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Please create issues for HiLive2 at https://gitlab.com/lokat/HiLive2.", + "uid": "gitlab/cosapp/cosapp", + "url": "https://gitlab.com/cosapp/cosapp", + "rel": "/software/repository/gitlab/cosapp/cosapp", + "avatar": "https://gitlab.com/uploads/-/system/project/avatar/19967329/cosapp_web.png", + "description": "CoSApp core package", "topics": [] }, { - "uid": "gitlab/octopus-code/octopus", - "url": "https://gitlab.com/octopus-code/octopus", - "rel": "/software/repository/gitlab/octopus-code/octopus", - "avatar": "https://gitlab.com/uploads/-/system/project/avatar/2018405/octopus.png", - "description": "Real-space Time-Dependent Density Functional Theory code", - "topics": [] + "uid": "gitlab/picos-api/picos", + "url": "https://gitlab.com/picos-api/picos", + "rel": "/software/repository/gitlab/picos-api/picos", + "avatar": "https://gitlab.com/uploads/-/system/project/avatar/7353603/logo.png", + "description": "A Python interface to conic optimization solvers.", + "topics": [ + "math", + "optimization", + "python" + ] }, { - "uid": "gitlab/ChemBioHub/tpmap", - "url": "https://gitlab.com/ChemBioHub/tpmap", - "rel": "/software/repository/gitlab/ChemBioHub/tpmap", - "avatar": "https://assets.gitlab-static.net/uploads/-/system/project/avatar/18237261/favicon.png", - "description": "Thermal Profiling Meltome Analysis Program", + "uid": "gitlab/pythia-uq/pythia", + "url": "https://gitlab.com/pythia-uq/pythia", + "rel": "/software/repository/gitlab/pythia-uq/pythia", + "avatar": "https://gitlab.com/uploads/-/system/project/avatar/45854627/logo_small.png", + "description": "PyThia Uncertainty Quantification Toolbox", "topics": [] }, { - "uid": "gitlab/robizzard/libcdict", - "url": "https://gitlab.com/rob.izzard/libcdict", - "rel": "/software/repository/gitlab/robizzard/libcdict", + "uid": "gitlab/chaver/choco-mining", + "url": "https://gitlab.com/chaver/choco-mining", + "rel": "/software/repository/gitlab/chaver/choco-mining", "avatar": "https://gitlab.comNone", - "description": "A generic associative array, also know as dictionary or hash, library in C, based on uthash and extended to be more user friendly and include integration features such as JSON output.", - "topics": [] + "description": "Data mining with Choco solver", + "topics": [ + "Association Rules Mining", + "Choco solver", + "Constraint Programming", + "Pareto", + "Skypattern", + "data mining", + "pattern mining" + ] }, { - "uid": "gitlab/ffaucher/hawen", - "url": "https://gitlab.com/ffaucher/hawen", - "rel": "/software/repository/gitlab/ffaucher/hawen", + "uid": "gitlab/astron-idg/idg", + "url": "https://gitlab.com/astron-idg/idg", + "rel": "/software/repository/gitlab/astron-idg/idg", "avatar": "https://gitlab.comNone", - "description": "time-HArmonic Wave modEling and INversion using Hybridizable Discontinuous Galerkin Discretization (hawen). The code is written in Fortran90, for forward and inverse time-harmonic wave problems. It uses mpi and openmp parallelism.", + "description": "Mirror of git.astron.nl/rd/idg", "topics": [] }, { - "uid": "gitlab/pvst/asi", - "url": "https://gitlab.com/pvst/asi", - "rel": "/software/repository/gitlab/pvst/asi", + "uid": "gitlab/mcfrith/paraclu", + "url": "https://gitlab.com/mcfrith/paraclu", + "rel": "/software/repository/gitlab/mcfrith/paraclu", "avatar": "https://gitlab.comNone", - "description": "Atomic Simulations Interface", + "description": "Parametric clustering of genomic and transcriptomic features", "topics": [] }, { - "uid": "gitlab/sissopp_developers/sissopp", - "url": "https://gitlab.com/sissopp_developers/sissopp", - "rel": "/software/repository/gitlab/sissopp_developers/sissopp", + "uid": "gitlab/mcfrith/last", + "url": "https://gitlab.com/mcfrith/last", + "rel": "/software/repository/gitlab/mcfrith/last", "avatar": "https://gitlab.comNone", - "description": "C++ implementation of sisso.", + "description": "finds & aligns related regions of sequences. LAST is designed for moderately large data (e.g. genomes, DNA reads, proteomes).", "topics": [] }, { - "uid": "gitlab/InspectorCell/inspectorcell", - "url": "https://gitlab.com/InspectorCell/inspectorcell", - "rel": "/software/repository/gitlab/InspectorCell/inspectorcell", + "uid": "gitlab/mcfrith/lamassemble", + "url": "https://gitlab.com/mcfrith/lamassemble", + "rel": "/software/repository/gitlab/mcfrith/lamassemble", "avatar": "https://gitlab.comNone", - "description": "InspectorCell provides an efficient workflow and graphical interface to generate high-quality training datasets from\r\nhighly multiplexed microscopy images.", + "description": "Merges overlapping \"long\" DNA reads into a consensus sequences", "topics": [] }, { - "uid": "gitlab/esa/pyxel", - "url": "https://gitlab.com/esa/pyxel", - "rel": "/software/repository/gitlab/esa/pyxel", - "avatar": "https://gitlab.com/uploads/-/system/project/avatar/10410719/square_logo.png", - "description": "Pyxel is a general detector simulation framework. An easy-to-use framework that can simulate a variety of imaging detector effects combined on images (e.g. radiation and optical effects, noises) made by CCD or CMOS-based detectors.", - "topics": [ - "astronomy", - "camera", - "ccd", - "cmos", - "detector", - "imaging", - "mct", - "pixel", - "python", - "simulation" - ] - }, - { - "uid": "gitlab/geekysquirrel/bigx", - "url": "https://gitlab.com/geekysquirrel/bigx", - "rel": "/software/repository/gitlab/geekysquirrel/bigx", - "avatar": "https://assets.gitlab-static.net/uploads/-/system/project/avatar/10925765/bigx.png", - "description": "A data visualisation tool for geographic datasets", + "uid": "gitlab/mcfrith/tantan", + "url": "https://gitlab.com/mcfrith/tantan", + "rel": "/software/repository/gitlab/mcfrith/tantan", + "avatar": "https://gitlab.comNone", + "description": "low complexity and tandem repeat masker for biosequences", "topics": [] }, { - "uid": "gitlab/binary_c/binary_c-python", - "url": "https://gitlab.com/binary_c/binary_c-python", - "rel": "/software/repository/gitlab/binary_c/binary_c-python", - "avatar": "https://gitlab.comNone", - "description": "Python module to interface with the binary_c stellar population framework.\r\n\r\nThe current stable branch is 1.0.0 which you can find in the [releases/1.0.0/2.2.4 branch](https://gitlab.com/binary_c/binary_c-python/-/tree/releases/1.0.0/2.2.4) which works with [binary_c version 2.2.4](https://gitlab.com/binary_c/binary_c/-/tree/development/2.2.4)", + "uid": "gitlab/petsc/petsc", + "url": "https://gitlab.com/petsc/petsc", + "rel": "/software/repository/gitlab/petsc/petsc", + "avatar": "https://gitlab.com/uploads/-/system/project/avatar/13882401/PETSc_RBG-logo.png", + "description": "PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations.", "topics": [] }, { @@ -423,118 +289,128 @@ ] }, { - "uid": "gitlab/ampere2/metalwalls", - "url": "https://gitlab.com/ampere2/metalwalls", - "rel": "/software/repository/gitlab/ampere2/metalwalls", + "uid": "gitlab/habermann_lab/phasik", + "url": "https://gitlab.com/habermann_lab/phasik", + "rel": "/software/repository/gitlab/habermann_lab/phasik", "avatar": "https://gitlab.comNone", - "description": "", + "description": "Scientific tools for extracting cyclic data via hierarchical clustering", "topics": [] }, { - "uid": "gitlab/permafrostnet/teaspoon", - "url": "https://gitlab.com/permafrostnet/teaspoon", - "rel": "/software/repository/gitlab/permafrostnet/teaspoon", - "avatar": "https://gitlab.com/uploads/-/system/project/avatar/35916406/teaspooncolor_p.png", - "description": "Python for permafrost temperature data", - "topics": [ - "dataset", - "earth science", - "geography" - ] - }, - { - "uid": "gitlab/mainlabwsu/bims", - "url": "https://gitlab.com/mainlabwsu/bims", - "rel": "/software/repository/gitlab/mainlabwsu/bims", + "uid": "gitlab/ags-data-format-wg/ags-python-library", + "url": "https://gitlab.com/ags-data-format-wg/ags-python-library", + "rel": "/software/repository/gitlab/ags-data-format-wg/ags-python-library", "avatar": "https://gitlab.comNone", - "description": "BIMS", + "description": "A library to read and write AGS files using Pandas DataFrames", "topics": [] }, { - "uid": "gitlab/picos-api/picos", - "url": "https://gitlab.com/picos-api/picos", - "rel": "/software/repository/gitlab/picos-api/picos", - "avatar": "https://gitlab.com/uploads/-/system/project/avatar/7353603/logo.png", - "description": "A Python interface to conic optimization solvers.", - "topics": [ - "math", - "optimization", - "python" - ] + "uid": "gitlab/project-dare/dare-platform", + "url": "https://gitlab.com/project-dare/dare-platform", + "rel": "/software/repository/gitlab/project-dare/dare-platform", + "avatar": "https://assets.gitlab-static.net/uploads/-/system/project/avatar/14873006/dare.png", + "description": "", + "topics": [] }, { - "uid": "gitlab/Molcas/OpenMolcas", - "url": "https://gitlab.com/Molcas/OpenMolcas", - "rel": "/software/repository/gitlab/Molcas/OpenMolcas", - "avatar": "https://gitlab.com/uploads/-/system/project/avatar/3536517/logo_open_flat.png", - "description": "OpenMolcas is a quantum chemistry software package.\r\n\r\nThe key feature of OpenMolcas is the multiconfigurational approach to the electronic structure.", + "uid": "gitlab/remram44/taguette", + "url": "https://gitlab.com/remram44/taguette", + "rel": "/software/repository/gitlab/remram44/taguette", + "avatar": "https://gitlab.com/uploads/-/system/project/avatar/8339211/taguette.png", + "description": "Free and open source qualitative research tool", "topics": [ - "chemistry", - "physics", - "quantum" + "document", + "hacktoberfest", + "highlights", + "notes", + "qual", + "qualitative", + "research", + "tagging", + "tags", + "text" ] }, { - "uid": "gitlab/metafundev/metafun", - "url": "https://gitlab.com/metafundev/metafun", - "rel": "/software/repository/gitlab/metafundev/metafun", + "uid": "gitlab/wpettersson/kep_solver", + "url": "https://gitlab.com/wpettersson/kep_solver", + "rel": "/software/repository/gitlab/wpettersson/kep_solver", "avatar": "https://gitlab.comNone", - "description": "", + "description": "A Python package for reading and solving single instances of kidney exchange problems. ", "topics": [] }, { - "uid": "gitlab/gmamon/MAMPOSSt", - "url": "https://gitlab.com/gmamon/MAMPOSSt", - "rel": "/software/repository/gitlab/gmamon/MAMPOSSt", - "avatar": "https://gitlab.com/uploads/-/system/project/avatar/6066861/MAMPOSSt_logo.png", - "description": null, - "topics": [ - "Mass/orbit modeling" - ] - }, - { - "uid": "gitlab/cosmograil/starred", - "url": "https://gitlab.com/cosmograil/starred", - "rel": "/software/repository/gitlab/cosmograil/starred", - "avatar": "https://gitlab.com/uploads/-/system/project/avatar/38194257/starred_main_image.png", - "description": "A two-channel deconvolution method with Starlet regularization", + "uid": "gitlab/sevecekp/sph", + "url": "https://gitlab.com/sevecekp/sph", + "rel": "/software/repository/gitlab/sevecekp/sph", + "avatar": "https://gitlab.comNone", + "description": "Library and graphical tools for running SPH and N-body simulations.", "topics": [ - "Deconvolution", - "astronomy", - "psf", - "python" + "SPH", + "nbody", + "opensph", + "simulation" ] }, { - "uid": "gitlab/cosmograil/PyCS3", - "url": "https://gitlab.com/cosmograil/PyCS3", - "rel": "/software/repository/gitlab/cosmograil/PyCS3", - "avatar": "https://assets.gitlab-static.net/uploads/-/system/project/avatar/7888463/cover_image_1.png", - "description": "PyCS for python 3", + "uid": "gitlab/mobse/source-code", + "url": "https://gitlab.com/mobse/source-code", + "rel": "/software/repository/gitlab/mobse/source-code", + "avatar": "https://gitlab.com/uploads/-/system/project/avatar/15981708/mobse_code_copia.png", + "description": null, "topics": [] }, { - "uid": "gitlab/gims-developers/gims", - "url": "https://gitlab.com/gims-developers/gims", - "rel": "/software/repository/gitlab/gims-developers/gims", - "avatar": "https://assets.gitlab-static.net/uploads/-/system/project/avatar/16358286/GIMSLogo.png", - "description": "GIMS -- Graphical Interface for Materials Simulations -- is an open-source, browser-based toolbox for electronic structure codes. Try it here: [gims.ms1p.org](https://gims.ms1p.org)", + "uid": "gitlab/cracklet/cracklet", + "url": "https://gitlab.com/cracklet/cracklet", + "rel": "/software/repository/gitlab/cracklet/cracklet", + "avatar": "https://gitlab.com/uploads/-/system/project/avatar/25188173/logo_large.png", + "description": "cRacklet is a C++ boundary element library based on a spectral formulation of the elastodynamic wave equations in continuum solids.", "topics": [] }, { - "uid": "gitlab/aroffringa/aoflagger", - "url": "https://gitlab.com/aroffringa/aoflagger", - "rel": "/software/repository/gitlab/aroffringa/aoflagger", + "uid": "gitlab/AstroVian/bmarxiv", + "url": "https://gitlab.com/AstroVian/bmarxiv", + "rel": "/software/repository/gitlab/AstroVian/bmarxiv", + "avatar": "https://gitlab.com/uploads/-/system/project/avatar/28500894/PAph_dog.gif", + "description": null, + "topics": [] + }, + { + "uid": "gitlab/loic.cg.rossi/pymiedap", + "url": "https://gitlab.com/loic.cg.rossi/pymiedap", + "rel": "/software/repository/gitlab/loic.cg.rossi/pymiedap", "avatar": "https://gitlab.comNone", - "description": "The AOFlagger is a tool that can find and remove radio-frequency interference (RFI) in radio astronomical observations. It can make use of Lua scripts to make flagging strategies flexible, and the tools are applicable to a wide set of telescopes.", + "description": "PyMieDAP = Python Mie Doubling Adding Program. A radiative transfer code with polarization.", + "topics": [ + "astronomy", + "atmospheres", + "polarization", + "radiative transfer" + ] + }, + { + "uid": "gitlab/kmrajwade/iqrm_apollo", + "url": "https://gitlab.com/kmrajwade/iqrm_apollo", + "rel": "/software/repository/gitlab/kmrajwade/iqrm_apollo", + "avatar": "https://gitlab.comNone", + "description": "A standalone code to clean narrow-band RFI using Inter-Quartile Range Mitigation (IQRM) algorithm. The code works on SIGPROC format data and outputs a cleaned SIGRPOC format file. The output file is compatible with other standard pulsar software.", "topics": [] }, { - "uid": "gitlab/aroffringa/wsclean", - "url": "https://gitlab.com/aroffringa/wsclean", - "rel": "/software/repository/gitlab/aroffringa/wsclean", + "uid": "gitlab/davidtourigny/dynamic-fba", + "url": "https://gitlab.com/davidtourigny/dynamic-fba", + "rel": "/software/repository/gitlab/davidtourigny/dynamic-fba", "avatar": "https://gitlab.comNone", - "description": "WSClean (w-stacking clean) is a fast generic widefield imager. It implements several gridding algorithms and offers fully-automated multi-scale multi-frequency deconvolution. Manual: https://wsclean.readthedocs.io/", + "description": "", + "topics": [] + }, + { + "uid": "gitlab/chiemotono/mdcontactcom", + "url": "https://gitlab.com/chiemotono/mdcontactcom", + "rel": "/software/repository/gitlab/chiemotono/mdcontactcom", + "avatar": "https://gitlab.comNone", + "description": "", "topics": [] }, { @@ -546,146 +422,177 @@ "topics": [] }, { - "uid": "gitlab/chaver/choco-mining", - "url": "https://gitlab.com/chaver/choco-mining", - "rel": "/software/repository/gitlab/chaver/choco-mining", - "avatar": "https://gitlab.comNone", - "description": "Data mining with Choco solver", + "uid": "gitlab/gmamon/MAMPOSSt", + "url": "https://gitlab.com/gmamon/MAMPOSSt", + "rel": "/software/repository/gitlab/gmamon/MAMPOSSt", + "avatar": "https://gitlab.com/uploads/-/system/project/avatar/6066861/MAMPOSSt_logo.png", + "description": null, "topics": [ - "Association Rules Mining", - "Choco solver", - "Constraint Programming", - "Pareto", - "Skypattern", - "data mining", - "pattern mining" + "Mass/orbit modeling" ] }, { - "uid": "gitlab/libreumg/dataquier", - "url": "https://gitlab.com/libreumg/dataquier", - "rel": "/software/repository/gitlab/libreumg/dataquier", - "avatar": "https://assets.gitlab-static.net/uploads/-/system/project/avatar/14144828/logo_ship.png", - "description": "", + "uid": "gitlab/ENKI-portal/ThermoCodegen", + "url": "https://gitlab.com/ENKI-portal/ThermoCodegen", + "rel": "/software/repository/gitlab/ENKI-portal/ThermoCodegen", + "avatar": "https://gitlab.com/uploads/-/system/project/avatar/37653498/tcg_logo_cropped.png", + "description": "ThermoCodegen: a python/C++ package for the generation of custom thermodynamic models", "topics": [] }, { - "uid": "gitlab/petsc/petsc", - "url": "https://gitlab.com/petsc/petsc", - "rel": "/software/repository/gitlab/petsc/petsc", - "avatar": "https://gitlab.com/uploads/-/system/project/avatar/13882401/PETSc_RBG-logo.png", - "description": "PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations.", + "uid": "gitlab/ENKI-portal/vaporock", + "url": "https://gitlab.com/ENKI-portal/vaporock", + "rel": "/software/repository/gitlab/ENKI-portal/vaporock", + "avatar": "https://gitlab.com/uploads/-/system/project/avatar/18914416/vaporock.png", + "description": "Thermodynamics of vaporized silicate rocks & melts for modeling magma ocean atmospheres and stellar nebula", "topics": [] }, { - "uid": "gitlab/JuditGG/trumpetplots", - "url": "https://gitlab.com/JuditGG/trumpetplots", - "rel": "/software/repository/gitlab/JuditGG/trumpetplots", - "avatar": "https://gitlab.com/uploads/-/system/project/avatar/45249770/trumpet-icon-design-free-vector.jpg", - "description": "Rpackage for Trumpet plots", - "topics": [ - "genetics", - "gwas", - "visualization" - ] + "uid": "gitlab/ENKI-portal/ThermoEngine", + "url": "https://gitlab.com/ENKI-portal/ThermoEngine", + "rel": "/software/repository/gitlab/ENKI-portal/ThermoEngine", + "avatar": "https://gitlab.com/uploads/-/system/project/avatar/2313798/Untitled.png", + "description": "Python, C, C++ and Objective C code that Implement thermodynamic properties of stoichiometric phases and solutions. This is the main code repository of the ENKI project.", + "topics": [] }, { - "uid": "gitlab/thartwig/asloth", - "url": "https://gitlab.com/thartwig/asloth", - "rel": "/software/repository/gitlab/thartwig/asloth", - "avatar": "https://gitlab.com/uploads/-/system/project/avatar/35049365/ASLOTH_logo_official.jpg", - "description": "Semi-analytical model A-SLOTH (Ancient Stars and Local Observables by Tracing Halos)", + "uid": "gitlab/fibreglass/pivc", + "url": "https://gitlab.com/fibreglass/pivc", + "rel": "/software/repository/gitlab/fibreglass/pivc", + "avatar": "https://gitlab.comNone", + "description": null, "topics": [] }, { - "uid": "gitlab/ztzou/phydl", - "url": "https://gitlab.com/ztzou/phydl", - "rel": "/software/repository/gitlab/ztzou/phydl", + "uid": "gitlab/aroffringa/aoflagger", + "url": "https://gitlab.com/aroffringa/aoflagger", + "rel": "/software/repository/gitlab/aroffringa/aoflagger", "avatar": "https://gitlab.comNone", - "description": "Phylogenetics by Deep Learning. A residual neural network for inference of quartet phylogenetic tree topology.", + "description": "The AOFlagger is a tool that can find and remove radio-frequency interference (RFI) in radio astronomical observations. It can make use of Lua scripts to make flagging strategies flexible, and the tools are applicable to a wide set of telescopes.", "topics": [] }, { - "uid": "gitlab/wpettersson/kep_solver", - "url": "https://gitlab.com/wpettersson/kep_solver", - "rel": "/software/repository/gitlab/wpettersson/kep_solver", + "uid": "gitlab/aroffringa/wsclean", + "url": "https://gitlab.com/aroffringa/wsclean", + "rel": "/software/repository/gitlab/aroffringa/wsclean", "avatar": "https://gitlab.comNone", - "description": "A Python package for reading and solving single instances of kidney exchange problems. ", + "description": "WSClean (w-stacking clean) is a fast generic widefield imager. It implements several gridding algorithms and offers fully-automated multi-scale multi-frequency deconvolution. Manual: https://wsclean.readthedocs.io/", "topics": [] }, { - "uid": "gitlab/gpagano/lensinggw", - "url": "https://gitlab.com/gpagano/lensinggw", - "rel": "/software/repository/gitlab/gpagano/lensinggw", + "uid": "gitlab/sigcorr/sigcorr", + "url": "https://gitlab.com/sigcorr/sigcorr", + "rel": "/software/repository/gitlab/sigcorr/sigcorr", "avatar": "https://gitlab.comNone", "description": null, - "topics": [ - "lensing of gravitational waves" - ] + "topics": [] }, { - "uid": "gitlab/paulklemm_PHD/proteinortho", - "url": "https://gitlab.com/paulklemm_PHD/proteinortho", - "rel": "/software/repository/gitlab/paulklemm_PHD/proteinortho", - "avatar": "https://gitlab.com/uploads/-/system/project/avatar/7278443/icon4.png", - "description": "Proteinortho is a tool to detect orthologous genes within different species. [(Download)](https://gitlab.com/paulklemm_PHD/proteinortho/-/archive/master/proteinortho-master.tar.gz)", - "topics": [ - "bioinformatics", - "orthology", - "orthology inference" - ] + "uid": "gitlab/joseaher/astroplotlib", + "url": "https://gitlab.com/joseaher/astroplotlib", + "rel": "/software/repository/gitlab/joseaher/astroplotlib", + "avatar": "https://gitlab.comNone", + "description": null, + "topics": [] }, { - "uid": "gitlab/sevecekp/sph", - "url": "https://gitlab.com/sevecekp/sph", - "rel": "/software/repository/gitlab/sevecekp/sph", + "uid": "gitlab/dalton/dalton", + "url": "https://gitlab.com/dalton/dalton", + "rel": "/software/repository/gitlab/dalton/dalton", + "avatar": "https://gitlab.com/uploads/-/system/project/avatar/4007652/pRZ6xe8j_400x400.jpg", + "description": "Public Dalton source code repository.", + "topics": [] + }, + { + "uid": "gitlab/octopus-code/octopus", + "url": "https://gitlab.com/octopus-code/octopus", + "rel": "/software/repository/gitlab/octopus-code/octopus", + "avatar": "https://gitlab.com/uploads/-/system/project/avatar/2018405/octopus.png", + "description": "Real-space Time-Dependent Density Functional Theory code", + "topics": [] + }, + { + "uid": "gitlab/ffaucher/hawen", + "url": "https://gitlab.com/ffaucher/hawen", + "rel": "/software/repository/gitlab/ffaucher/hawen", "avatar": "https://gitlab.comNone", - "description": "Library and graphical tools for running SPH and N-body simulations.", + "description": "time-HArmonic Wave modEling and INversion using Hybridizable Discontinuous Galerkin Discretization (hawen). The code is written in Fortran90, for forward and inverse time-harmonic wave problems. It uses mpi and openmp parallelism.", + "topics": [] + }, + { + "uid": "gitlab/esa/pyxel", + "url": "https://gitlab.com/esa/pyxel", + "rel": "/software/repository/gitlab/esa/pyxel", + "avatar": "https://gitlab.com/uploads/-/system/project/avatar/10410719/square_logo.png", + "description": "Pyxel is a general detector simulation framework. An easy-to-use framework that can simulate a variety of imaging detector effects combined on images (e.g. radiation and optical effects, noises) made by CCD or CMOS-based detectors.", "topics": [ - "SPH", - "nbody", - "opensph", + "astronomy", + "camera", + "ccd", + "cmos", + "detector", + "imaging", + "mct", + "pixel", + "python", "simulation" ] }, { - "uid": "gitlab/mcfrith/tantan", - "url": "https://gitlab.com/mcfrith/tantan", - "rel": "/software/repository/gitlab/mcfrith/tantan", + "uid": "gitlab/gpagano/lensinggw", + "url": "https://gitlab.com/gpagano/lensinggw", + "rel": "/software/repository/gitlab/gpagano/lensinggw", "avatar": "https://gitlab.comNone", - "description": "low complexity and tandem repeat masker for biosequences", - "topics": [] + "description": null, + "topics": [ + "lensing of gravitational waves" + ] }, { - "uid": "gitlab/mcfrith/paraclu", - "url": "https://gitlab.com/mcfrith/paraclu", - "rel": "/software/repository/gitlab/mcfrith/paraclu", + "uid": "gitlab/BioimageInformaticsGroup/openphi", + "url": "https://gitlab.com/BioimageInformaticsGroup/openphi", + "rel": "/software/repository/gitlab/BioimageInformaticsGroup/openphi", "avatar": "https://gitlab.comNone", - "description": "Parametric clustering of genomic and transcriptomic features", + "description": "Open PatHology Interface - A Python API for accessing iSyntax digital pathology images", "topics": [] }, { - "uid": "gitlab/mcfrith/lamassemble", - "url": "https://gitlab.com/mcfrith/lamassemble", - "rel": "/software/repository/gitlab/mcfrith/lamassemble", - "avatar": "https://gitlab.comNone", - "description": "Merges overlapping \"long\" DNA reads into a consensus sequences", + "uid": "gitlab/dglaeser/fieldcompare", + "url": "https://gitlab.com/dglaeser/fieldcompare", + "rel": "/software/repository/gitlab/dglaeser/fieldcompare", + "avatar": "https://gitlab.com/uploads/-/system/project/avatar/32838547/fcompare_logo.png", + "description": "Python package with command-line interface to compare field data", "topics": [] }, { - "uid": "gitlab/mcfrith/last", - "url": "https://gitlab.com/mcfrith/last", - "rel": "/software/repository/gitlab/mcfrith/last", - "avatar": "https://gitlab.comNone", - "description": "finds & aligns related regions of sequences. LAST is designed for moderately large data (e.g. genomes, DNA reads, proteomes).", + "uid": "gitlab/eduardo-vitral/balrogo", + "url": "https://gitlab.com/eduardo-vitral/balrogo", + "rel": "/software/repository/gitlab/eduardo-vitral/balrogo", + "avatar": "https://gitlab.com/eduardo-vitral/balrogo/-/avatar", + "description": "Bayesian Astrometric Likelihood Recovery of Galactic Objects", "topics": [] }, { - "uid": "gitlab/AstroVian/bmarxiv", - "url": "https://gitlab.com/AstroVian/bmarxiv", - "rel": "/software/repository/gitlab/AstroVian/bmarxiv", - "avatar": "https://gitlab.com/uploads/-/system/project/avatar/28500894/PAph_dog.gif", - "description": null, + "uid": "gitlab/pipe3d/pyPipe3D", + "url": "https://gitlab.com/pipe3d/pyPipe3D", + "rel": "/software/repository/gitlab/pipe3d/pyPipe3D", + "avatar": "https://gitlab.com/uploads/-/system/project/avatar/26080505/pyPipe3D_colorido_avatar.png", + "description": "pyPipe3D is a spectroscopy analysis pipeline which produces coherent, easy to distribute and compare, parameters of the stellar populations and the ionized gas, suited in particular for data from the most recent optical IFS surveys.", + "topics": [ + "ifs", + "ionized gas", + "ism", + "spectroscopy", + "stellar population synthesis", + "techniques" + ] + }, + { + "uid": "gitlab/polmag/PORTA", + "url": "https://gitlab.com/polmag/PORTA", + "rel": "/software/repository/gitlab/polmag/PORTA", + "avatar": "https://gitlab.com/uploads/-/system/project/avatar/12210898/porta-logo-bw.png", + "description": "PORTA: A three-dimensional multilevel radiative transfer code for modeling the intensity and polarization of spectral lines with massively parallel computers", "topics": [] }, { @@ -705,96 +612,117 @@ ] }, { - "uid": "gitlab/etienne.behar/menura", - "url": "https://gitlab.com/etienne.behar/menura", - "rel": "/software/repository/gitlab/etienne.behar/menura", - "avatar": "https://gitlab.com/uploads/-/system/project/avatar/24686946/menura_logo2_thumb.png", - "description": "Menura is a space plasma simulation code. It is built around a hybrid Particle In Cell (PIC) solver, running on Graphics Processing Units. More informations on https://menura.readthedocs.io", - "topics": [ - "plasma", - "simulation", - "solar wind", - "turbulence" - ] + "uid": "gitlab/pvst/asi", + "url": "https://gitlab.com/pvst/asi", + "rel": "/software/repository/gitlab/pvst/asi", + "avatar": "https://gitlab.comNone", + "description": "Atomic Simulations Interface", + "topics": [] }, { - "uid": "gitlab/vincent-sater/umigen", - "url": "https://gitlab.com/vincent-sater/umigen", - "rel": "/software/repository/gitlab/vincent-sater/umigen", + "uid": "gitlab/leelamichaels/Elysium", + "url": "https://gitlab.com/leelamichaels/Elysium", + "rel": "/software/repository/gitlab/leelamichaels/Elysium", "avatar": "https://gitlab.comNone", - "description": "UMI-based reads simulator for variant calling evaluation in paired-end sequencing NGS libraries", + "description": "Code Elysium release copy", "topics": [] }, { - "uid": "gitlab/andrea-tango/ficos", - "url": "https://gitlab.com/andrea-tango/ficos", - "rel": "/software/repository/gitlab/andrea-tango/ficos", + "uid": "gitlab/leelamichaels/Burning_Arrow", + "url": "https://gitlab.com/leelamichaels/Burning_Arrow", + "rel": "/software/repository/gitlab/leelamichaels/Burning_Arrow", "avatar": "https://gitlab.comNone", - "description": "", + "description": "Code Burning Arrow release copy", "topics": [] }, { - "uid": "gitlab/moerman1/fhi-cc4s", - "url": "https://gitlab.com/moerman1/fhi-cc4s", - "rel": "/software/repository/gitlab/moerman1/fhi-cc4s", + "uid": "gitlab/leelamichaels/Infinity", + "url": "https://gitlab.com/leelamichaels/Infinity", + "rel": "/software/repository/gitlab/leelamichaels/Infinity", "avatar": "https://gitlab.comNone", - "description": "This project constitutes the interface between the Fritz Haber Institute ab initio molecular simulations (FHI-aims) and the Coupled Cluster for Solids (CC4S) code developed by Felix Hummel and Adreas Grueneis at the TU Wien. \r\n", + "description": "Code Infinity release copy", "topics": [] }, { - "uid": "gitlab/sigcorr/sigcorr", - "url": "https://gitlab.com/sigcorr/sigcorr", - "rel": "/software/repository/gitlab/sigcorr/sigcorr", + "uid": "gitlab/leelamichaels/Tranquillity", + "url": "https://gitlab.com/leelamichaels/Tranquillity", + "rel": "/software/repository/gitlab/leelamichaels/Tranquillity", "avatar": "https://gitlab.comNone", - "description": null, + "description": "Code Tranquillity release copy", "topics": [] }, { - "uid": "gitlab/programgreg/tagginglatencyestimator", - "url": "https://gitlab.com/programgreg/tagginglatencyestimator", - "rel": "/software/repository/gitlab/programgreg/tagginglatencyestimator", + "uid": "gitlab/leelamichaels/Omega", + "url": "https://gitlab.com/leelamichaels/Omega", + "rel": "/software/repository/gitlab/leelamichaels/Omega", "avatar": "https://gitlab.comNone", - "description": "Software to estimate the latency of the tagging process.", + "description": "Code Omega release copy", "topics": [] }, { - "uid": "gitlab/eduardo-vitral/balrogo", - "url": "https://gitlab.com/eduardo-vitral/balrogo", - "rel": "/software/repository/gitlab/eduardo-vitral/balrogo", - "avatar": "https://gitlab.com/eduardo-vitral/balrogo/-/avatar", - "description": "Bayesian Astrometric Likelihood Recovery of Galactic Objects", + "uid": "gitlab/jesseds/apav", + "url": "https://gitlab.com/jesseds/apav", + "rel": "/software/repository/gitlab/jesseds/apav", + "avatar": "https://gitlab.com/uploads/-/system/project/avatar/10414782/g39334.png", + "description": "APAV (Atom Probe Analysis and Visualization) is a Python library for the analysis and\r\nvisualization of atom probe tomography experiments.", + "topics": [ + "Atom Probe", + "Field Evaporation", + "data analysis", + "science", + "tomography" + ] + }, + { + "uid": "gitlab/magnumpi/magnumpi", + "url": "https://gitlab.com/magnumpi/magnumpi", + "rel": "/software/repository/gitlab/magnumpi/magnumpi", + "avatar": "https://gitlab.com/uploads/-/system/project/avatar/8913469/Tom_20Selleck_20as_20Thomas_20Magnum_20P.I._large.jpg", + "description": "Potential Integrator", "topics": [] }, { - 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"uid": "gitlab/magnumpi/magnumpi", - "url": "https://gitlab.com/magnumpi/magnumpi", - "rel": "/software/repository/gitlab/magnumpi/magnumpi", - "avatar": "https://gitlab.com/uploads/-/system/project/avatar/8913469/Tom_20Selleck_20as_20Thomas_20Magnum_20P.I._large.jpg", - "description": "Potential Integrator", + "uid": "gitlab/chrjan/seq-seq-pan", + "url": "https://gitlab.com/chrjan/seq-seq-pan", + "rel": "/software/repository/gitlab/chrjan/seq-seq-pan", + "avatar": "https://gitlab.comNone", + "description": "seq-seq-pan is a workflow for the SEQuential alignment of SEQuences to build a PAN-genome data structure and a whole-genome-alignment.", "topics": [] }, { - "uid": "gitlab/kmrajwade/iqrm_apollo", - "url": "https://gitlab.com/kmrajwade/iqrm_apollo", - "rel": "/software/repository/gitlab/kmrajwade/iqrm_apollo", + "uid": "gitlab/permafrostnet/teaspoon", + "url": "https://gitlab.com/permafrostnet/teaspoon", + "rel": "/software/repository/gitlab/permafrostnet/teaspoon", + "avatar": "https://gitlab.com/uploads/-/system/project/avatar/35916406/teaspooncolor_p.png", + "description": "Python for permafrost temperature data", + "topics": [ + "dataset", + "earth science", + "geography" + ] + }, + { + "uid": "gitlab/sissopp_developers/sissopp", + "url": "https://gitlab.com/sissopp_developers/sissopp", + "rel": "/software/repository/gitlab/sissopp_developers/sissopp", "avatar": "https://gitlab.comNone", - "description": "A standalone code to clean narrow-band RFI using Inter-Quartile Range Mitigation (IQRM) algorithm. The code works on SIGPROC format data and outputs a cleaned SIGRPOC format file. The output file is compatible with other standard pulsar software.", + "description": "C++ implementation of sisso.", "topics": [] }, { @@ -820,235 +748,164 @@ ] }, { - "uid": "gitlab/emd-dev/emd", - "url": "https://gitlab.com/emd-dev/emd", - "rel": "/software/repository/gitlab/emd-dev/emd", + "uid": "gitlab/german.tischler/biobambam2", + "url": "https://gitlab.com/german.tischler/biobambam2", + "rel": "/software/repository/gitlab/german.tischler/biobambam2", "avatar": "https://gitlab.comNone", - "description": "Empirical Mode Decomposition in Python\r\n\r\n\"pipeline", + "description": "Tools for early stage alignment file processing", "topics": [] }, { - "uid": "gitlab/joseaher/astroplotlib", - "url": "https://gitlab.com/joseaher/astroplotlib", - "rel": "/software/repository/gitlab/joseaher/astroplotlib", + "uid": "gitlab/german.tischler/libmaus2", + "url": "https://gitlab.com/german.tischler/libmaus2", + "rel": "/software/repository/gitlab/german.tischler/libmaus2", "avatar": "https://gitlab.comNone", - "description": null, + "description": "collection of data structures and algorithms", "topics": [] }, { - "uid": "gitlab/davidtourigny/dynamic-fba", - "url": "https://gitlab.com/davidtourigny/dynamic-fba", - "rel": "/software/repository/gitlab/davidtourigny/dynamic-fba", + "uid": "gitlab/binary_c/binary_c-python", + "url": "https://gitlab.com/binary_c/binary_c-python", + "rel": "/software/repository/gitlab/binary_c/binary_c-python", "avatar": "https://gitlab.comNone", - "description": "", + "description": "Python module to interface with the binary_c stellar population framework.\r\n\r\nThe current stable branch is 1.0.0 which you can find in the [releases/1.0.0/2.2.4 branch](https://gitlab.com/binary_c/binary_c-python/-/tree/releases/1.0.0/2.2.4) which works with [binary_c version 2.2.4](https://gitlab.com/binary_c/binary_c/-/tree/development/2.2.4)", "topics": [] }, { - "uid": "gitlab/BioimageInformaticsGroup/openphi", - "url": "https://gitlab.com/BioimageInformaticsGroup/openphi", - "rel": "/software/repository/gitlab/BioimageInformaticsGroup/openphi", - "avatar": "https://gitlab.comNone", - "description": "Open PatHology Interface - A Python API for accessing iSyntax digital pathology images", + "uid": "gitlab/rki_bioinformatics/HiLive2", + "url": "https://gitlab.com/rki_bioinformatics/HiLive2", + "rel": "/software/repository/gitlab/rki_bioinformatics/HiLive2", + "avatar": "https://gitlab.com/uploads/-/system/project/avatar/7428486/hilive2_logo.png", + "description": "HiLive2 is a read mapping tool that maps Illumina HiSeq (or comparable) reads right in the moment when they are produced. Please create issues for HiLive2 at https://gitlab.com/lokat/HiLive2.", "topics": [] }, { - "uid": "gitlab/chrjan/seq-seq-pan", - "url": "https://gitlab.com/chrjan/seq-seq-pan", - "rel": "/software/repository/gitlab/chrjan/seq-seq-pan", - "avatar": "https://gitlab.comNone", - "description": "seq-seq-pan is a workflow for the SEQuential alignment of SEQuences to build a PAN-genome data structure and a whole-genome-alignment.", + "uid": "gitlab/rki_bioinformatics/purple", + "url": "https://gitlab.com/rki_bioinformatics/purple", + "rel": "/software/repository/gitlab/rki_bioinformatics/purple", + "avatar": "https://gitlab.com/uploads/-/system/project/avatar/11392663/Purple_128.png", + "description": "Picking Unique Relevant Peptides for viraL Experiments\r\n\r\nAuthors: Johanna Lechner [@LechnerJ], Pauline Hiortand Felix Hartkopf [@HartkopfF]\r\n\r\nSupport: https://gitlab.com/HartkopfF/Purple\r\n\r\nDownload: https://gitlab.com/HartkopfF/Purple/releases", "topics": [] }, { - "uid": "gitlab/casi-project/casi-2d", - "url": "https://gitlab.com/casi-project/casi-2d", - "rel": "/software/repository/gitlab/casi-project/casi-2d", + "uid": "gitlab/rki_bioinformatics/IDeFIX", + "url": "https://gitlab.com/rki_bioinformatics/IDeFIX", + "rel": "/software/repository/gitlab/rki_bioinformatics/IDeFIX", "avatar": "https://gitlab.comNone", - "description": "Identification of stellar feedback signatures in simulated molecular clouds using methods from deep learning.", + "description": "Index checking for improved demultiplexing of NGS data", "topics": [] }, { - "uid": "gitlab/casi-project/casi-3d", - "url": "https://gitlab.com/casi-project/casi-3d", - "rel": "/software/repository/gitlab/casi-project/casi-3d", + "uid": "gitlab/ProjectRHEA/flowsolverrhea", + "url": "https://gitlab.com/ProjectRHEA/flowsolverrhea", + "rel": "/software/repository/gitlab/ProjectRHEA/flowsolverrhea", "avatar": "https://gitlab.comNone", - "description": null, + "description": "RHEA: an open-source Reproducible and Hybrid-architecture flow solver Engineered for Academia", "topics": [] }, { - "uid": "gitlab/RKIBioinformaticsPipelines/QCumber", - "url": "https://gitlab.com/RKIBioinformaticsPipelines/QCumber", - "rel": "/software/repository/gitlab/RKIBioinformaticsPipelines/QCumber", + "uid": "gitlab/dsbowen/conditional-inference", + "url": "https://gitlab.com/dsbowen/conditional-inference", + "rel": "/software/repository/gitlab/dsbowen/conditional-inference", "avatar": "https://gitlab.comNone", - "description": "quality control of genomic sequences", + "description": null, "topics": [] }, { - "uid": "gitlab/treangenlab/vulcan", - "url": "https://gitlab.com/treangenlab/vulcan", - "rel": "/software/repository/gitlab/treangenlab/vulcan", - "avatar": "https://gitlab.comNone", - "description": "", + "uid": "gitlab/elsi_project/elsi_interface", + "url": "https://gitlab.com/elsi_project/elsi_interface", + "rel": "/software/repository/gitlab/elsi_project/elsi_interface", + "avatar": "https://gitlab.com/uploads/-/system/project/avatar/20804728/elsi_200629.png", + "description": "ELSI: A software interface designed for electronic structure codes to connect with ELPA, libOMM, PEXSI, EigenExa, SLEPc, NTPoly, BSEPACK, LAPACK, MAGMA, and other solver libraries.", "topics": [] }, { - "uid": "gitlab/treangenlab/emu", - "url": "https://gitlab.com/treangenlab/emu", - "rel": "/software/repository/gitlab/treangenlab/emu", - "avatar": "https://gitlab.com/treangenlab/emu/-/avatar", - "description": "EMu is a relative abundance estimator for 16S genomic sequences", - "topics": [] - }, - { - "uid": "gitlab/loic.cg.rossi/pymiedap", - "url": "https://gitlab.com/loic.cg.rossi/pymiedap", - "rel": "/software/repository/gitlab/loic.cg.rossi/pymiedap", - "avatar": "https://gitlab.comNone", - "description": "PyMieDAP = Python Mie Doubling Adding Program. 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In addition, the software architecture is designed in different modules that make Cytomorph an adaptive computational tool in which new advances can be integrated.", - "topics": [] + "uid": "github/ScialdoneLab/MitoHEAR", + "url": "https://github.com/ScialdoneLab/MitoHEAR", + "rel": "/software/repository/github/ScialdoneLab/MitoHEAR", + "avatar": "https://avatars.githubusercontent.com/u/42929618?v=4", + "description": "MitoHEAR (Mitochondrial HEteroplasmy AnalyzeR) is an R package that allows the estimation as well as downstream statistical analysis of the mtDNA heteroplasmy calculated from single-cell datasets.", + "topics": [ + "bioinformatics-analysis", + "heteroplasmy", + "open-source", + "rstats-package" + ] }, { - "uid": "github/doriancazeneuve/ODNet", - "url": "https://github.com/doriancazeneuve/ODNet", - "rel": "/software/repository/github/doriancazeneuve/ODNet", - "avatar": "https://avatars.githubusercontent.com/u/112989778?v=4", - "description": "ODNet : Asteroid Occultation Detection Convolutional Neural Network", + "uid": "github/Ambuj-UF/APOP", + "url": "https://github.com/Ambuj-UF/APOP", + "rel": "/software/repository/github/Ambuj-UF/APOP", + "avatar": "https://avatars.githubusercontent.com/u/7588003?v=4", + "description": "Allostery pocket prediction", "topics": [] }, { - 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Performs benchmarks against datasets and SotA algorithms, and implements training, validation and testing procedures.", + "topics": [ + "collaborative-filtering", + "drug-repurposing", + "open-science", + "python", + "science-reproducibility" + ] + }, + { + "uid": "github/pybamm-team/PyBaMM", + "url": "https://github.com/pybamm-team/PyBaMM", + "rel": "/software/repository/github/pybamm-team/PyBaMM", + "avatar": "https://avatars.githubusercontent.com/u/48961907?v=4", + "description": "Fast and flexible physics-based battery models in Python", + "topics": [ + "pybamm", + "battery-models", + "solvers", + "python", + "batteries", + "simulation" + ] + }, + { + "uid": "github/pybamm-team/liionpack", + "url": "https://github.com/pybamm-team/liionpack", + "rel": "/software/repository/github/pybamm-team/liionpack", + "avatar": "https://avatars.githubusercontent.com/u/48961907?v=4", + "description": "A battery pack simulation tool that uses the PyBaMM framework", "topics": [] }, { - "uid": "github/PaulRitsche/DLTrack", - "url": "https://github.com/PaulRitsche/DL_Track_US", - "rel": "/software/repository/github/PaulRitsche/DLTrack", - "avatar": "https://avatars.githubusercontent.com/u/71383228?v=4", - "description": "This repositories contains code for automatic analysis of human lower limb ultrasonography images.", + "uid": "github/jgducoin/galclaim", + "url": "https://github.com/jgducoin/galclaim", + "rel": "/software/repository/github/jgducoin/galclaim", + "avatar": "https://avatars.githubusercontent.com/u/44273935?v=4", + "description": "GALaxy Chance of Local Alignment algorIthM", "topics": [] }, { - "uid": "github/yiwenstat/MCPCA_PopGen", - "url": "https://github.com/yiwenstat/MCPCA_PopGen", - "rel": "/software/repository/github/yiwenstat/MCPCA_PopGen", - "avatar": "https://avatars.githubusercontent.com/u/44883065?v=4", + "uid": "github/ot483/NetCom", + "url": "https://github.com/ot483/NetCom", + "rel": "/software/repository/github/ot483/NetCom", + "avatar": "https://avatars.githubusercontent.com/u/78791373?v=4", "description": null, "topics": [] }, { - "uid": "github/Oftatkofta/cellocity", - "url": "https://github.com/Oftatkofta/cellocity", - "rel": "/software/repository/github/Oftatkofta/cellocity", - "avatar": "https://avatars.githubusercontent.com/u/6969742?v=4", - "description": "Scientific software for analysis of confluent cell dynamics.", + "uid": "github/vembrane/vembrane", + "url": "https://github.com/vembrane/vembrane", + "rel": "/software/repository/github/vembrane/vembrane", + "avatar": "https://avatars.githubusercontent.com/u/68063743?v=4", + "description": "vembrane filters VCF records using python expressions", "topics": [ - "microscopy", - "time-series-analysis", - "analysis", - "vector-analysis", - "microscopy-data", - "cell-dynamics" + "bioinformatics", + "filter", + "filter-expression", + "vcf", + "vcf-filtering" ] }, { - "uid": "github/miguelzuma/hi_class_public", - "url": "https://github.com/miguelzuma/hi_class_public", - "rel": "/software/repository/github/miguelzuma/hi_class_public", - "avatar": "https://avatars.githubusercontent.com/u/5014027?v=4", - "description": "Public version of Horndeski in the Cosmic Linear Anisotropy Solving System", + "uid": "github/johannesulf/dsigma", + "url": "https://github.com/johannesulf/dsigma", + "rel": "/software/repository/github/johannesulf/dsigma", + "avatar": "https://avatars.githubusercontent.com/u/4167911?v=4", + "description": "A Galaxy-Galaxy Lensing Python Package", "topics": [] }, { - "uid": "github/pennucci/PulsePortraiture", - "url": "https://github.com/pennucci/PulsePortraiture", - "rel": "/software/repository/github/pennucci/PulsePortraiture", - "avatar": "https://avatars.githubusercontent.com/u/1768226?v=4", - "description": "PulsePortraiture (PP): a wideband pulsar timing code written in python. It uses an extension of Joe Taylor's FFTFIT algorithm (Taylor 1992) to simultaneously measure a phase (TOA) and dispersion measure (DM). PSRCHIVE, lmfit, and the latest vertsions of numpy and scipy are required.", + "uid": "github/andymummeryastro/tidalspin", + "url": "https://github.com/andymummeryastro/tidalspin", + "rel": "/software/repository/github/andymummeryastro/tidalspin", + "avatar": "https://avatars.githubusercontent.com/u/87980281?v=4", + "description": "Python package for constraining black hole spins using the properties of relativistic tidal forces", "topics": [] }, { - "uid": "github/GEUS-Glaciology-and-Climate/pypromice", - "url": "https://github.com/GEUS-Glaciology-and-Climate/pypromice", - "rel": "/software/repository/github/GEUS-Glaciology-and-Climate/pypromice", - "avatar": "https://avatars.githubusercontent.com/u/71171316?v=4", - "description": "Process AWS data from L0 (raw logger) through Lx (end user)", + "uid": "github/jodyphelan/tb-ml", + "url": "https://github.com/jodyphelan/tb-ml", + "rel": "/software/repository/github/jodyphelan/tb-ml", + "avatar": "https://avatars.githubusercontent.com/u/8697224?v=4", + "description": "A simple tool for creating machine learning antimicrobial resistance prediction pipelines using Docker containers for M. tuberculosis", "topics": [ - "greenland", - "weather", - "weather-station" + "amr", + "ml" ] }, { - "uid": "github/hsocasnavarro/NICOLE", - "url": "https://github.com/hsocasnavarro/NICOLE", - "rel": "/software/repository/github/hsocasnavarro/NICOLE", - "avatar": "https://avatars.githubusercontent.com/u/5393130?v=4", - "description": "NLTE Stokes Synthesis/Inversion Code", - "topics": [] - }, - { - "uid": "github/alastair-droop/fqtools", - "url": "https://github.com/alastair-droop/fqtools", - "rel": "/software/repository/github/alastair-droop/fqtools", - "avatar": "https://avatars.githubusercontent.com/u/13238060?v=4", - "description": "An efficient FASTQ manipulation suite", + "uid": "github/jodyphelan/TBProfiler", + "url": "https://github.com/jodyphelan/TBProfiler", + "rel": "/software/repository/github/jodyphelan/TBProfiler", + "avatar": "https://avatars.githubusercontent.com/u/8697224?v=4", + "description": "Profiling tool for Mycobacterium tuberculosis to detect ressistance and strain type from WGS data", "topics": [ - "fastq", - "fastq-files", - "next-generation-sequencing", - "bioinformatics" + "drug-resistance", + "tb-profiler" ] } ] \ No newline at end of file diff --git a/docs/repository/github/CEA-MetroCarac/fitspy/annotate-criteria/index.html b/docs/repository/github/CEA-MetroCarac/fitspy/annotate-criteria/index.html new file mode 100644 index 000000000..f5db8274e --- /dev/null +++ b/docs/repository/github/CEA-MetroCarac/fitspy/annotate-criteria/index.html @@ -0,0 +1,169 @@ + + + + + Annotate Criteria for github/CEA-MetroCarac/fitspy + + + + + + + + + + + +
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+

What do you think about github/CEA-MetroCarac/fitspy + +

+

Generic tool dedicated to fit spectra in python

+

If you don't know an answer, don't answer it!

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+
+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
QuestionYour Response
Would taking away the software be a detriment to research? + + + + +
Has the software been cited? + + + + +
Is the software intended for a particular domain? + + + + +
Was the software created with intention to solve a research question? + + + + +
Is the software intended for research? + + + + +
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+ + + + + + + + + + + + + \ No newline at end of file diff --git a/docs/repository/github/CEA-MetroCarac/fitspy/annotate-taxonomy/index.html b/docs/repository/github/CEA-MetroCarac/fitspy/annotate-taxonomy/index.html new file mode 100644 index 000000000..66346761c --- /dev/null +++ b/docs/repository/github/CEA-MetroCarac/fitspy/annotate-taxonomy/index.html @@ -0,0 +1,254 @@ + + + + + Annotate Criteria + + + + + + + + + + + +
+
+
+
+

github/CEA-MetroCarac/fitspy

+

How would you categorize this software? Choose more than one. See examples and visual

+

Your submission will be posted as a new GitHub issue, with automation to update the database.

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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Software to directly conduct research Domain-specific software +
Software to directly conduct research Domain-specific software +
Software to directly conduct research Domain-specific software +
Software to directly conduct research General software +
Software to directly conduct research General software +
Software to directly conduct research General software +
Software to support research Explicitly for research +
Software to support research Explicitly for research +
Software to support research Explicitly for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Used for research but not explicitly for it +
Software to support research Used for research but not explicitly for it +
Software to support research Used for research but not explicitly for it +
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+ + + + + + + + + + + + + \ No newline at end of file diff --git a/docs/repository/github/Markusjsommer/BalrogCPP/annotate-criteria/index.html b/docs/repository/github/Markusjsommer/BalrogCPP/annotate-criteria/index.html new file mode 100644 index 000000000..2e35efb51 --- /dev/null +++ b/docs/repository/github/Markusjsommer/BalrogCPP/annotate-criteria/index.html @@ -0,0 +1,169 @@ + + + + + Annotate Criteria for github/Markusjsommer/BalrogCPP + + + + + + + + + + + +
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What do you think about github/Markusjsommer/BalrogCPP + +

+

A universal protein model for prokaryotic gene prediction

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If you don't know an answer, don't answer it!

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+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
QuestionYour Response
Would taking away the software be a detriment to research? + + + + +
Has the software been cited? + + + + +
Is the software intended for a particular domain? + + + + +
Was the software created with intention to solve a research question? + + + + +
Is the software intended for research? + + + + +
Has the software been used by researchers? + + + + +
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+ + + + + + + + + + + + + \ No newline at end of file diff --git a/docs/repository/github/Markusjsommer/BalrogCPP/annotate-taxonomy/index.html b/docs/repository/github/Markusjsommer/BalrogCPP/annotate-taxonomy/index.html new file mode 100644 index 000000000..35258146f --- /dev/null +++ b/docs/repository/github/Markusjsommer/BalrogCPP/annotate-taxonomy/index.html @@ -0,0 +1,254 @@ + + + + + Annotate Criteria + + + + + + + + + + + +
+
+
+
+

github/Markusjsommer/BalrogCPP

+

How would you categorize this software? Choose more than one. See examples and visual

+

Your submission will be posted as a new GitHub issue, with automation to update the database.

+
+
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+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Software to directly conduct research Domain-specific software +
Software to directly conduct research Domain-specific software +
Software to directly conduct research Domain-specific software +
Software to directly conduct research General software +
Software to directly conduct research General software +
Software to directly conduct research General software +
Software to support research Explicitly for research +
Software to support research Explicitly for research +
Software to support research Explicitly for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Used for research but not explicitly for it +
Software to support research Used for research but not explicitly for it +
Software to support research Used for research but not explicitly for it +
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+ + + + + + + + + + + + + \ No newline at end of file diff --git a/docs/repository/github/MatthijsHak/MetalDock/annotate-criteria/index.html b/docs/repository/github/MatthijsHak/MetalDock/annotate-criteria/index.html new file mode 100644 index 000000000..b734ac52a --- /dev/null +++ b/docs/repository/github/MatthijsHak/MetalDock/annotate-criteria/index.html @@ -0,0 +1,169 @@ + + + + + Annotate Criteria for github/MatthijsHak/MetalDock + + + + + + + + + + + +
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What do you think about github/MatthijsHak/MetalDock + +

+

Dock organometallic compounds to proteins/DNA/biomolecules

+

If you don't know an answer, don't answer it!

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+
+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
QuestionYour Response
Would taking away the software be a detriment to research? + + + + +
Has the software been cited? + + + + +
Is the software intended for a particular domain? + + + + +
Was the software created with intention to solve a research question? + + + + +
Is the software intended for research? + + + + +
Has the software been used by researchers? + + + + +
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+ + + + + + + + + + + + + \ No newline at end of file diff --git a/docs/repository/github/MatthijsHak/MetalDock/annotate-taxonomy/index.html b/docs/repository/github/MatthijsHak/MetalDock/annotate-taxonomy/index.html new file mode 100644 index 000000000..2faecc00b --- /dev/null +++ b/docs/repository/github/MatthijsHak/MetalDock/annotate-taxonomy/index.html @@ -0,0 +1,254 @@ + + + + + Annotate Criteria + + + + + + + + + + + +
+
+
+
+

github/MatthijsHak/MetalDock

+

How would you categorize this software? Choose more than one. See examples and visual

+

Your submission will be posted as a new GitHub issue, with automation to update the database.

+
+
+
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Software to directly conduct research Domain-specific software +
Software to directly conduct research Domain-specific software +
Software to directly conduct research Domain-specific software +
Software to directly conduct research General software +
Software to directly conduct research General software +
Software to directly conduct research General software +
Software to support research Explicitly for research +
Software to support research Explicitly for research +
Software to support research Explicitly for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Used for research but not explicitly for it +
Software to support research Used for research but not explicitly for it +
Software to support research Used for research but not explicitly for it +
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+ + + + + + + + + + + + + \ No newline at end of file diff --git a/docs/repository/github/PopGenClustering/Clumppling/annotate-criteria/index.html b/docs/repository/github/PopGenClustering/Clumppling/annotate-criteria/index.html new file mode 100644 index 000000000..8c6c59059 --- /dev/null +++ b/docs/repository/github/PopGenClustering/Clumppling/annotate-criteria/index.html @@ -0,0 +1,169 @@ + + + + + Annotate Criteria for github/PopGenClustering/Clumppling + + + + + + + + + + + +
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What do you think about github/PopGenClustering/Clumppling + +

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None

+

If you don't know an answer, don't answer it!

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+
+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
QuestionYour Response
Would taking away the software be a detriment to research? + + + + +
Has the software been cited? + + + + +
Is the software intended for a particular domain? + + + + +
Was the software created with intention to solve a research question? + + + + +
Is the software intended for research? + + + + +
Has the software been used by researchers? + + + + +
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+ + + + + + + + + + + + + \ No newline at end of file diff --git a/docs/repository/github/PopGenClustering/Clumppling/annotate-taxonomy/index.html b/docs/repository/github/PopGenClustering/Clumppling/annotate-taxonomy/index.html new file mode 100644 index 000000000..1fcbac58e --- /dev/null +++ b/docs/repository/github/PopGenClustering/Clumppling/annotate-taxonomy/index.html @@ -0,0 +1,254 @@ + + + + + Annotate Criteria + + + + + + + + + + + +
+
+
+
+

github/PopGenClustering/Clumppling

+

How would you categorize this software? Choose more than one. See examples and visual

+

Your submission will be posted as a new GitHub issue, with automation to update the database.

+
+
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+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Software to directly conduct research Domain-specific software +
Software to directly conduct research Domain-specific software +
Software to directly conduct research Domain-specific software +
Software to directly conduct research General software +
Software to directly conduct research General software +
Software to directly conduct research General software +
Software to support research Explicitly for research +
Software to support research Explicitly for research +
Software to support research Explicitly for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Used for research but not explicitly for it +
Software to support research Used for research but not explicitly for it +
Software to support research Used for research but not explicitly for it +
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+ + + + + + + + + + + + + \ No newline at end of file diff --git a/docs/repository/github/SMTG-Bham/doped/annotate-criteria/index.html b/docs/repository/github/SMTG-Bham/doped/annotate-criteria/index.html new file mode 100644 index 000000000..58fd3ea5e --- /dev/null +++ b/docs/repository/github/SMTG-Bham/doped/annotate-criteria/index.html @@ -0,0 +1,169 @@ + + + + + Annotate Criteria for github/SMTG-Bham/doped + + + + + + + + + + + +
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+

What do you think about github/SMTG-Bham/doped + +

+

doped is a Python software for the generation, pre-/post-processing and analysis of defect supercell calculations, implementing the defect simulation workflow in an efficient, reproducible, user-friendly yet powerful and fully-customisable manner.

+

If you don't know an answer, don't answer it!

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QuestionYour Response
Would taking away the software be a detriment to research? + + + + +
Has the software been cited? + + + + +
Is the software intended for a particular domain? + + + + +
Was the software created with intention to solve a research question? + + + + +
Is the software intended for research? + + + + +
Has the software been used by researchers? + + + + +
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+ database: filesystem +
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+ + + + + + + + + + + + + \ No newline at end of file diff --git a/docs/repository/github/SMTG-Bham/doped/annotate-taxonomy/index.html b/docs/repository/github/SMTG-Bham/doped/annotate-taxonomy/index.html new file mode 100644 index 000000000..85024e6ba --- /dev/null +++ b/docs/repository/github/SMTG-Bham/doped/annotate-taxonomy/index.html @@ -0,0 +1,254 @@ + + + + + Annotate Criteria + + + + + + + + + + + +
+
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+
+

github/SMTG-Bham/doped

+

How would you categorize this software? Choose more than one. See examples and visual

+

Your submission will be posted as a new GitHub issue, with automation to update the database.

+
+
+
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Software to directly conduct research Domain-specific software +
Software to directly conduct research Domain-specific software +
Software to directly conduct research Domain-specific software +
Software to directly conduct research General software +
Software to directly conduct research General software +
Software to directly conduct research General software +
Software to support research Explicitly for research +
Software to support research Explicitly for research +
Software to support research Explicitly for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Used for research but not explicitly for it +
Software to support research Used for research but not explicitly for it +
Software to support research Used for research but not explicitly for it +
+
+ +
+
+ + +
+
+ + +
+ database: filesystem +
+
+
+ + + + + + + + + + + + + \ No newline at end of file diff --git a/docs/repository/github/TravisWheelerLab/VIBES/annotate-criteria/index.html b/docs/repository/github/TravisWheelerLab/VIBES/annotate-criteria/index.html new file mode 100644 index 000000000..96d9c8560 --- /dev/null +++ b/docs/repository/github/TravisWheelerLab/VIBES/annotate-criteria/index.html @@ -0,0 +1,169 @@ + + + + + Annotate Criteria for github/TravisWheelerLab/VIBES + + + + + + + + + + + +
+
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+
+

What do you think about github/TravisWheelerLab/VIBES + +

+

Viral Integrations in Bacterial genomES

+

If you don't know an answer, don't answer it!

+
+
+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
QuestionYour Response
Would taking away the software be a detriment to research? + + + + +
Has the software been cited? + + + + +
Is the software intended for a particular domain? + + + + +
Was the software created with intention to solve a research question? + + + + +
Is the software intended for research? + + + + +
Has the software been used by researchers? + + + + +
+ +
+ +
+
+ + + +
+
+
+
+
+ +
+ database: filesystem +
+
+
+ + + + + + + + + + + + + \ No newline at end of file diff --git a/docs/repository/github/TravisWheelerLab/VIBES/annotate-taxonomy/index.html b/docs/repository/github/TravisWheelerLab/VIBES/annotate-taxonomy/index.html new file mode 100644 index 000000000..c4242014a --- /dev/null +++ b/docs/repository/github/TravisWheelerLab/VIBES/annotate-taxonomy/index.html @@ -0,0 +1,254 @@ + + + + + Annotate Criteria + + + + + + + + + + + +
+
+
+
+

github/TravisWheelerLab/VIBES

+

How would you categorize this software? Choose more than one. See examples and visual

+

Your submission will be posted as a new GitHub issue, with automation to update the database.

+
+
+
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Software to directly conduct research Domain-specific software +
Software to directly conduct research Domain-specific software +
Software to directly conduct research Domain-specific software +
Software to directly conduct research General software +
Software to directly conduct research General software +
Software to directly conduct research General software +
Software to support research Explicitly for research +
Software to support research Explicitly for research +
Software to support research Explicitly for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Used for research but not explicitly for it +
Software to support research Used for research but not explicitly for it +
Software to support research Used for research but not explicitly for it +
+
+ +
+
+ + +
+
+ + +
+ database: filesystem +
+
+
+ + + + + + + + + + + + + \ No newline at end of file diff --git a/docs/repository/github/chemprop/chemprop_benchmark/annotate-criteria/index.html b/docs/repository/github/chemprop/chemprop_benchmark/annotate-criteria/index.html new file mode 100644 index 000000000..f6d8ede49 --- /dev/null +++ b/docs/repository/github/chemprop/chemprop_benchmark/annotate-criteria/index.html @@ -0,0 +1,169 @@ + + + + + Annotate Criteria for github/chemprop/chemprop_benchmark + + + + + + + + + + + +
+
+
+
+
+
+
+
+
+
+
+

What do you think about github/chemprop/chemprop_benchmark + +

+

Chemprop benchmarking scripts and data

+

If you don't know an answer, don't answer it!

+
+
+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
QuestionYour Response
Would taking away the software be a detriment to research? + + + + +
Has the software been cited? + + + + +
Is the software intended for a particular domain? + + + + +
Was the software created with intention to solve a research question? + + + + +
Is the software intended for research? + + + + +
Has the software been used by researchers? + + + + +
+ +
+ +
+
+ + + +
+
+
+
+
+ +
+ database: filesystem +
+
+
+ + + + + + + + + + + + + \ No newline at end of file diff --git a/docs/repository/github/chemprop/chemprop_benchmark/annotate-taxonomy/index.html b/docs/repository/github/chemprop/chemprop_benchmark/annotate-taxonomy/index.html new file mode 100644 index 000000000..af80d5531 --- /dev/null +++ b/docs/repository/github/chemprop/chemprop_benchmark/annotate-taxonomy/index.html @@ -0,0 +1,254 @@ + + + + + Annotate Criteria + + + + + + + + + + + +
+
+
+
+

github/chemprop/chemprop_benchmark

+

How would you categorize this software? Choose more than one. See examples and visual

+

Your submission will be posted as a new GitHub issue, with automation to update the database.

+
+
+
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Software to directly conduct research Domain-specific software +
Software to directly conduct research Domain-specific software +
Software to directly conduct research Domain-specific software +
Software to directly conduct research General software +
Software to directly conduct research General software +
Software to directly conduct research General software +
Software to support research Explicitly for research +
Software to support research Explicitly for research +
Software to support research Explicitly for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Used for research but not explicitly for it +
Software to support research Used for research but not explicitly for it +
Software to support research Used for research but not explicitly for it +
+
+ +
+
+ + +
+
+ + +
+ database: filesystem +
+
+
+ + + + + + + + + + + + + \ No newline at end of file diff --git a/docs/repository/github/eisascience/HISTA/annotate-criteria/index.html b/docs/repository/github/eisascience/HISTA/annotate-criteria/index.html new file mode 100644 index 000000000..c7ee951ea --- /dev/null +++ b/docs/repository/github/eisascience/HISTA/annotate-criteria/index.html @@ -0,0 +1,169 @@ + + + + + Annotate Criteria for github/eisascience/HISTA + + + + + + + + + + + +
+
+
+
+
+
+
+
+
+
+
+

What do you think about github/eisascience/HISTA + +

+

Human Infertility Single-cell Testis Atlas

+

If you don't know an answer, don't answer it!

+
+
+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
QuestionYour Response
Would taking away the software be a detriment to research? + + + + +
Has the software been cited? + + + + +
Is the software intended for a particular domain? + + + + +
Was the software created with intention to solve a research question? + + + + +
Is the software intended for research? + + + + +
Has the software been used by researchers? + + + + +
+ +
+ +
+
+ + + +
+
+
+
+
+ +
+ database: filesystem +
+
+
+ + + + + + + + + + + + + \ No newline at end of file diff --git a/docs/repository/github/eisascience/HISTA/annotate-taxonomy/index.html b/docs/repository/github/eisascience/HISTA/annotate-taxonomy/index.html new file mode 100644 index 000000000..91145d90c --- /dev/null +++ b/docs/repository/github/eisascience/HISTA/annotate-taxonomy/index.html @@ -0,0 +1,254 @@ + + + + + Annotate Criteria + + + + + + + + + + + +
+
+
+
+

github/eisascience/HISTA

+

How would you categorize this software? Choose more than one. See examples and visual

+

Your submission will be posted as a new GitHub issue, with automation to update the database.

+
+
+
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Software to directly conduct research Domain-specific software +
Software to directly conduct research Domain-specific software +
Software to directly conduct research Domain-specific software +
Software to directly conduct research General software +
Software to directly conduct research General software +
Software to directly conduct research General software +
Software to support research Explicitly for research +
Software to support research Explicitly for research +
Software to support research Explicitly for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Used for research but not explicitly for it +
Software to support research Used for research but not explicitly for it +
Software to support research Used for research but not explicitly for it +
+
+ +
+
+ + +
+
+ + +
+ database: filesystem +
+
+
+ + + + + + + + + + + + + \ No newline at end of file diff --git a/docs/repository/github/hpc-maths/samurai/annotate-criteria/index.html b/docs/repository/github/hpc-maths/samurai/annotate-criteria/index.html new file mode 100644 index 000000000..0ab04ac2a --- /dev/null +++ b/docs/repository/github/hpc-maths/samurai/annotate-criteria/index.html @@ -0,0 +1,169 @@ + + + + + Annotate Criteria for github/hpc-maths/samurai + + + + + + + + + + + +
+
+
+
+
+
+
+
+
+
+
+

What do you think about github/hpc-maths/samurai + +

+

Intervals coupled with algebra of set to handle adaptive mesh refinement and operators on it.

+

If you don't know an answer, don't answer it!

+
+
+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
QuestionYour Response
Would taking away the software be a detriment to research? + + + + +
Has the software been cited? + + + + +
Is the software intended for a particular domain? + + + + +
Was the software created with intention to solve a research question? + + + + +
Is the software intended for research? + + + + +
Has the software been used by researchers? + + + + +
+ +
+ +
+
+ + + +
+
+
+
+
+ +
+ database: filesystem +
+
+
+ + + + + + + + + + + + + \ No newline at end of file diff --git a/docs/repository/github/hpc-maths/samurai/annotate-taxonomy/index.html b/docs/repository/github/hpc-maths/samurai/annotate-taxonomy/index.html new file mode 100644 index 000000000..6fcab8876 --- /dev/null +++ b/docs/repository/github/hpc-maths/samurai/annotate-taxonomy/index.html @@ -0,0 +1,254 @@ + + + + + Annotate Criteria + + + + + + + + + + + +
+
+
+
+

github/hpc-maths/samurai

+

How would you categorize this software? Choose more than one. See examples and visual

+

Your submission will be posted as a new GitHub issue, with automation to update the database.

+
+
+
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Software to directly conduct research Domain-specific software +
Software to directly conduct research Domain-specific software +
Software to directly conduct research Domain-specific software +
Software to directly conduct research General software +
Software to directly conduct research General software +
Software to directly conduct research General software +
Software to support research Explicitly for research +
Software to support research Explicitly for research +
Software to support research Explicitly for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Used for research but not explicitly for it +
Software to support research Used for research but not explicitly for it +
Software to support research Used for research but not explicitly for it +
+
+ +
+
+ + +
+
+ + +
+ database: filesystem +
+
+
+ + + + + + + + + + + + + \ No newline at end of file diff --git a/docs/repository/github/lemene/PECAT/annotate-criteria/index.html b/docs/repository/github/lemene/PECAT/annotate-criteria/index.html new file mode 100644 index 000000000..63b13ac47 --- /dev/null +++ b/docs/repository/github/lemene/PECAT/annotate-criteria/index.html @@ -0,0 +1,169 @@ + + + + + Annotate Criteria for github/lemene/PECAT + + + + + + + + + + + +
+
+
+
+
+
+
+
+
+
+
+

What do you think about github/lemene/PECAT + +

+

PECAT, a phased error correct and assembly tool

+

If you don't know an answer, don't answer it!

+
+
+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
QuestionYour Response
Would taking away the software be a detriment to research? + + + + +
Has the software been cited? + + + + +
Is the software intended for a particular domain? + + + + +
Was the software created with intention to solve a research question? + + + + +
Is the software intended for research? + + + + +
Has the software been used by researchers? + + + + +
+ +
+ +
+
+ + + +
+
+
+
+
+ +
+ database: filesystem +
+
+
+ + + + + + + + + + + + + \ No newline at end of file diff --git a/docs/repository/github/lemene/PECAT/annotate-taxonomy/index.html b/docs/repository/github/lemene/PECAT/annotate-taxonomy/index.html new file mode 100644 index 000000000..93401e875 --- /dev/null +++ b/docs/repository/github/lemene/PECAT/annotate-taxonomy/index.html @@ -0,0 +1,254 @@ + + + + + Annotate Criteria + + + + + + + + + + + +
+
+
+
+

github/lemene/PECAT

+

How would you categorize this software? Choose more than one. See examples and visual

+

Your submission will be posted as a new GitHub issue, with automation to update the database.

+
+
+
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Software to directly conduct research Domain-specific software +
Software to directly conduct research Domain-specific software +
Software to directly conduct research Domain-specific software +
Software to directly conduct research General software +
Software to directly conduct research General software +
Software to directly conduct research General software +
Software to support research Explicitly for research +
Software to support research Explicitly for research +
Software to support research Explicitly for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Used for research but not explicitly for it +
Software to support research Used for research but not explicitly for it +
Software to support research Used for research but not explicitly for it +
+
+ +
+
+ + +
+
+ + +
+ database: filesystem +
+
+
+ + + + + + + + + + + + + \ No newline at end of file diff --git a/docs/repository/github/metabolomicsworkbench/MetGENE/annotate-criteria/index.html b/docs/repository/github/metabolomicsworkbench/MetGENE/annotate-criteria/index.html new file mode 100644 index 000000000..000525cd9 --- /dev/null +++ b/docs/repository/github/metabolomicsworkbench/MetGENE/annotate-criteria/index.html @@ -0,0 +1,169 @@ + + + + + Annotate Criteria for github/metabolomicsworkbench/MetGENE + + + + + + + + + + + +
+
+
+
+
+
+
+
+
+
+
+

What do you think about github/metabolomicsworkbench/MetGENE + +

+

Gene-centric Metabolomics Information Retrieval Tool

+

If you don't know an answer, don't answer it!

+
+
+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
QuestionYour Response
Would taking away the software be a detriment to research? + + + + +
Has the software been cited? + + + + +
Is the software intended for a particular domain? + + + + +
Was the software created with intention to solve a research question? + + + + +
Is the software intended for research? + + + + +
Has the software been used by researchers? + + + + +
+ +
+ +
+
+ + + +
+
+
+
+
+ +
+ database: filesystem +
+
+
+ + + + + + + + + + + + + \ No newline at end of file diff --git a/docs/repository/github/metabolomicsworkbench/MetGENE/annotate-taxonomy/index.html b/docs/repository/github/metabolomicsworkbench/MetGENE/annotate-taxonomy/index.html new file mode 100644 index 000000000..3fa6bab62 --- /dev/null +++ b/docs/repository/github/metabolomicsworkbench/MetGENE/annotate-taxonomy/index.html @@ -0,0 +1,254 @@ + + + + + Annotate Criteria + + + + + + + + + + + +
+
+
+
+

github/metabolomicsworkbench/MetGENE

+

How would you categorize this software? Choose more than one. See examples and visual

+

Your submission will be posted as a new GitHub issue, with automation to update the database.

+
+
+
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Software to directly conduct research Domain-specific software +
Software to directly conduct research Domain-specific software +
Software to directly conduct research Domain-specific software +
Software to directly conduct research General software +
Software to directly conduct research General software +
Software to directly conduct research General software +
Software to support research Explicitly for research +
Software to support research Explicitly for research +
Software to support research Explicitly for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Used for research but not explicitly for it +
Software to support research Used for research but not explicitly for it +
Software to support research Used for research but not explicitly for it +
+
+ +
+
+ + +
+
+ + +
+ database: filesystem +
+
+
+ + + + + + + + + + + + + \ No newline at end of file diff --git a/docs/repository/github/mikejohnson51/AHGestimation/annotate-criteria/index.html b/docs/repository/github/mikejohnson51/AHGestimation/annotate-criteria/index.html new file mode 100644 index 000000000..75032d98a --- /dev/null +++ b/docs/repository/github/mikejohnson51/AHGestimation/annotate-criteria/index.html @@ -0,0 +1,169 @@ + + + + + Annotate Criteria for github/mikejohnson51/AHGestimation + + + + + + + + + + + +
+
+
+
+
+
+
+
+
+
+
+

What do you think about github/mikejohnson51/AHGestimation + +

+

Estimating robust, mass conserving AHG relationships

+

If you don't know an answer, don't answer it!

+
+
+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
QuestionYour Response
Would taking away the software be a detriment to research? + + + + +
Has the software been cited? + + + + +
Is the software intended for a particular domain? + + + + +
Was the software created with intention to solve a research question? + + + + +
Is the software intended for research? + + + + +
Has the software been used by researchers? + + + + +
+ +
+ +
+
+ + + +
+
+
+
+
+ +
+ database: filesystem +
+
+
+ + + + + + + + + + + + + \ No newline at end of file diff --git a/docs/repository/github/mikejohnson51/AHGestimation/annotate-taxonomy/index.html b/docs/repository/github/mikejohnson51/AHGestimation/annotate-taxonomy/index.html new file mode 100644 index 000000000..d37133ffe --- /dev/null +++ b/docs/repository/github/mikejohnson51/AHGestimation/annotate-taxonomy/index.html @@ -0,0 +1,254 @@ + + + + + Annotate Criteria + + + + + + + + + + + +
+
+
+
+

github/mikejohnson51/AHGestimation

+

How would you categorize this software? Choose more than one. See examples and visual

+

Your submission will be posted as a new GitHub issue, with automation to update the database.

+
+
+
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Software to directly conduct research Domain-specific software +
Software to directly conduct research Domain-specific software +
Software to directly conduct research Domain-specific software +
Software to directly conduct research General software +
Software to directly conduct research General software +
Software to directly conduct research General software +
Software to support research Explicitly for research +
Software to support research Explicitly for research +
Software to support research Explicitly for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Used for research but not explicitly for it +
Software to support research Used for research but not explicitly for it +
Software to support research Used for research but not explicitly for it +
+
+ +
+
+ + +
+
+ + +
+ database: filesystem +
+
+
+ + + + + + + + + + + + + \ No newline at end of file diff --git a/docs/repository/github/musoke/UltraDark.jl/annotate-criteria/index.html b/docs/repository/github/musoke/UltraDark.jl/annotate-criteria/index.html new file mode 100644 index 000000000..3d323f7e4 --- /dev/null +++ b/docs/repository/github/musoke/UltraDark.jl/annotate-criteria/index.html @@ -0,0 +1,169 @@ + + + + + Annotate Criteria for github/musoke/UltraDark.jl + + + + + + + + + + + +
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Simulations of cosmological scalar fields

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+ + + + + + + + + + + + + \ No newline at end of file diff --git a/docs/repository/github/musoke/UltraDark.jl/annotate-taxonomy/index.html b/docs/repository/github/musoke/UltraDark.jl/annotate-taxonomy/index.html new file mode 100644 index 000000000..3727a58d9 --- /dev/null +++ b/docs/repository/github/musoke/UltraDark.jl/annotate-taxonomy/index.html @@ -0,0 +1,254 @@ + + + + + Annotate Criteria + + + + + + + + + + + +
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github/musoke/UltraDark.jl

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+ + + + + + + + + + + + + \ No newline at end of file diff --git a/docs/repository/github/robbievanleeuwen/section-properties/annotate-criteria/index.html b/docs/repository/github/robbievanleeuwen/section-properties/annotate-criteria/index.html new file mode 100644 index 000000000..de9e3b199 --- /dev/null +++ b/docs/repository/github/robbievanleeuwen/section-properties/annotate-criteria/index.html @@ -0,0 +1,169 @@ + + + + + Annotate Criteria for github/robbievanleeuwen/section-properties + + + + + + + + + + + +
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Analysis of an arbitrary cross-section in python using the finite element method.

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github/robbievanleeuwen/section-properties

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Alignment of RNAs

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github/s-will/LocARNA

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+
+ +
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+ + + + + + + + + + + + + \ No newline at end of file diff --git a/docs/repository/github/tberlok/paicos/annotate-criteria/index.html b/docs/repository/github/tberlok/paicos/annotate-criteria/index.html new file mode 100644 index 000000000..cb0ce15e8 --- /dev/null +++ b/docs/repository/github/tberlok/paicos/annotate-criteria/index.html @@ -0,0 +1,169 @@ + + + + + Annotate Criteria for github/tberlok/paicos + + + + + + + + + + + +
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An object-oriented Python package for analysis of (cosmological) simulations performed with Arepo

+

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github/tberlok/paicos

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Software to support research Used for research but not explicitly for it +
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+
+ +
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+ + +
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+ + +
+ database: filesystem +
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+ + + + + + + + + + + + + \ No newline at end of file diff --git a/docs/repository/github/tomoyukif/MCPtaggR/annotate-criteria/index.html b/docs/repository/github/tomoyukif/MCPtaggR/annotate-criteria/index.html new file mode 100644 index 000000000..b80e7a8f5 --- /dev/null +++ b/docs/repository/github/tomoyukif/MCPtaggR/annotate-criteria/index.html @@ -0,0 +1,169 @@ + + + + + Annotate Criteria for github/tomoyukif/MCPtaggR + + + + + + + + + + + +
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What do you think about github/tomoyukif/MCPtaggR + +

+

None

+

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QuestionYour Response
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+ database: filesystem +
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github/tomoyukif/MCPtaggR

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Software to directly conduct research Domain-specific software +
Software to directly conduct research Domain-specific software +
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Software to directly conduct research General software +
Software to directly conduct research General software +
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Software to support research Explicitly for research +
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Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Incidentally used for research +
Software to support research Used for research but not explicitly for it +
Software to support research Used for research but not explicitly for it +
Software to support research Used for research but not explicitly for it +
+
+ +
+
+ + +
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+ database: filesystem +
+
+
+ + + + + + + + + + + + + \ No newline at end of file diff --git a/docs/search/index.html b/docs/search/index.html index 710cb3aa1..352a90763 100644 --- a/docs/search/index.html +++ b/docs/search/index.html @@ -69,29 +69,71 @@ "url": " https://rseng.github.io/software/repository/gitlab/mauricemolli/petitRADTRANS", "content": "None" }, - "gitlab/german.tischler/biobambam2": { - "id": "gitlab/german.tischler/biobambam2", - "title": "gitlab/german.tischler/biobambam2", - "url": " https://rseng.github.io/software/repository/gitlab/german.tischler/biobambam2", - "content": "Tools for early stage alignment file processing" + "gitlab/aegge/comet-emu": { + "id": "gitlab/aegge/comet-emu", + "title": "gitlab/aegge/comet-emu", + "url": " https://rseng.github.io/software/repository/gitlab/aegge/comet-emu", + "content": "None" }, - "gitlab/german.tischler/libmaus2": { - "id": "gitlab/german.tischler/libmaus2", - "title": "gitlab/german.tischler/libmaus2", - "url": " https://rseng.github.io/software/repository/gitlab/german.tischler/libmaus2", - "content": "collection of data structures and algorithms" + "gitlab/casi-project/casi-3d": { + "id": "gitlab/casi-project/casi-3d", + "title": "gitlab/casi-project/casi-3d", + "url": " https://rseng.github.io/software/repository/gitlab/casi-project/casi-3d", + "content": "None" }, - "gitlab/eleonoraalei/exo-mercat-gui": { - "id": "gitlab/eleonoraalei/exo-mercat-gui", - "title": "gitlab/eleonoraalei/exo-mercat-gui", - "url": " https://rseng.github.io/software/repository/gitlab/eleonoraalei/exo-mercat-gui", - "content": "The Graphical User Interface of Exo-MerCat." + "gitlab/casi-project/casi-2d": { + "id": "gitlab/casi-project/casi-2d", + "title": "gitlab/casi-project/casi-2d", + "url": " https://rseng.github.io/software/repository/gitlab/casi-project/casi-2d", + "content": "Identification of stellar feedback signatures in simulated molecular clouds using methods from deep learning." }, - "gitlab/ProjectRHEA/flowsolverrhea": { - "id": "gitlab/ProjectRHEA/flowsolverrhea", - "title": "gitlab/ProjectRHEA/flowsolverrhea", - "url": " https://rseng.github.io/software/repository/gitlab/ProjectRHEA/flowsolverrhea", - "content": "RHEA: an open-source Reproducible and Hybrid-architecture flow solver Engineered for Academia" + "gitlab/clairedavies/sedbys": { + "id": "gitlab/clairedavies/sedbys", + "title": "gitlab/clairedavies/sedbys", + "url": " https://rseng.github.io/software/repository/gitlab/clairedavies/sedbys", + "content": "A python-based spectral energy distribution builder for young stars" + }, + "gitlab/andreas.andrusch/paipline": { + "id": "gitlab/andreas.andrusch/paipline", + "title": "gitlab/andreas.andrusch/paipline", + "url": " https://rseng.github.io/software/repository/gitlab/andreas.andrusch/paipline", + "content": "Pipeline for the Automatic Identification of Pathogens" + }, + "gitlab/metafundev/metafun": { + "id": "gitlab/metafundev/metafun", + "title": "gitlab/metafundev/metafun", + "url": " https://rseng.github.io/software/repository/gitlab/metafundev/metafun", + "content": "" + }, + "gitlab/treangenlab/vulcan": { + "id": "gitlab/treangenlab/vulcan", + "title": "gitlab/treangenlab/vulcan", + "url": " https://rseng.github.io/software/repository/gitlab/treangenlab/vulcan", + "content": "" + }, + "gitlab/treangenlab/emu": { + "id": "gitlab/treangenlab/emu", + "title": "gitlab/treangenlab/emu", + "url": " https://rseng.github.io/software/repository/gitlab/treangenlab/emu", + "content": "EMu is a relative abundance estimator for 16S genomic sequences" + }, + "gitlab/programgreg/tagginglatencyestimator": { + "id": "gitlab/programgreg/tagginglatencyestimator", + "title": "gitlab/programgreg/tagginglatencyestimator", + "url": " https://rseng.github.io/software/repository/gitlab/programgreg/tagginglatencyestimator", + "content": "Software to estimate the latency of the tagging process." + }, + "gitlab/pyFBS/pyFBS": { + "id": "gitlab/pyFBS/pyFBS", + "title": "gitlab/pyFBS/pyFBS", + "url": " https://rseng.github.io/software/repository/gitlab/pyFBS/pyFBS", + "content": "A Python package for Frequency Based Substructuring and Transfer Path Analysis" + }, + "gitlab/ChemBioHub/tpmap": { + "id": "gitlab/ChemBioHub/tpmap", + "title": "gitlab/ChemBioHub/tpmap", + "url": " https://rseng.github.io/software/repository/gitlab/ChemBioHub/tpmap", + "content": "Thermal Profiling Meltome Analysis Program" }, "gitlab/ostrokach/proteinsolver": { "id": "gitlab/ostrokach/proteinsolver", @@ -101,11 +143,17 @@ " }, - "gitlab/project-dare/dare-platform": { - "id": "gitlab/project-dare/dare-platform", - "title": "gitlab/project-dare/dare-platform", - "url": " https://rseng.github.io/software/repository/gitlab/project-dare/dare-platform", - "content": "" + "gitlab/robizzard/libcdict": { + "id": "gitlab/robizzard/libcdict", + "title": "gitlab/robizzard/libcdict", + "url": " https://rseng.github.io/software/repository/gitlab/robizzard/libcdict", + "content": "A generic associative array, also know as dictionary or hash, library in C, based on uthash and extended to be more user friendly and include integration features such as JSON output." + }, + "gitlab/JuditGG/trumpetplots": { + "id": "gitlab/JuditGG/trumpetplots", + "title": "gitlab/JuditGG/trumpetplots", + "url": " https://rseng.github.io/software/repository/gitlab/JuditGG/trumpetplots", + "content": "Rpackage for Trumpet plots" }, "gitlab/souvlaki/thalassa": { "id": "gitlab/souvlaki/thalassa", @@ -113,102 +161,35 @@ "url": " https://rseng.github.io/software/repository/gitlab/souvlaki/thalassa", "content": "None" }, - "gitlab/fduchate/predihood": { - "id": "gitlab/fduchate/predihood", - "title": "gitlab/fduchate/predihood", - "url": " https://rseng.github.io/software/repository/gitlab/fduchate/predihood", - "content": "" - }, - "gitlab/pipe3d/pyPipe3D": { - "id": "gitlab/pipe3d/pyPipe3D", - "title": "gitlab/pipe3d/pyPipe3D", - "url": " https://rseng.github.io/software/repository/gitlab/pipe3d/pyPipe3D", - "content": "pyPipe3D is a spectroscopy analysis pipeline which produces coherent, easy to distribute and compare, parameters of the stellar populations and the ionized gas, suited in particular for data from the most recent optical IFS surveys." - }, - "gitlab/polmag/PORTA": { - "id": "gitlab/polmag/PORTA", - "title": "gitlab/polmag/PORTA", - "url": " https://rseng.github.io/software/repository/gitlab/polmag/PORTA", - "content": "PORTA: A three-dimensional multilevel radiative transfer code for modeling the intensity and polarization of spectral lines with massively parallel computers" - }, "gitlab/aceteam.kaist/ACE-Molecule": { "id": "gitlab/aceteam.kaist/ACE-Molecule", "title": "gitlab/aceteam.kaist/ACE-Molecule", "url": " https://rseng.github.io/software/repository/gitlab/aceteam.kaist/ACE-Molecule", "content": "GitLab repository for ACE-Molecule." }, - "gitlab/astron-idg/idg": { - "id": "gitlab/astron-idg/idg", - "title": "gitlab/astron-idg/idg", - "url": " https://rseng.github.io/software/repository/gitlab/astron-idg/idg", - "content": "Mirror of git.astron.nl/rd/idg" - }, - "gitlab/jesseds/apav": { - "id": "gitlab/jesseds/apav", - "title": "gitlab/jesseds/apav", - "url": " https://rseng.github.io/software/repository/gitlab/jesseds/apav", - "content": "APAV (Atom Probe Analysis and Visualization) is a Python library for the analysis and -visualization of atom probe tomography experiments." - }, - "gitlab/multigris/mgris": { - "id": "gitlab/multigris/mgris", - "title": "gitlab/multigris/mgris", - "url": " https://rseng.github.io/software/repository/gitlab/multigris/mgris", - "content": "MULTIGRIS ("mgris") is a Bayesian multi-dimensional grid search using PyMC to extract the posterior distributions of primary grid parameters and predict unobserved parameters/observables." - }, - "gitlab/dglaeser/fieldcompare": { - "id": "gitlab/dglaeser/fieldcompare", - "title": "gitlab/dglaeser/fieldcompare", - "url": " https://rseng.github.io/software/repository/gitlab/dglaeser/fieldcompare", - "content": "Python package with command-line interface to compare field data" - }, - "gitlab/clairedavies/sedbys": { - "id": "gitlab/clairedavies/sedbys", - "title": "gitlab/clairedavies/sedbys", - "url": " https://rseng.github.io/software/repository/gitlab/clairedavies/sedbys", - "content": "A python-based spectral energy distribution builder for young stars" - }, - "gitlab/fibreglass/pivc": { - "id": "gitlab/fibreglass/pivc", - "title": "gitlab/fibreglass/pivc", - "url": " https://rseng.github.io/software/repository/gitlab/fibreglass/pivc", - "content": "None" + "gitlab/ampere2/metalwalls": { + "id": "gitlab/ampere2/metalwalls", + "title": "gitlab/ampere2/metalwalls", + "url": " https://rseng.github.io/software/repository/gitlab/ampere2/metalwalls", + "content": "" }, - "gitlab/remikz/nccmp": { - "id": "gitlab/remikz/nccmp", - "title": "gitlab/remikz/nccmp", - "url": " https://rseng.github.io/software/repository/gitlab/remikz/nccmp", - "content": "nccmp - Compare 2 NetCDF files. " + "gitlab/bu_cnio/vulcanspot": { + "id": "gitlab/bu_cnio/vulcanspot", + "title": "gitlab/bu_cnio/vulcanspot", + "url": " https://rseng.github.io/software/repository/gitlab/bu_cnio/vulcanspot", + "content": "" }, - "gitlab/jtagusari/hrisk-noisemodelling": { - "id": "gitlab/jtagusari/hrisk-noisemodelling", - "title": "gitlab/jtagusari/hrisk-noisemodelling", - "url": " https://rseng.github.io/software/repository/gitlab/jtagusari/hrisk-noisemodelling", + "gitlab/imoralc/malu-ifs-visualization-tool": { + "id": "gitlab/imoralc/malu-ifs-visualization-tool", + "title": "gitlab/imoralc/malu-ifs-visualization-tool", + "url": " https://rseng.github.io/software/repository/gitlab/imoralc/malu-ifs-visualization-tool", "content": "None" }, - "gitlab/pyFBS/pyFBS": { - "id": "gitlab/pyFBS/pyFBS", - "title": "gitlab/pyFBS/pyFBS", - "url": " https://rseng.github.io/software/repository/gitlab/pyFBS/pyFBS", - "content": "A Python package for Frequency Based Substructuring and Transfer Path Analysis" - }, - "gitlab/cirad-apps/phylostems": { - "id": "gitlab/cirad-apps/phylostems", - "title": "gitlab/cirad-apps/phylostems", - "url": " https://rseng.github.io/software/repository/gitlab/cirad-apps/phylostems", - "content": "**phylostems** is a graphical tool developped by CIRAD (UMR PVBMT) to explore temporal signal at various evolutionary scales in heterochronous nucleic acid sequences datasets." - }, - "gitlab/vibes-developers/vibes": { - "id": "gitlab/vibes-developers/vibes", - "title": "gitlab/vibes-developers/vibes", - "url": " https://rseng.github.io/software/repository/gitlab/vibes-developers/vibes", - "content": "[FHI-vibes](https://vibes-developers.gitlab.io/vibes/): Vibrational simulations with python powered by ASE and FHI-aims." - }, - "gitlab/ezlab/busco": { - "id": "gitlab/ezlab/busco", - "title": "gitlab/ezlab/busco", - "url": " https://rseng.github.io/software/repository/gitlab/ezlab/busco", - "content": "Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs (BUSCO)" + "gitlab/sybreton/apollinaire": { + "id": "gitlab/sybreton/apollinaire", + "title": "gitlab/sybreton/apollinaire", + "url": " https://rseng.github.io/software/repository/gitlab/sybreton/apollinaire", + "content": "Python tools for helio- and asteroseismic peakbagging frameworks." }, "gitlab/cosapp/cosapp": { "id": "gitlab/cosapp/cosapp", @@ -216,208 +197,179 @@ "url": " https://rseng.github.io/software/repository/gitlab/cosapp/cosapp", "content": "CoSApp core package" }, - "gitlab/leelamichaels/Omega": { - "id": "gitlab/leelamichaels/Omega", - "title": "gitlab/leelamichaels/Omega", - "url": " https://rseng.github.io/software/repository/gitlab/leelamichaels/Omega", - "content": "Code Omega release copy" + "gitlab/picos-api/picos": { + "id": "gitlab/picos-api/picos", + "title": "gitlab/picos-api/picos", + "url": " https://rseng.github.io/software/repository/gitlab/picos-api/picos", + "content": "A Python interface to conic optimization solvers." }, - "gitlab/leelamichaels/Tranquillity": { - "id": "gitlab/leelamichaels/Tranquillity", - "title": "gitlab/leelamichaels/Tranquillity", - "url": " https://rseng.github.io/software/repository/gitlab/leelamichaels/Tranquillity", - "content": "Code Tranquillity release copy" + "gitlab/pythia-uq/pythia": { + "id": "gitlab/pythia-uq/pythia", + "title": "gitlab/pythia-uq/pythia", + "url": " https://rseng.github.io/software/repository/gitlab/pythia-uq/pythia", + "content": "PyThia Uncertainty Quantification Toolbox" }, - "gitlab/leelamichaels/Elysium": { - "id": "gitlab/leelamichaels/Elysium", - "title": "gitlab/leelamichaels/Elysium", - "url": " https://rseng.github.io/software/repository/gitlab/leelamichaels/Elysium", - "content": "Code Elysium release copy" + "gitlab/chaver/choco-mining": { + "id": "gitlab/chaver/choco-mining", + "title": "gitlab/chaver/choco-mining", + "url": " https://rseng.github.io/software/repository/gitlab/chaver/choco-mining", + "content": "Data mining with Choco solver" }, - "gitlab/leelamichaels/Burning_Arrow": { - "id": "gitlab/leelamichaels/Burning_Arrow", - "title": "gitlab/leelamichaels/Burning_Arrow", - "url": " https://rseng.github.io/software/repository/gitlab/leelamichaels/Burning_Arrow", - "content": "Code Burning Arrow release copy" + "gitlab/astron-idg/idg": { + "id": "gitlab/astron-idg/idg", + "title": "gitlab/astron-idg/idg", + "url": " https://rseng.github.io/software/repository/gitlab/astron-idg/idg", + "content": "Mirror of git.astron.nl/rd/idg" }, - "gitlab/leelamichaels/Infinity": { - "id": "gitlab/leelamichaels/Infinity", - "title": "gitlab/leelamichaels/Infinity", - "url": " https://rseng.github.io/software/repository/gitlab/leelamichaels/Infinity", - "content": "Code Infinity release copy" + "gitlab/mcfrith/paraclu": { + "id": "gitlab/mcfrith/paraclu", + "title": "gitlab/mcfrith/paraclu", + "url": " https://rseng.github.io/software/repository/gitlab/mcfrith/paraclu", + "content": "Parametric clustering of genomic and transcriptomic features" }, - "gitlab/imoralc/malu-ifs-visualization-tool": { - "id": "gitlab/imoralc/malu-ifs-visualization-tool", - "title": "gitlab/imoralc/malu-ifs-visualization-tool", - "url": " https://rseng.github.io/software/repository/gitlab/imoralc/malu-ifs-visualization-tool", - "content": "None" - }, - "gitlab/aegge/comet-emu": { - "id": "gitlab/aegge/comet-emu", - "title": "gitlab/aegge/comet-emu", - "url": " https://rseng.github.io/software/repository/gitlab/aegge/comet-emu", - "content": "None" + "gitlab/mcfrith/last": { + "id": "gitlab/mcfrith/last", + "title": "gitlab/mcfrith/last", + "url": " https://rseng.github.io/software/repository/gitlab/mcfrith/last", + "content": "finds & aligns related regions of sequences. LAST is designed for moderately large data (e.g. genomes, DNA reads, proteomes)." }, - "gitlab/cracklet/cracklet": { - "id": "gitlab/cracklet/cracklet", - "title": "gitlab/cracklet/cracklet", - "url": " https://rseng.github.io/software/repository/gitlab/cracklet/cracklet", - "content": "cRacklet is a C++ boundary element library based on a spectral formulation of the elastodynamic wave equations in continuum solids." + "gitlab/mcfrith/lamassemble": { + "id": "gitlab/mcfrith/lamassemble", + "title": "gitlab/mcfrith/lamassemble", + "url": " https://rseng.github.io/software/repository/gitlab/mcfrith/lamassemble", + "content": "Merges overlapping "long" DNA reads into a consensus sequences" }, - "gitlab/rki_bioinformatics/IDeFIX": { - "id": "gitlab/rki_bioinformatics/IDeFIX", - "title": "gitlab/rki_bioinformatics/IDeFIX", - "url": " https://rseng.github.io/software/repository/gitlab/rki_bioinformatics/IDeFIX", - "content": "Index checking for improved demultiplexing of NGS data" + "gitlab/mcfrith/tantan": { + "id": "gitlab/mcfrith/tantan", + "title": "gitlab/mcfrith/tantan", + "url": " https://rseng.github.io/software/repository/gitlab/mcfrith/tantan", + "content": "low complexity and tandem repeat masker for biosequences" }, - "gitlab/rki_bioinformatics/purple": { - "id": "gitlab/rki_bioinformatics/purple", - "title": "gitlab/rki_bioinformatics/purple", - "url": " https://rseng.github.io/software/repository/gitlab/rki_bioinformatics/purple", - "content": "Picking Unique Relevant Peptides for viraL Experiments - -Authors: Johanna Lechner [@LechnerJ], Pauline Hiortand Felix Hartkopf [@HartkopfF] - -Support: https://gitlab.com/HartkopfF/Purple - -Download: https://gitlab.com/HartkopfF/Purple/releases" + "gitlab/petsc/petsc": { + "id": "gitlab/petsc/petsc", + "title": "gitlab/petsc/petsc", + "url": " https://rseng.github.io/software/repository/gitlab/petsc/petsc", + "content": "PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations." }, - "gitlab/rki_bioinformatics/HiLive2": { - "id": "gitlab/rki_bioinformatics/HiLive2", - "title": "gitlab/rki_bioinformatics/HiLive2", - "url": " https://rseng.github.io/software/repository/gitlab/rki_bioinformatics/HiLive2", - "content": "HiLive2 is a read mapping tool that maps Illumina HiSeq (or comparable) reads right in the moment when they are produced. Please create issues for HiLive2 at https://gitlab.com/lokat/HiLive2." + "gitlab/jason-rumengan/pyarma": { + "id": "gitlab/jason-rumengan/pyarma", + "title": "gitlab/jason-rumengan/pyarma", + "url": " https://rseng.github.io/software/repository/gitlab/jason-rumengan/pyarma", + "content": "PyArmadillo - linear algebra library for Python with MATLAB-like syntax - https://pyarma.sourceforge.io" }, - "gitlab/octopus-code/octopus": { - "id": "gitlab/octopus-code/octopus", - "title": "gitlab/octopus-code/octopus", - "url": " https://rseng.github.io/software/repository/gitlab/octopus-code/octopus", - "content": "Real-space Time-Dependent Density Functional Theory code" + "gitlab/habermann_lab/phasik": { + "id": "gitlab/habermann_lab/phasik", + "title": "gitlab/habermann_lab/phasik", + "url": " https://rseng.github.io/software/repository/gitlab/habermann_lab/phasik", + "content": "Scientific tools for extracting cyclic data via hierarchical clustering" }, - "gitlab/ChemBioHub/tpmap": { - "id": "gitlab/ChemBioHub/tpmap", - "title": "gitlab/ChemBioHub/tpmap", - "url": " https://rseng.github.io/software/repository/gitlab/ChemBioHub/tpmap", - "content": "Thermal Profiling Meltome Analysis Program" + "gitlab/ags-data-format-wg/ags-python-library": { + "id": "gitlab/ags-data-format-wg/ags-python-library", + "title": "gitlab/ags-data-format-wg/ags-python-library", + "url": " https://rseng.github.io/software/repository/gitlab/ags-data-format-wg/ags-python-library", + "content": "A library to read and write AGS files using Pandas DataFrames" }, - "gitlab/robizzard/libcdict": { - "id": "gitlab/robizzard/libcdict", - "title": "gitlab/robizzard/libcdict", - "url": " https://rseng.github.io/software/repository/gitlab/robizzard/libcdict", - "content": "A generic associative array, also know as dictionary or hash, library in C, based on uthash and extended to be more user friendly and include integration features such as JSON output." + "gitlab/project-dare/dare-platform": { + "id": "gitlab/project-dare/dare-platform", + "title": "gitlab/project-dare/dare-platform", + "url": " https://rseng.github.io/software/repository/gitlab/project-dare/dare-platform", + "content": "" }, - "gitlab/ffaucher/hawen": { - "id": "gitlab/ffaucher/hawen", - "title": "gitlab/ffaucher/hawen", - "url": " https://rseng.github.io/software/repository/gitlab/ffaucher/hawen", - "content": "time-HArmonic Wave modEling and INversion using Hybridizable Discontinuous Galerkin Discretization (hawen). The code is written in Fortran90, for forward and inverse time-harmonic wave problems. It uses mpi and openmp parallelism." + "gitlab/remram44/taguette": { + "id": "gitlab/remram44/taguette", + "title": "gitlab/remram44/taguette", + "url": " https://rseng.github.io/software/repository/gitlab/remram44/taguette", + "content": "Free and open source qualitative research tool" }, - "gitlab/pvst/asi": { - "id": "gitlab/pvst/asi", - "title": "gitlab/pvst/asi", - "url": " https://rseng.github.io/software/repository/gitlab/pvst/asi", - "content": "Atomic Simulations Interface" + "gitlab/wpettersson/kep_solver": { + "id": "gitlab/wpettersson/kep_solver", + "title": "gitlab/wpettersson/kep_solver", + "url": " https://rseng.github.io/software/repository/gitlab/wpettersson/kep_solver", + "content": "A Python package for reading and solving single instances of kidney exchange problems. " }, - "gitlab/sissopp_developers/sissopp": { - "id": "gitlab/sissopp_developers/sissopp", - "title": "gitlab/sissopp_developers/sissopp", - "url": " https://rseng.github.io/software/repository/gitlab/sissopp_developers/sissopp", - "content": "C++ implementation of sisso." + "gitlab/sevecekp/sph": { + "id": "gitlab/sevecekp/sph", + "title": "gitlab/sevecekp/sph", + "url": " https://rseng.github.io/software/repository/gitlab/sevecekp/sph", + "content": "Library and graphical tools for running SPH and N-body simulations." }, - "gitlab/InspectorCell/inspectorcell": { - "id": "gitlab/InspectorCell/inspectorcell", - "title": "gitlab/InspectorCell/inspectorcell", - "url": " https://rseng.github.io/software/repository/gitlab/InspectorCell/inspectorcell", - "content": "InspectorCell provides an efficient workflow and graphical interface to generate high-quality training datasets from -highly multiplexed microscopy images." + "gitlab/mobse/source-code": { + "id": "gitlab/mobse/source-code", + "title": "gitlab/mobse/source-code", + "url": " https://rseng.github.io/software/repository/gitlab/mobse/source-code", + "content": "None" }, - "gitlab/esa/pyxel": { - "id": "gitlab/esa/pyxel", - "title": "gitlab/esa/pyxel", - "url": " https://rseng.github.io/software/repository/gitlab/esa/pyxel", - "content": "Pyxel is a general detector simulation framework. An easy-to-use framework that can simulate a variety of imaging detector effects combined on images (e.g. radiation and optical effects, noises) made by CCD or CMOS-based detectors." + "gitlab/cracklet/cracklet": { + "id": "gitlab/cracklet/cracklet", + "title": "gitlab/cracklet/cracklet", + "url": " https://rseng.github.io/software/repository/gitlab/cracklet/cracklet", + "content": "cRacklet is a C++ boundary element library based on a spectral formulation of the elastodynamic wave equations in continuum solids." }, - "gitlab/geekysquirrel/bigx": { - "id": "gitlab/geekysquirrel/bigx", - "title": "gitlab/geekysquirrel/bigx", - "url": " https://rseng.github.io/software/repository/gitlab/geekysquirrel/bigx", - "content": "A data visualisation tool for geographic datasets" + "gitlab/AstroVian/bmarxiv": { + "id": "gitlab/AstroVian/bmarxiv", + "title": "gitlab/AstroVian/bmarxiv", + "url": " https://rseng.github.io/software/repository/gitlab/AstroVian/bmarxiv", + "content": "None" }, - "gitlab/binary_c/binary_c-python": { - "id": "gitlab/binary_c/binary_c-python", - "title": "gitlab/binary_c/binary_c-python", - "url": " https://rseng.github.io/software/repository/gitlab/binary_c/binary_c-python", - "content": "Python module to interface with the binary_c stellar population framework. - -The current stable branch is 1.0.0 which you can find in the [releases/1.0.0/2.2.4 branch](https://gitlab.com/binary_c/binary_c-python/-/tree/releases/1.0.0/2.2.4) which works with [binary_c version 2.2.4](https://gitlab.com/binary_c/binary_c/-/tree/development/2.2.4)" + "gitlab/loic.cg.rossi/pymiedap": { + "id": "gitlab/loic.cg.rossi/pymiedap", + "title": "gitlab/loic.cg.rossi/pymiedap", + "url": " https://rseng.github.io/software/repository/gitlab/loic.cg.rossi/pymiedap", + "content": "PyMieDAP = Python Mie Doubling Adding Program. A radiative transfer code with polarization." }, - "gitlab/jason-rumengan/pyarma": { - "id": "gitlab/jason-rumengan/pyarma", - "title": "gitlab/jason-rumengan/pyarma", - "url": " https://rseng.github.io/software/repository/gitlab/jason-rumengan/pyarma", - "content": "PyArmadillo - linear algebra library for Python with MATLAB-like syntax - https://pyarma.sourceforge.io" + "gitlab/kmrajwade/iqrm_apollo": { + "id": "gitlab/kmrajwade/iqrm_apollo", + "title": "gitlab/kmrajwade/iqrm_apollo", + "url": " https://rseng.github.io/software/repository/gitlab/kmrajwade/iqrm_apollo", + "content": "A standalone code to clean narrow-band RFI using Inter-Quartile Range Mitigation (IQRM) algorithm. The code works on SIGPROC format data and outputs a cleaned SIGRPOC format file. The output file is compatible with other standard pulsar software." }, - "gitlab/ampere2/metalwalls": { - "id": "gitlab/ampere2/metalwalls", - "title": "gitlab/ampere2/metalwalls", - "url": " https://rseng.github.io/software/repository/gitlab/ampere2/metalwalls", + "gitlab/davidtourigny/dynamic-fba": { + "id": "gitlab/davidtourigny/dynamic-fba", + "title": "gitlab/davidtourigny/dynamic-fba", + "url": " https://rseng.github.io/software/repository/gitlab/davidtourigny/dynamic-fba", "content": "" }, - "gitlab/permafrostnet/teaspoon": { - "id": "gitlab/permafrostnet/teaspoon", - "title": "gitlab/permafrostnet/teaspoon", - "url": " https://rseng.github.io/software/repository/gitlab/permafrostnet/teaspoon", - "content": "Python for permafrost temperature data" - }, - "gitlab/mainlabwsu/bims": { - "id": "gitlab/mainlabwsu/bims", - "title": "gitlab/mainlabwsu/bims", - "url": " https://rseng.github.io/software/repository/gitlab/mainlabwsu/bims", - "content": "BIMS" - }, - "gitlab/picos-api/picos": { - "id": "gitlab/picos-api/picos", - "title": "gitlab/picos-api/picos", - "url": " https://rseng.github.io/software/repository/gitlab/picos-api/picos", - "content": "A Python interface to conic optimization solvers." - }, - "gitlab/Molcas/OpenMolcas": { - "id": "gitlab/Molcas/OpenMolcas", - "title": "gitlab/Molcas/OpenMolcas", - "url": " https://rseng.github.io/software/repository/gitlab/Molcas/OpenMolcas", - "content": "OpenMolcas is a quantum chemistry software package. - -The key feature of OpenMolcas is the multiconfigurational approach to the electronic structure." - }, - "gitlab/metafundev/metafun": { - "id": "gitlab/metafundev/metafun", - "title": "gitlab/metafundev/metafun", - "url": " https://rseng.github.io/software/repository/gitlab/metafundev/metafun", + "gitlab/chiemotono/mdcontactcom": { + "id": "gitlab/chiemotono/mdcontactcom", + "title": "gitlab/chiemotono/mdcontactcom", + "url": " https://rseng.github.io/software/repository/gitlab/chiemotono/mdcontactcom", "content": "" }, + "gitlab/random-quintessence/random-quintessence": { + "id": "gitlab/random-quintessence/random-quintessence", + "title": "gitlab/random-quintessence/random-quintessence", + "url": " https://rseng.github.io/software/repository/gitlab/random-quintessence/random-quintessence", + "content": "None" + }, "gitlab/gmamon/MAMPOSSt": { "id": "gitlab/gmamon/MAMPOSSt", "title": "gitlab/gmamon/MAMPOSSt", "url": " https://rseng.github.io/software/repository/gitlab/gmamon/MAMPOSSt", "content": "None" }, - "gitlab/cosmograil/starred": { - "id": "gitlab/cosmograil/starred", - "title": "gitlab/cosmograil/starred", - "url": " https://rseng.github.io/software/repository/gitlab/cosmograil/starred", - "content": "A two-channel deconvolution method with Starlet regularization" + "gitlab/ENKI-portal/ThermoCodegen": { + "id": "gitlab/ENKI-portal/ThermoCodegen", + "title": "gitlab/ENKI-portal/ThermoCodegen", + "url": " https://rseng.github.io/software/repository/gitlab/ENKI-portal/ThermoCodegen", + "content": "ThermoCodegen: a python/C++ package for the generation of custom thermodynamic models" }, - "gitlab/cosmograil/PyCS3": { - "id": "gitlab/cosmograil/PyCS3", - "title": "gitlab/cosmograil/PyCS3", - "url": " https://rseng.github.io/software/repository/gitlab/cosmograil/PyCS3", - "content": "PyCS for python 3" + "gitlab/ENKI-portal/vaporock": { + "id": "gitlab/ENKI-portal/vaporock", + "title": "gitlab/ENKI-portal/vaporock", + "url": " https://rseng.github.io/software/repository/gitlab/ENKI-portal/vaporock", + "content": "Thermodynamics of vaporized silicate rocks & melts for modeling magma ocean atmospheres and stellar nebula" }, - "gitlab/gims-developers/gims": { - "id": "gitlab/gims-developers/gims", - "title": "gitlab/gims-developers/gims", - "url": " https://rseng.github.io/software/repository/gitlab/gims-developers/gims", - "content": "GIMS -- Graphical Interface for Materials Simulations -- is an open-source, browser-based toolbox for electronic structure codes. Try it here: [gims.ms1p.org](https://gims.ms1p.org)" + "gitlab/ENKI-portal/ThermoEngine": { + "id": "gitlab/ENKI-portal/ThermoEngine", + "title": "gitlab/ENKI-portal/ThermoEngine", + "url": " https://rseng.github.io/software/repository/gitlab/ENKI-portal/ThermoEngine", + "content": "Python, C, C++ and Objective C code that Implement thermodynamic properties of stoichiometric phases and solutions. This is the main code repository of the ENKI project." + }, + "gitlab/fibreglass/pivc": { + "id": "gitlab/fibreglass/pivc", + "title": "gitlab/fibreglass/pivc", + "url": " https://rseng.github.io/software/repository/gitlab/fibreglass/pivc", + "content": "None" }, "gitlab/aroffringa/aoflagger": { "id": "gitlab/aroffringa/aoflagger", @@ -431,53 +383,41 @@ "url": " https://rseng.github.io/software/repository/gitlab/aroffringa/wsclean", "content": "WSClean (w-stacking clean) is a fast generic widefield imager. It implements several gridding algorithms and offers fully-automated multi-scale multi-frequency deconvolution. Manual: https://wsclean.readthedocs.io/" }, - "gitlab/random-quintessence/random-quintessence": { - "id": "gitlab/random-quintessence/random-quintessence", - "title": "gitlab/random-quintessence/random-quintessence", - "url": " https://rseng.github.io/software/repository/gitlab/random-quintessence/random-quintessence", + "gitlab/sigcorr/sigcorr": { + "id": "gitlab/sigcorr/sigcorr", + "title": "gitlab/sigcorr/sigcorr", + "url": " https://rseng.github.io/software/repository/gitlab/sigcorr/sigcorr", "content": "None" }, - "gitlab/chaver/choco-mining": { - "id": "gitlab/chaver/choco-mining", - "title": "gitlab/chaver/choco-mining", - "url": " https://rseng.github.io/software/repository/gitlab/chaver/choco-mining", - "content": "Data mining with Choco solver" - }, - "gitlab/libreumg/dataquier": { - "id": "gitlab/libreumg/dataquier", - "title": "gitlab/libreumg/dataquier", - "url": " https://rseng.github.io/software/repository/gitlab/libreumg/dataquier", - "content": "" - }, - "gitlab/petsc/petsc": { - "id": "gitlab/petsc/petsc", - "title": "gitlab/petsc/petsc", - "url": " https://rseng.github.io/software/repository/gitlab/petsc/petsc", - "content": "PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations." + "gitlab/joseaher/astroplotlib": { + "id": "gitlab/joseaher/astroplotlib", + "title": "gitlab/joseaher/astroplotlib", + "url": " https://rseng.github.io/software/repository/gitlab/joseaher/astroplotlib", + "content": "None" }, - "gitlab/JuditGG/trumpetplots": { - "id": "gitlab/JuditGG/trumpetplots", - "title": "gitlab/JuditGG/trumpetplots", - "url": " https://rseng.github.io/software/repository/gitlab/JuditGG/trumpetplots", - "content": "Rpackage for Trumpet plots" + "gitlab/dalton/dalton": { + "id": "gitlab/dalton/dalton", + "title": "gitlab/dalton/dalton", + "url": " https://rseng.github.io/software/repository/gitlab/dalton/dalton", + "content": "Public Dalton source code repository." }, - "gitlab/thartwig/asloth": { - "id": "gitlab/thartwig/asloth", - "title": "gitlab/thartwig/asloth", - "url": " https://rseng.github.io/software/repository/gitlab/thartwig/asloth", - "content": "Semi-analytical model A-SLOTH (Ancient Stars and Local Observables by Tracing Halos)" + "gitlab/octopus-code/octopus": { + "id": "gitlab/octopus-code/octopus", + "title": "gitlab/octopus-code/octopus", + "url": " https://rseng.github.io/software/repository/gitlab/octopus-code/octopus", + "content": "Real-space Time-Dependent Density Functional Theory code" }, - "gitlab/ztzou/phydl": { - "id": "gitlab/ztzou/phydl", - "title": "gitlab/ztzou/phydl", - "url": " https://rseng.github.io/software/repository/gitlab/ztzou/phydl", - "content": "Phylogenetics by Deep Learning. A residual neural network for inference of quartet phylogenetic tree topology." + "gitlab/ffaucher/hawen": { + "id": "gitlab/ffaucher/hawen", + "title": "gitlab/ffaucher/hawen", + "url": " https://rseng.github.io/software/repository/gitlab/ffaucher/hawen", + "content": "time-HArmonic Wave modEling and INversion using Hybridizable Discontinuous Galerkin Discretization (hawen). The code is written in Fortran90, for forward and inverse time-harmonic wave problems. It uses mpi and openmp parallelism." }, - "gitlab/wpettersson/kep_solver": { - "id": "gitlab/wpettersson/kep_solver", - "title": "gitlab/wpettersson/kep_solver", - "url": " https://rseng.github.io/software/repository/gitlab/wpettersson/kep_solver", - "content": "A Python package for reading and solving single instances of kidney exchange problems. " + "gitlab/esa/pyxel": { + "id": "gitlab/esa/pyxel", + "title": "gitlab/esa/pyxel", + "url": " https://rseng.github.io/software/repository/gitlab/esa/pyxel", + "content": "Pyxel is a general detector simulation framework. An easy-to-use framework that can simulate a variety of imaging detector effects combined on images (e.g. radiation and optical effects, noises) made by CCD or CMOS-based detectors." }, "gitlab/gpagano/lensinggw": { "id": "gitlab/gpagano/lensinggw", @@ -485,47 +425,35 @@ "url": " https://rseng.github.io/software/repository/gitlab/gpagano/lensinggw", "content": "None" }, - "gitlab/paulklemm_PHD/proteinortho": { - "id": "gitlab/paulklemm_PHD/proteinortho", - "title": "gitlab/paulklemm_PHD/proteinortho", - "url": " https://rseng.github.io/software/repository/gitlab/paulklemm_PHD/proteinortho", - "content": "Proteinortho is a tool to detect orthologous genes within different species. [(Download)](https://gitlab.com/paulklemm_PHD/proteinortho/-/archive/master/proteinortho-master.tar.gz)" - }, - "gitlab/sevecekp/sph": { - "id": "gitlab/sevecekp/sph", - "title": "gitlab/sevecekp/sph", - "url": " https://rseng.github.io/software/repository/gitlab/sevecekp/sph", - "content": "Library and graphical tools for running SPH and N-body simulations." - }, - "gitlab/mcfrith/tantan": { - "id": "gitlab/mcfrith/tantan", - "title": "gitlab/mcfrith/tantan", - "url": " https://rseng.github.io/software/repository/gitlab/mcfrith/tantan", - "content": "low complexity and tandem repeat masker for biosequences" + "gitlab/BioimageInformaticsGroup/openphi": { + "id": "gitlab/BioimageInformaticsGroup/openphi", + "title": "gitlab/BioimageInformaticsGroup/openphi", + "url": " https://rseng.github.io/software/repository/gitlab/BioimageInformaticsGroup/openphi", + "content": "Open PatHology Interface - A Python API for accessing iSyntax digital pathology images" }, - "gitlab/mcfrith/paraclu": { - "id": "gitlab/mcfrith/paraclu", - "title": "gitlab/mcfrith/paraclu", - "url": " https://rseng.github.io/software/repository/gitlab/mcfrith/paraclu", - "content": "Parametric clustering of genomic and transcriptomic features" + "gitlab/dglaeser/fieldcompare": { + "id": "gitlab/dglaeser/fieldcompare", + "title": "gitlab/dglaeser/fieldcompare", + "url": " https://rseng.github.io/software/repository/gitlab/dglaeser/fieldcompare", + "content": "Python package with command-line interface to compare field data" }, - "gitlab/mcfrith/lamassemble": { - "id": "gitlab/mcfrith/lamassemble", - "title": "gitlab/mcfrith/lamassemble", - "url": " https://rseng.github.io/software/repository/gitlab/mcfrith/lamassemble", - "content": "Merges overlapping "long" DNA reads into a consensus sequences" + "gitlab/eduardo-vitral/balrogo": { + "id": "gitlab/eduardo-vitral/balrogo", + "title": "gitlab/eduardo-vitral/balrogo", + "url": " https://rseng.github.io/software/repository/gitlab/eduardo-vitral/balrogo", + "content": "Bayesian Astrometric Likelihood Recovery of Galactic Objects" }, - "gitlab/mcfrith/last": { - "id": "gitlab/mcfrith/last", - "title": "gitlab/mcfrith/last", - "url": " https://rseng.github.io/software/repository/gitlab/mcfrith/last", - "content": "finds & aligns related regions of sequences. LAST is designed for moderately large data (e.g. genomes, DNA reads, proteomes)." + "gitlab/pipe3d/pyPipe3D": { + "id": "gitlab/pipe3d/pyPipe3D", + "title": "gitlab/pipe3d/pyPipe3D", + "url": " https://rseng.github.io/software/repository/gitlab/pipe3d/pyPipe3D", + "content": "pyPipe3D is a spectroscopy analysis pipeline which produces coherent, easy to distribute and compare, parameters of the stellar populations and the ionized gas, suited in particular for data from the most recent optical IFS surveys." }, - "gitlab/AstroVian/bmarxiv": { - "id": "gitlab/AstroVian/bmarxiv", - "title": "gitlab/AstroVian/bmarxiv", - "url": " https://rseng.github.io/software/repository/gitlab/AstroVian/bmarxiv", - "content": "None" + "gitlab/polmag/PORTA": { + "id": "gitlab/polmag/PORTA", + "title": "gitlab/polmag/PORTA", + "url": " https://rseng.github.io/software/repository/gitlab/polmag/PORTA", + "content": "PORTA: A three-dimensional multilevel radiative transfer code for modeling the intensity and polarization of spectral lines with massively parallel computers" }, "gitlab/mbiagetti/persistent_homology_lss": { "id": "gitlab/mbiagetti/persistent_homology_lss", @@ -533,60 +461,48 @@ "url": " https://rseng.github.io/software/repository/gitlab/mbiagetti/persistent_homology_lss", "content": "Analyze halo catalogs using persistent homology to constrain cosmological parameters" }, - "gitlab/etienne.behar/menura": { - "id": "gitlab/etienne.behar/menura", - "title": "gitlab/etienne.behar/menura", - "url": " https://rseng.github.io/software/repository/gitlab/etienne.behar/menura", - "content": "Menura is a space plasma simulation code. It is built around a hybrid Particle In Cell (PIC) solver, running on Graphics Processing Units. More informations on https://menura.readthedocs.io" - }, - "gitlab/vincent-sater/umigen": { - "id": "gitlab/vincent-sater/umigen", - "title": "gitlab/vincent-sater/umigen", - "url": " https://rseng.github.io/software/repository/gitlab/vincent-sater/umigen", - "content": "UMI-based reads simulator for variant calling evaluation in paired-end sequencing NGS libraries" - }, - "gitlab/andrea-tango/ficos": { - "id": "gitlab/andrea-tango/ficos", - "title": "gitlab/andrea-tango/ficos", - "url": " https://rseng.github.io/software/repository/gitlab/andrea-tango/ficos", - "content": "" + "gitlab/pvst/asi": { + "id": "gitlab/pvst/asi", + "title": "gitlab/pvst/asi", + "url": " https://rseng.github.io/software/repository/gitlab/pvst/asi", + "content": "Atomic Simulations Interface" }, - "gitlab/moerman1/fhi-cc4s": { - "id": "gitlab/moerman1/fhi-cc4s", - "title": "gitlab/moerman1/fhi-cc4s", - "url": " https://rseng.github.io/software/repository/gitlab/moerman1/fhi-cc4s", - "content": "This project constitutes the interface between the Fritz Haber Institute ab initio molecular simulations (FHI-aims) and the Coupled Cluster for Solids (CC4S) code developed by Felix Hummel and Adreas Grueneis at the TU Wien. -" + "gitlab/leelamichaels/Elysium": { + "id": "gitlab/leelamichaels/Elysium", + "title": "gitlab/leelamichaels/Elysium", + "url": " https://rseng.github.io/software/repository/gitlab/leelamichaels/Elysium", + "content": "Code Elysium release copy" }, - "gitlab/sigcorr/sigcorr": { - "id": "gitlab/sigcorr/sigcorr", - "title": "gitlab/sigcorr/sigcorr", - "url": " https://rseng.github.io/software/repository/gitlab/sigcorr/sigcorr", - "content": "None" + "gitlab/leelamichaels/Burning_Arrow": { + "id": "gitlab/leelamichaels/Burning_Arrow", + "title": "gitlab/leelamichaels/Burning_Arrow", + "url": " https://rseng.github.io/software/repository/gitlab/leelamichaels/Burning_Arrow", + "content": "Code Burning Arrow release copy" }, - "gitlab/programgreg/tagginglatencyestimator": { - "id": "gitlab/programgreg/tagginglatencyestimator", - "title": "gitlab/programgreg/tagginglatencyestimator", - "url": " https://rseng.github.io/software/repository/gitlab/programgreg/tagginglatencyestimator", - "content": "Software to estimate the latency of the tagging process." + "gitlab/leelamichaels/Infinity": { + "id": "gitlab/leelamichaels/Infinity", + "title": "gitlab/leelamichaels/Infinity", + "url": " https://rseng.github.io/software/repository/gitlab/leelamichaels/Infinity", + "content": "Code Infinity release copy" }, - "gitlab/eduardo-vitral/balrogo": { - "id": "gitlab/eduardo-vitral/balrogo", - "title": "gitlab/eduardo-vitral/balrogo", - "url": " https://rseng.github.io/software/repository/gitlab/eduardo-vitral/balrogo", - "content": "Bayesian Astrometric Likelihood Recovery of Galactic Objects" + "gitlab/leelamichaels/Tranquillity": { + "id": "gitlab/leelamichaels/Tranquillity", + "title": "gitlab/leelamichaels/Tranquillity", + "url": " https://rseng.github.io/software/repository/gitlab/leelamichaels/Tranquillity", + "content": "Code Tranquillity release copy" }, - "gitlab/bu_cnio/vulcanspot": { - "id": "gitlab/bu_cnio/vulcanspot", - "title": "gitlab/bu_cnio/vulcanspot", - "url": " https://rseng.github.io/software/repository/gitlab/bu_cnio/vulcanspot", - "content": "" + "gitlab/leelamichaels/Omega": { + "id": "gitlab/leelamichaels/Omega", + "title": "gitlab/leelamichaels/Omega", + "url": " https://rseng.github.io/software/repository/gitlab/leelamichaels/Omega", + "content": "Code Omega release copy" }, - "gitlab/mobse/source-code": { - "id": "gitlab/mobse/source-code", - "title": "gitlab/mobse/source-code", - "url": " https://rseng.github.io/software/repository/gitlab/mobse/source-code", - "content": "None" + "gitlab/jesseds/apav": { + "id": "gitlab/jesseds/apav", + "title": "gitlab/jesseds/apav", + "url": " https://rseng.github.io/software/repository/gitlab/jesseds/apav", + "content": "APAV (Atom Probe Analysis and Visualization) is a Python library for the analysis and +visualization of atom probe tomography experiments." }, "gitlab/magnumpi/magnumpi": { "id": "gitlab/magnumpi/magnumpi", @@ -594,11 +510,35 @@ "url": " https://rseng.github.io/software/repository/gitlab/magnumpi/magnumpi", "content": "Potential Integrator" }, - "gitlab/kmrajwade/iqrm_apollo": { - "id": "gitlab/kmrajwade/iqrm_apollo", - "title": "gitlab/kmrajwade/iqrm_apollo", - "url": " https://rseng.github.io/software/repository/gitlab/kmrajwade/iqrm_apollo", - "content": "A standalone code to clean narrow-band RFI using Inter-Quartile Range Mitigation (IQRM) algorithm. The code works on SIGPROC format data and outputs a cleaned SIGRPOC format file. The output file is compatible with other standard pulsar software." + "gitlab/cirad-apps/phylostems": { + "id": "gitlab/cirad-apps/phylostems", + "title": "gitlab/cirad-apps/phylostems", + "url": " https://rseng.github.io/software/repository/gitlab/cirad-apps/phylostems", + "content": "**phylostems** is a graphical tool developped by CIRAD (UMR PVBMT) to explore temporal signal at various evolutionary scales in heterochronous nucleic acid sequences datasets." + }, + "gitlab/vincent-sater/umigen": { + "id": "gitlab/vincent-sater/umigen", + "title": "gitlab/vincent-sater/umigen", + "url": " https://rseng.github.io/software/repository/gitlab/vincent-sater/umigen", + "content": "UMI-based reads simulator for variant calling evaluation in paired-end sequencing NGS libraries" + }, + "gitlab/chrjan/seq-seq-pan": { + "id": "gitlab/chrjan/seq-seq-pan", + "title": "gitlab/chrjan/seq-seq-pan", + "url": " https://rseng.github.io/software/repository/gitlab/chrjan/seq-seq-pan", + "content": "seq-seq-pan is a workflow for the SEQuential alignment of SEQuences to build a PAN-genome data structure and a whole-genome-alignment." + }, + "gitlab/permafrostnet/teaspoon": { + "id": "gitlab/permafrostnet/teaspoon", + "title": "gitlab/permafrostnet/teaspoon", + "url": " https://rseng.github.io/software/repository/gitlab/permafrostnet/teaspoon", + "content": "Python for permafrost temperature data" + }, + "gitlab/sissopp_developers/sissopp": { + "id": "gitlab/sissopp_developers/sissopp", + "title": "gitlab/sissopp_developers/sissopp", + "url": " https://rseng.github.io/software/repository/gitlab/sissopp_developers/sissopp", + "content": "C++ implementation of sisso." }, "gitlab/materials-modeling/calorine": { "id": "gitlab/materials-modeling/calorine", @@ -606,97 +546,55 @@ "url": " https://rseng.github.io/software/repository/gitlab/materials-modeling/calorine", "content": "[A python tool box for GPUMD simulations](https://calorine.materialsmodeling.org/)" }, - "gitlab/emd-dev/emd": { - "id": "gitlab/emd-dev/emd", - "title": "gitlab/emd-dev/emd", - "url": " https://rseng.github.io/software/repository/gitlab/emd-dev/emd", - "content": "Empirical Mode Decomposition in Python - -<a href="https://gitlab.com/ajquinn/emd/commits/master"><img alt="pipeline status" src="https://gitlab.com/ajquinn/emd/badges/master/pipeline.svg" /></a>" - }, - "gitlab/joseaher/astroplotlib": { - "id": "gitlab/joseaher/astroplotlib", - "title": "gitlab/joseaher/astroplotlib", - "url": " https://rseng.github.io/software/repository/gitlab/joseaher/astroplotlib", - "content": "None" - }, - "gitlab/davidtourigny/dynamic-fba": { - "id": "gitlab/davidtourigny/dynamic-fba", - "title": "gitlab/davidtourigny/dynamic-fba", - "url": " https://rseng.github.io/software/repository/gitlab/davidtourigny/dynamic-fba", - "content": "" - }, - "gitlab/BioimageInformaticsGroup/openphi": { - "id": "gitlab/BioimageInformaticsGroup/openphi", - "title": "gitlab/BioimageInformaticsGroup/openphi", - "url": " https://rseng.github.io/software/repository/gitlab/BioimageInformaticsGroup/openphi", - "content": "Open PatHology Interface - A Python API for accessing iSyntax digital pathology images" - }, - "gitlab/chrjan/seq-seq-pan": { - "id": "gitlab/chrjan/seq-seq-pan", - "title": "gitlab/chrjan/seq-seq-pan", - "url": " https://rseng.github.io/software/repository/gitlab/chrjan/seq-seq-pan", - "content": "seq-seq-pan is a workflow for the SEQuential alignment of SEQuences to build a PAN-genome data structure and a whole-genome-alignment." - }, - "gitlab/casi-project/casi-2d": { - "id": "gitlab/casi-project/casi-2d", - "title": "gitlab/casi-project/casi-2d", - "url": " https://rseng.github.io/software/repository/gitlab/casi-project/casi-2d", - "content": "Identification of stellar feedback signatures in simulated molecular clouds using methods from deep learning." - }, - "gitlab/casi-project/casi-3d": { - "id": "gitlab/casi-project/casi-3d", - "title": "gitlab/casi-project/casi-3d", - "url": " https://rseng.github.io/software/repository/gitlab/casi-project/casi-3d", - "content": "None" - }, - "gitlab/RKIBioinformaticsPipelines/QCumber": { - "id": "gitlab/RKIBioinformaticsPipelines/QCumber", - "title": "gitlab/RKIBioinformaticsPipelines/QCumber", - "url": " https://rseng.github.io/software/repository/gitlab/RKIBioinformaticsPipelines/QCumber", - "content": "quality control of genomic sequences" - }, - "gitlab/treangenlab/vulcan": { - "id": "gitlab/treangenlab/vulcan", - "title": "gitlab/treangenlab/vulcan", - "url": " https://rseng.github.io/software/repository/gitlab/treangenlab/vulcan", - "content": "" + "gitlab/german.tischler/biobambam2": { + "id": "gitlab/german.tischler/biobambam2", + "title": "gitlab/german.tischler/biobambam2", + "url": " https://rseng.github.io/software/repository/gitlab/german.tischler/biobambam2", + "content": "Tools for early stage alignment file processing" }, - "gitlab/treangenlab/emu": { - "id": "gitlab/treangenlab/emu", - "title": "gitlab/treangenlab/emu", - "url": " https://rseng.github.io/software/repository/gitlab/treangenlab/emu", - "content": "EMu is a relative abundance estimator for 16S genomic sequences" + "gitlab/german.tischler/libmaus2": { + "id": "gitlab/german.tischler/libmaus2", + "title": "gitlab/german.tischler/libmaus2", + "url": " https://rseng.github.io/software/repository/gitlab/german.tischler/libmaus2", + "content": "collection of data structures and algorithms" }, - "gitlab/loic.cg.rossi/pymiedap": { - "id": "gitlab/loic.cg.rossi/pymiedap", - "title": "gitlab/loic.cg.rossi/pymiedap", - "url": " https://rseng.github.io/software/repository/gitlab/loic.cg.rossi/pymiedap", - "content": "PyMieDAP = Python Mie Doubling Adding Program. A radiative transfer code with polarization." + "gitlab/binary_c/binary_c-python": { + "id": "gitlab/binary_c/binary_c-python", + "title": "gitlab/binary_c/binary_c-python", + "url": " https://rseng.github.io/software/repository/gitlab/binary_c/binary_c-python", + "content": "Python module to interface with the binary_c stellar population framework. + +The current stable branch is 1.0.0 which you can find in the [releases/1.0.0/2.2.4 branch](https://gitlab.com/binary_c/binary_c-python/-/tree/releases/1.0.0/2.2.4) which works with [binary_c version 2.2.4](https://gitlab.com/binary_c/binary_c/-/tree/development/2.2.4)" }, - "gitlab/ENKI-portal/vaporock": { - "id": "gitlab/ENKI-portal/vaporock", - "title": "gitlab/ENKI-portal/vaporock", - "url": " https://rseng.github.io/software/repository/gitlab/ENKI-portal/vaporock", - "content": "Thermodynamics of vaporized silicate rocks & melts for modeling magma ocean atmospheres and stellar nebula" + "gitlab/rki_bioinformatics/HiLive2": { + "id": "gitlab/rki_bioinformatics/HiLive2", + "title": "gitlab/rki_bioinformatics/HiLive2", + "url": " https://rseng.github.io/software/repository/gitlab/rki_bioinformatics/HiLive2", + "content": "HiLive2 is a read mapping tool that maps Illumina HiSeq (or comparable) reads right in the moment when they are produced. Please create issues for HiLive2 at https://gitlab.com/lokat/HiLive2." }, - "gitlab/ENKI-portal/ThermoCodegen": { - "id": "gitlab/ENKI-portal/ThermoCodegen", - "title": "gitlab/ENKI-portal/ThermoCodegen", - "url": " https://rseng.github.io/software/repository/gitlab/ENKI-portal/ThermoCodegen", - "content": "ThermoCodegen: a python/C++ package for the generation of custom thermodynamic models" + "gitlab/rki_bioinformatics/purple": { + "id": "gitlab/rki_bioinformatics/purple", + "title": "gitlab/rki_bioinformatics/purple", + "url": " https://rseng.github.io/software/repository/gitlab/rki_bioinformatics/purple", + "content": "Picking Unique Relevant Peptides for viraL Experiments + +Authors: Johanna Lechner [@LechnerJ], Pauline Hiortand Felix Hartkopf [@HartkopfF] + +Support: https://gitlab.com/HartkopfF/Purple + +Download: https://gitlab.com/HartkopfF/Purple/releases" }, - "gitlab/ENKI-portal/ThermoEngine": { - "id": "gitlab/ENKI-portal/ThermoEngine", - "title": "gitlab/ENKI-portal/ThermoEngine", - "url": " https://rseng.github.io/software/repository/gitlab/ENKI-portal/ThermoEngine", - "content": "Python, C, C++ and Objective C code that Implement thermodynamic properties of stoichiometric phases and solutions. This is the main code repository of the ENKI project." + "gitlab/rki_bioinformatics/IDeFIX": { + "id": "gitlab/rki_bioinformatics/IDeFIX", + "title": "gitlab/rki_bioinformatics/IDeFIX", + "url": " https://rseng.github.io/software/repository/gitlab/rki_bioinformatics/IDeFIX", + "content": "Index checking for improved demultiplexing of NGS data" }, - "gitlab/chjordan/sslf": { - "id": "gitlab/chjordan/sslf", - "title": "gitlab/chjordan/sslf", - "url": " https://rseng.github.io/software/repository/gitlab/chjordan/sslf", - "content": "Simple Spectral Line Finder" + "gitlab/ProjectRHEA/flowsolverrhea": { + "id": "gitlab/ProjectRHEA/flowsolverrhea", + "title": "gitlab/ProjectRHEA/flowsolverrhea", + "url": " https://rseng.github.io/software/repository/gitlab/ProjectRHEA/flowsolverrhea", + "content": "RHEA: an open-source Reproducible and Hybrid-architecture flow solver Engineered for Academia" }, "gitlab/dsbowen/conditional-inference": { "id": "gitlab/dsbowen/conditional-inference", @@ -704,59 +602,17 @@ "url": " https://rseng.github.io/software/repository/gitlab/dsbowen/conditional-inference", "content": "None" }, - "gitlab/pythia-uq/pythia": { - "id": "gitlab/pythia-uq/pythia", - "title": "gitlab/pythia-uq/pythia", - "url": " https://rseng.github.io/software/repository/gitlab/pythia-uq/pythia", - "content": "PyThia Uncertainty Quantification Toolbox" - }, - "gitlab/ags-data-format-wg/ags-python-library": { - "id": "gitlab/ags-data-format-wg/ags-python-library", - "title": "gitlab/ags-data-format-wg/ags-python-library", - "url": " https://rseng.github.io/software/repository/gitlab/ags-data-format-wg/ags-python-library", - "content": "A library to read and write AGS files using Pandas DataFrames" - }, - "gitlab/chiemotono/mdcontactcom": { - "id": "gitlab/chiemotono/mdcontactcom", - "title": "gitlab/chiemotono/mdcontactcom", - "url": " https://rseng.github.io/software/repository/gitlab/chiemotono/mdcontactcom", - "content": "" - }, - "gitlab/remram44/taguette": { - "id": "gitlab/remram44/taguette", - "title": "gitlab/remram44/taguette", - "url": " https://rseng.github.io/software/repository/gitlab/remram44/taguette", - "content": "Free and open source qualitative research tool" - }, "gitlab/elsi_project/elsi_interface": { "id": "gitlab/elsi_project/elsi_interface", "title": "gitlab/elsi_project/elsi_interface", "url": " https://rseng.github.io/software/repository/gitlab/elsi_project/elsi_interface", "content": "ELSI: A software interface designed for electronic structure codes to connect with ELPA, libOMM, PEXSI, EigenExa, SLEPc, NTPoly, BSEPACK, LAPACK, MAGMA, and other solver libraries." }, - "gitlab/sybreton/apollinaire": { - "id": "gitlab/sybreton/apollinaire", - "title": "gitlab/sybreton/apollinaire", - "url": " https://rseng.github.io/software/repository/gitlab/sybreton/apollinaire", - "content": "Python tools for helio- and asteroseismic peakbagging frameworks." - }, - "gitlab/jerrytheo16/exoplanet": { - "id": "gitlab/jerrytheo16/exoplanet", - "title": "gitlab/jerrytheo16/exoplanet", - "url": " https://rseng.github.io/software/repository/gitlab/jerrytheo16/exoplanet", - "content": "Desktop-based application to aid in constructing a machine learning model for predictive analysis. The application further allows the model to be evaluated through statistical results and interactive graphs." - }, - "gitlab/dalton/dalton": { - "id": "gitlab/dalton/dalton", - "title": "gitlab/dalton/dalton", - "url": " https://rseng.github.io/software/repository/gitlab/dalton/dalton", - "content": "Public Dalton source code repository." - }, - "gitlab/andreas.andrusch/paipline": { - "id": "gitlab/andreas.andrusch/paipline", - "title": "gitlab/andreas.andrusch/paipline", - "url": " https://rseng.github.io/software/repository/gitlab/andreas.andrusch/paipline", - "content": "Pipeline for the Automatic Identification of Pathogens" + "gitlab/paulklemm_PHD/proteinortho": { + "id": "gitlab/paulklemm_PHD/proteinortho", + "title": "gitlab/paulklemm_PHD/proteinortho", + "url": " https://rseng.github.io/software/repository/gitlab/paulklemm_PHD/proteinortho", + "content": "Proteinortho is a tool to detect orthologous genes within different species. [(Download)](https://gitlab.com/paulklemm_PHD/proteinortho/-/archive/master/proteinortho-master.tar.gz)" }, "gitlab/mcfuman/SpectraPy": { "id": "gitlab/mcfuman/SpectraPy", @@ -764,11 +620,54 @@ "url": " https://rseng.github.io/software/repository/gitlab/mcfuman/SpectraPy", "content": "Python module to extract and reduce astronomical spectral data" }, - "gitlab/habermann_lab/phasik": { - "id": "gitlab/habermann_lab/phasik", - "title": "gitlab/habermann_lab/phasik", - "url": " https://rseng.github.io/software/repository/gitlab/habermann_lab/phasik", - "content": "Scientific tools for extracting cyclic data via hierarchical clustering" + "gitlab/fduchate/predihood": { + "id": "gitlab/fduchate/predihood", + "title": "gitlab/fduchate/predihood", + "url": " https://rseng.github.io/software/repository/gitlab/fduchate/predihood", + "content": "" + }, + "gitlab/InspectorCell/inspectorcell": { + "id": "gitlab/InspectorCell/inspectorcell", + "title": "gitlab/InspectorCell/inspectorcell", + "url": " https://rseng.github.io/software/repository/gitlab/InspectorCell/inspectorcell", + "content": "InspectorCell provides an efficient workflow and graphical interface to generate high-quality training datasets from +highly multiplexed microscopy images." + }, + "gitlab/RKIBioinformaticsPipelines/QCumber": { + "id": "gitlab/RKIBioinformaticsPipelines/QCumber", + "title": "gitlab/RKIBioinformaticsPipelines/QCumber", + "url": " https://rseng.github.io/software/repository/gitlab/RKIBioinformaticsPipelines/QCumber", + "content": "quality control of genomic sequences" + }, + "gitlab/cosmograil/starred": { + "id": "gitlab/cosmograil/starred", + "title": "gitlab/cosmograil/starred", + "url": " https://rseng.github.io/software/repository/gitlab/cosmograil/starred", + "content": "A two-channel deconvolution method with Starlet regularization" + }, + "gitlab/cosmograil/PyCS3": { + "id": "gitlab/cosmograil/PyCS3", + "title": "gitlab/cosmograil/PyCS3", + "url": " https://rseng.github.io/software/repository/gitlab/cosmograil/PyCS3", + "content": "PyCS for python 3" + }, + "gitlab/jtagusari/hrisk-noisemodelling": { + "id": "gitlab/jtagusari/hrisk-noisemodelling", + "title": "gitlab/jtagusari/hrisk-noisemodelling", + "url": " https://rseng.github.io/software/repository/gitlab/jtagusari/hrisk-noisemodelling", + "content": "None" + }, + "gitlab/libreumg/dataquier": { + "id": "gitlab/libreumg/dataquier", + "title": "gitlab/libreumg/dataquier", + "url": " https://rseng.github.io/software/repository/gitlab/libreumg/dataquier", + "content": "" + }, + "gitlab/remikz/nccmp": { + "id": "gitlab/remikz/nccmp", + "title": "gitlab/remikz/nccmp", + "url": " https://rseng.github.io/software/repository/gitlab/remikz/nccmp", + "content": "nccmp - Compare 2 NetCDF files. " }, "gitlab/LouisLab/PiVR": { "id": "gitlab/LouisLab/PiVR", @@ -777,2333 +676,1396 @@ "content": "PiVR has been developed to track a variety of animals in real time and present them with light stimuli. Manual can be found at www.PiVR.org, scientific publication at https://doi.org/10.1371/journal.pbio.3000712 " }, - "github/bengeof/QPoweredCompound2DeNovoDrugPropMax": { - "id": "github/bengeof/QPoweredCompound2DeNovoDrugPropMax", - "title": "github/bengeof/QPoweredCompound2DeNovoDrugPropMax", - "url": " https://rseng.github.io/software/repository/github/bengeof/QPoweredCompound2DeNovoDrugPropMax", - "content": "None" - }, - "github/etiennepayet/nti": { - "id": "github/etiennepayet/nti", - "title": "github/etiennepayet/nti", - "url": " https://rseng.github.io/software/repository/github/etiennepayet/nti", - "content": "None" + "gitlab/moerman1/fhi-cc4s": { + "id": "gitlab/moerman1/fhi-cc4s", + "title": "gitlab/moerman1/fhi-cc4s", + "url": " https://rseng.github.io/software/repository/gitlab/moerman1/fhi-cc4s", + "content": "This project constitutes the interface between the Fritz Haber Institute ab initio molecular simulations (FHI-aims) and the Coupled Cluster for Solids (CC4S) code developed by Felix Hummel and Adreas Grueneis at the TU Wien. +" }, - "github/jpahlers/LASR": { - "id": "github/jpahlers/LASR", - "title": "github/jpahlers/LASR", - "url": " https://rseng.github.io/software/repository/github/jpahlers/LASR", - "content": "Code and dependencies for the Linear Algorithm for Significance Reduction, developed by various members of the University of Idaho's Department of Physics." + "gitlab/mainlabwsu/bims": { + "id": "gitlab/mainlabwsu/bims", + "title": "gitlab/mainlabwsu/bims", + "url": " https://rseng.github.io/software/repository/gitlab/mainlabwsu/bims", + "content": "BIMS" }, - "github/hendr1km/dropout": { - "id": "github/hendr1km/dropout", - "title": "github/hendr1km/dropout", - "url": " https://rseng.github.io/software/repository/github/hendr1km/dropout", - "content": "tools for dropout analysis when working with survey data" - }, - "github/matiscke/lcps": { - "id": "github/matiscke/lcps", - "title": "github/matiscke/lcps", - "url": " https://rseng.github.io/software/repository/github/matiscke/lcps", - "content": "A tool for pre-selecting light curves with possible transit signatures" - }, - "github/krober10nd/SeismicMesh": { - "id": "github/krober10nd/SeismicMesh", - "title": "github/krober10nd/SeismicMesh", - "url": " https://rseng.github.io/software/repository/github/krober10nd/SeismicMesh", - "content": "2D/3D serial and parallel triangular mesh generation tool for Finite Element Methods." - }, - "github/ycwu1030/EvoEMD": { - "id": "github/ycwu1030/EvoEMD", - "title": "github/ycwu1030/EvoEMD", - "url": " https://rseng.github.io/software/repository/github/ycwu1030/EvoEMD", - "content": "Evolution with an Early Matter-Dominated era" - }, - "github/astro-datalab/noaosourcecatalog": { - "id": "github/astro-datalab/noaosourcecatalog", - "title": "github/astro-datalab/noaosourcecatalog", - "url": " https://rseng.github.io/software/repository/github/astro-datalab/noaosourcecatalog", - "content": "Source catalog of all NOAO imaging data" - }, - "github/IBM/fold2seq": { - "id": "github/IBM/fold2seq", - "title": "github/IBM/fold2seq", - "url": " https://rseng.github.io/software/repository/github/IBM/fold2seq", - "content": "Code for Fold2Seq paper from ICML 2021" - }, - "github/jollejolles/pirecorder": { - "id": "github/jollejolles/pirecorder", - "title": "github/jollejolles/pirecorder", - "url": " https://rseng.github.io/software/repository/github/jollejolles/pirecorder", - "content": "Controlled and automated image and video recording with the raspberry pi" - }, - "github/SimonPfeifer/cows": { - "id": "github/SimonPfeifer/cows", - "title": "github/SimonPfeifer/cows", - "url": " https://rseng.github.io/software/repository/github/SimonPfeifer/cows", - "content": "None" - }, - "github/parallelwindfarms/byteparsing": { - "id": "github/parallelwindfarms/byteparsing", - "title": "github/parallelwindfarms/byteparsing", - "url": " https://rseng.github.io/software/repository/github/parallelwindfarms/byteparsing", - "content": "Parser for mixed binary/ASCII data in Python" - }, - "github/SchedMD/slurm": { - "id": "github/SchedMD/slurm", - "title": "github/SchedMD/slurm", - "url": " https://rseng.github.io/software/repository/github/SchedMD/slurm", - "content": "Slurm: A Highly Scalable Workload Manager" - }, - "github/SirSharpest/NarrowEscapeSimulator": { - "id": "github/SirSharpest/NarrowEscapeSimulator", - "title": "github/SirSharpest/NarrowEscapeSimulator", - "url": " https://rseng.github.io/software/repository/github/SirSharpest/NarrowEscapeSimulator", - "content": "Developed during my PhD at the John Innes Centre (Norwich Research Park, Doctoral Training Programme). " - }, - "github/DeepMIALab/UC-NfNet": { - "id": "github/DeepMIALab/UC-NfNet", - "title": "github/DeepMIALab/UC-NfNet", - "url": " https://rseng.github.io/software/repository/github/DeepMIALab/UC-NfNet", - "content": "None" - }, - "github/pengweixing/FACT": { - "id": "github/pengweixing/FACT", - "title": "github/pengweixing/FACT", - "url": " https://rseng.github.io/software/repository/github/pengweixing/FACT", - "content": "None" - }, - "github/hpparvi/opents": { - "id": "github/hpparvi/opents", - "title": "github/hpparvi/opents", - "url": " https://rseng.github.io/software/repository/github/hpparvi/opents", - "content": "Open exoplanet transit search pipeline" - }, - "github/hpparvi/ldtk": { - "id": "github/hpparvi/ldtk", - "title": "github/hpparvi/ldtk", - "url": " https://rseng.github.io/software/repository/github/hpparvi/ldtk", - "content": "Python toolkit for calculating stellar limb darkening profiles and model-specific coefficients using the stellar atmosphere spectrum library by Husser et al. (2013). Described in Parviainen & Aigrain, MNRAS 453, 3821–3826 (2015)." - }, - "github/hpparvi/MuSCAT2_transit_pipeline": { - "id": "github/hpparvi/MuSCAT2_transit_pipeline", - "title": "github/hpparvi/MuSCAT2_transit_pipeline", - "url": " https://rseng.github.io/software/repository/github/hpparvi/MuSCAT2_transit_pipeline", - "content": "MuSCAT2 transit analysis pipeline" - }, - "github/hpparvi/PyTransit": { - "id": "github/hpparvi/PyTransit", - "title": "github/hpparvi/PyTransit", - "url": " https://rseng.github.io/software/repository/github/hpparvi/PyTransit", - "content": "Fast and easy exoplanet transit light curve modelling." - }, - "github/YesselmanLab/rna_map": { - "id": "github/YesselmanLab/rna_map", - "title": "github/YesselmanLab/rna_map", - "url": " https://rseng.github.io/software/repository/github/YesselmanLab/rna_map", - "content": "tools to do mutational profiling (MaP) analysis for RNA chemical mapping experiments." - }, - "github/ORNL/tx2": { - "id": "github/ORNL/tx2", - "title": "github/ORNL/tx2", - "url": " https://rseng.github.io/software/repository/github/ORNL/tx2", - "content": "Transformer eXplainability and eXploration" - }, - "github/ORNL/curifactory": { - "id": "github/ORNL/curifactory", - "title": "github/ORNL/curifactory", - "url": " https://rseng.github.io/software/repository/github/ORNL/curifactory", - "content": "An experiment workflow and organization tool." - }, - "github/abrupt-climate/hyper-canny": { - "id": "github/abrupt-climate/hyper-canny", - "title": "github/abrupt-climate/hyper-canny", - "url": " https://rseng.github.io/software/repository/github/abrupt-climate/hyper-canny", - "content": "High dimensional Canny edge detection" - }, - "github/zhanghe9704/tpsa": { - "id": "github/zhanghe9704/tpsa", - "title": "github/zhanghe9704/tpsa", - "url": " https://rseng.github.io/software/repository/github/zhanghe9704/tpsa", - "content": "C++ and Python TPSA/DA codes" - }, - "github/putonti/virmine": { - "id": "github/putonti/virmine", - "title": "github/putonti/virmine", - 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"title": "github/brentp/vcfanno", - "url": " https://rseng.github.io/software/repository/github/brentp/vcfanno", - "content": "annotate a VCF with other VCFs/BEDs/tabixed files " - }, - "github/brentp/geneimpacts": { - "id": "github/brentp/geneimpacts", - "title": "github/brentp/geneimpacts", - "url": " https://rseng.github.io/software/repository/github/brentp/geneimpacts", - "content": "prioritize effects of variant annotations from VEP, SnpEff, et al." - }, - "github/brentp/cigar": { - "id": "github/brentp/cigar", - "title": "github/brentp/cigar", - "url": " https://rseng.github.io/software/repository/github/brentp/cigar", - "content": "simple library for dealing with SAM cigar strings" - }, - "github/brentp/somalier": { - "id": "github/brentp/somalier", - "title": "github/brentp/somalier", - "url": " https://rseng.github.io/software/repository/github/brentp/somalier", - "content": "fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... 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"id": "github/ParisAstronomicalDataCentre/OPUS", - "title": "github/ParisAstronomicalDataCentre/OPUS", - "url": " https://rseng.github.io/software/repository/github/ParisAstronomicalDataCentre/OPUS", - "content": "Observatoire de Paris UWS System (OPUS): UWS web client/server developped at the Paris Astronomical Data Centre." - }, - "github/jmason86/James-s-EVE-Dimming-Index-JEDI": { - "id": "github/jmason86/James-s-EVE-Dimming-Index-JEDI", - "title": "github/jmason86/James-s-EVE-Dimming-Index-JEDI", - "url": " https://rseng.github.io/software/repository/github/jmason86/James-s-EVE-Dimming-Index-JEDI", - "content": "Detect and characterize coronal dimming in the Solar Dynamics Observatory Extreme Ultraviolet Variability Experiment data" - }, - "github/byuflowlab/GXBeam.jl": { - "id": "github/byuflowlab/GXBeam.jl", - "title": "github/byuflowlab/GXBeam.jl", - "url": " https://rseng.github.io/software/repository/github/byuflowlab/GXBeam.jl", - "content": "Pure Julia Implementation of Geometrically Exact Beam Theory" - 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"content": "An object-oriented general relativity package for Mathematica." - }, - "github/MaudeDavidLab/GMEmbeddings": { - "id": "github/MaudeDavidLab/GMEmbeddings", - "title": "github/MaudeDavidLab/GMEmbeddings", - "url": " https://rseng.github.io/software/repository/github/MaudeDavidLab/GMEmbeddings", - "content": "None" - }, - "github/kevin218/Eureka": { - "id": "github/kevin218/Eureka", - "title": "github/kevin218/Eureka", - "url": " https://rseng.github.io/software/repository/github/kevin218/Eureka", - "content": "Eureka! is a data reduction and analysis pipeline intended for time-series observations with the James Webb Space Telescope (JWST)." - }, - "github/JelfsMaterialsGroup/stk": { - "id": "github/JelfsMaterialsGroup/stk", - "title": "github/JelfsMaterialsGroup/stk", - "url": " https://rseng.github.io/software/repository/github/JelfsMaterialsGroup/stk", - "content": "Mirror of lukasturcani/stk - please file issues / fork / star that repo. 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"content": "A Python/C++ package for three-point clustering measurements in LSS analyses" - }, - "github/MikeSWang/HorizonGRound": { - "id": "github/MikeSWang/HorizonGRound", - "title": "github/MikeSWang/HorizonGRound", - "url": " https://rseng.github.io/software/repository/github/MikeSWang/HorizonGRound", - "content": "Relativistic effects in ultra-large-scale galaxy clustering" - }, - "github/MikeSWang/Harmonia": { - "id": "github/MikeSWang/Harmonia", - "title": "github/MikeSWang/Harmonia", - "url": " https://rseng.github.io/software/repository/github/MikeSWang/Harmonia", - "content": "Hybrid-basis inference for large-scale galaxy clustering" - }, - "github/phil-mansfield/gotetra": { - "id": "github/phil-mansfield/gotetra", - "title": "github/phil-mansfield/gotetra", - "url": " https://rseng.github.io/software/repository/github/phil-mansfield/gotetra", - "content": "A Go-based tracking of cosmic velocity fields through the use of tetrahedra" - }, - "github/UNSW-CEEM/NEMSEER": { - "id": "github/UNSW-CEEM/NEMSEER", - "title": "github/UNSW-CEEM/NEMSEER", - "url": " https://rseng.github.io/software/repository/github/UNSW-CEEM/NEMSEER", - "content": "A package for downloading and handling forecasts for the National Electricity Market (NEM) from the Australian Energy Market Operator (AEMO)." - }, - "github/UNSW-CEEM/nempy": { - "id": "github/UNSW-CEEM/nempy", - "title": "github/UNSW-CEEM/nempy", - "url": " https://rseng.github.io/software/repository/github/UNSW-CEEM/nempy", - "content": "A flexible tool kit for modelling Australia's National Electricity Market dispatch procedure." - }, - "github/ilaudy/PIAO": { - "id": "github/ilaudy/PIAO", - "title": "github/ilaudy/PIAO", - "url": " https://rseng.github.io/software/repository/github/ilaudy/PIAO", - "content": "PIAO (漂) is efficient memory-controlled python code using the standard SO algorithm to identify halos." - }, - "github/pavanvyn/triple-stability": { - "id": "github/pavanvyn/triple-stability", - "title": "github/pavanvyn/triple-stability", - "url": " https://rseng.github.io/software/repository/github/pavanvyn/triple-stability", - 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Based on matrix completion of noisy matrix with low-rank regularization via nuclear norm." + "gitlab/chjordan/sslf": { + "id": "gitlab/chjordan/sslf", + "title": "gitlab/chjordan/sslf", + "url": " https://rseng.github.io/software/repository/gitlab/chjordan/sslf", + "content": "Simple Spectral Line Finder" }, - "github/nlesc/embodied-emotions-scripts": { - "id": "github/nlesc/embodied-emotions-scripts", - "title": "github/nlesc/embodied-emotions-scripts", - "url": " https://rseng.github.io/software/repository/github/nlesc/embodied-emotions-scripts", - "content": "None" + "gitlab/eleonoraalei/exo-mercat-gui": { + "id": "gitlab/eleonoraalei/exo-mercat-gui", + "title": "gitlab/eleonoraalei/exo-mercat-gui", + "url": " https://rseng.github.io/software/repository/gitlab/eleonoraalei/exo-mercat-gui", + "content": "The Graphical User Interface of Exo-MerCat." }, - "github/nlesc/scriptcwl": { - "id": "github/nlesc/scriptcwl", - "title": "github/nlesc/scriptcwl", - "url": " https://rseng.github.io/software/repository/github/nlesc/scriptcwl", - "content": "Create cwl workflows by writing a simple Python script" + "gitlab/geekysquirrel/bigx": { + "id": "gitlab/geekysquirrel/bigx", + "title": "gitlab/geekysquirrel/bigx", + "url": " https://rseng.github.io/software/repository/gitlab/geekysquirrel/bigx", + "content": "A data visualisation tool for geographic datasets" }, - "github/pyFFTW/pyFFTW": { - "id": "github/pyFFTW/pyFFTW", - "title": "github/pyFFTW/pyFFTW", - "url": " https://rseng.github.io/software/repository/github/pyFFTW/pyFFTW", - "content": "A pythonic python wrapper around FFTW" + "gitlab/emd-dev/emd": { + "id": "gitlab/emd-dev/emd", + "title": "gitlab/emd-dev/emd", + "url": " https://rseng.github.io/software/repository/gitlab/emd-dev/emd", + "content": "Empirical Mode Decomposition in Python + +<a href="https://gitlab.com/ajquinn/emd/commits/master"><img alt="pipeline status" src="https://gitlab.com/ajquinn/emd/badges/master/pipeline.svg" /></a>" }, - "github/emunte/vaRHC": { - "id": "github/emunte/vaRHC", - "title": "github/emunte/vaRHC", - "url": " https://rseng.github.io/software/repository/github/emunte/vaRHC", - "content": "None" + "gitlab/gims-developers/gims": { + "id": "gitlab/gims-developers/gims", + "title": "gitlab/gims-developers/gims", + "url": " https://rseng.github.io/software/repository/gitlab/gims-developers/gims", + "content": "GIMS -- Graphical Interface for Materials Simulations -- is an open-source, browser-based toolbox for electronic structure codes. Try it here: [gims.ms1p.org](https://gims.ms1p.org)" }, - "github/rvalieris/parallel-fastq-dump": { - "id": "github/rvalieris/parallel-fastq-dump", - "title": "github/rvalieris/parallel-fastq-dump", - "url": " https://rseng.github.io/software/repository/github/rvalieris/parallel-fastq-dump", - "content": "parallel fastq-dump wrapper" + "gitlab/ztzou/phydl": { + "id": "gitlab/ztzou/phydl", + "title": "gitlab/ztzou/phydl", + "url": " https://rseng.github.io/software/repository/gitlab/ztzou/phydl", + "content": "Phylogenetics by Deep Learning. A residual neural network for inference of quartet phylogenetic tree topology." }, - "github/qboxcode/qbox-public": { - "id": "github/qboxcode/qbox-public", - "title": "github/qboxcode/qbox-public", - "url": " https://rseng.github.io/software/repository/github/qboxcode/qbox-public", - "content": "Qbox public repository" + "gitlab/Molcas/OpenMolcas": { + "id": "gitlab/Molcas/OpenMolcas", + "title": "gitlab/Molcas/OpenMolcas", + "url": " https://rseng.github.io/software/repository/gitlab/Molcas/OpenMolcas", + "content": "OpenMolcas is a quantum chemistry software package. + +The key feature of OpenMolcas is the multiconfigurational approach to the electronic structure." }, - "github/lucian-ilie/DELPHI": { - "id": "github/lucian-ilie/DELPHI", - "title": "github/lucian-ilie/DELPHI", - "url": " https://rseng.github.io/software/repository/github/lucian-ilie/DELPHI", - "content": "Deep learning protein-protein binding sites prediction" + "gitlab/vibes-developers/vibes": { + "id": "gitlab/vibes-developers/vibes", + "title": "gitlab/vibes-developers/vibes", + "url": " https://rseng.github.io/software/repository/gitlab/vibes-developers/vibes", + "content": "[FHI-vibes](https://vibes-developers.gitlab.io/vibes/): Vibrational simulations with python powered by ASE and FHI-aims." }, - "github/zengzhenhuan/GFNet": { - "id": "github/zengzhenhuan/GFNet", - "title": "github/zengzhenhuan/GFNet", - "url": " https://rseng.github.io/software/repository/github/zengzhenhuan/GFNet", - "content": "None" + "gitlab/etienne.behar/menura": { + "id": "gitlab/etienne.behar/menura", + "title": "gitlab/etienne.behar/menura", + "url": " https://rseng.github.io/software/repository/gitlab/etienne.behar/menura", + "content": "Menura is a space plasma simulation code. It is built around a hybrid Particle In Cell (PIC) solver, running on Graphics Processing Units. 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"content": "Wally: Visualization of aligned sequencing reads and contigs" + "github/blebon/directChillFoam": { + "id": "github/blebon/directChillFoam", + "title": "github/blebon/directChillFoam", + "url": " https://rseng.github.io/software/repository/github/blebon/directChillFoam", + "content": "OpenFOAM solver for direct chill casting" }, - "github/tobiasrausch/lorax": { - "id": "github/tobiasrausch/lorax", - "title": "github/tobiasrausch/lorax", - "url": " https://rseng.github.io/software/repository/github/tobiasrausch/lorax", - "content": "A long-read analysis toolbox for cancer genomics" + "github/odb9402/CNNPeaks": { + "id": "github/odb9402/CNNPeaks", + "title": "github/odb9402/CNNPeaks", + "url": " https://rseng.github.io/software/repository/github/odb9402/CNNPeaks", + "content": "The ChIP-Seq peak calling algorithm using convolution neural networks" }, - "github/christinahedges/contaminante": { - "id": "github/christinahedges/contaminante", - "title": "github/christinahedges/contaminante", - "url": " https://rseng.github.io/software/repository/github/christinahedges/contaminante", - "content": "Find the contaminant transiting source in Kepler, K2 or TESS data." + "github/pynucastro/pynucastro": { + "id": "github/pynucastro/pynucastro", + "title": "github/pynucastro/pynucastro", + "url": " https://rseng.github.io/software/repository/github/pynucastro/pynucastro", + "content": "python interfaces to the nuclear reaction rate databases" }, - "github/fulcrumgenomics/fgbio": { - "id": "github/fulcrumgenomics/fgbio", - "title": "github/fulcrumgenomics/fgbio", - "url": " https://rseng.github.io/software/repository/github/fulcrumgenomics/fgbio", - "content": "Tools for working with genomic and high throughput sequencing data." + "github/ejmackrell/tidyproteomics-interactive": { + "id": "github/ejmackrell/tidyproteomics-interactive", + "title": "github/ejmackrell/tidyproteomics-interactive", + "url": " https://rseng.github.io/software/repository/github/ejmackrell/tidyproteomics-interactive", + "content": "Interactive Shiny application for tidyproteomics" }, - 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"github/florpi/sunbird": { - "id": "github/florpi/sunbird", - "title": "github/florpi/sunbird", - "url": " https://rseng.github.io/software/repository/github/florpi/sunbird", - "content": "COsmOlogical inference with dEnsity Split cluStering" + "github/mgckind/easyaccess": { + "id": "github/mgckind/easyaccess", + "title": "github/mgckind/easyaccess", + "url": " https://rseng.github.io/software/repository/github/mgckind/easyaccess", + "content": "SQL command line interpreter for astronomical surveys" }, - "github/PDB-REDO/libcifpp": { - "id": "github/PDB-REDO/libcifpp", - "title": "github/PDB-REDO/libcifpp", - "url": " https://rseng.github.io/software/repository/github/PDB-REDO/libcifpp", - "content": "Library containing code to manipulate mmCIF and PDB files" + "github/JeffLCoughlin/EphemMatch": { + "id": "github/JeffLCoughlin/EphemMatch", + "title": "github/JeffLCoughlin/EphemMatch", + "url": " https://rseng.github.io/software/repository/github/JeffLCoughlin/EphemMatch", + "content": "Code to do ephemeris matching of DR25 TCEs, KOIs, and EBs for false positive identificaiton." }, - 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"github/PDB-REDO/dssp": { - "id": "github/PDB-REDO/dssp", - "title": "github/PDB-REDO/dssp", - "url": " https://rseng.github.io/software/repository/github/PDB-REDO/dssp", - "content": "Application to assign secondary structure to proteins" + "github/prmunday/Immunolyser": { + "id": "github/prmunday/Immunolyser", + "title": "github/prmunday/Immunolyser", + "url": " https://rseng.github.io/software/repository/github/prmunday/Immunolyser", + "content": "None" }, - "github/lehtiolab/msstitch": { - "id": "github/lehtiolab/msstitch", - "title": "github/lehtiolab/msstitch", - "url": " https://rseng.github.io/software/repository/github/lehtiolab/msstitch", - "content": "MS proteomics post-processing utilities" + "github/malonge/RagTag": { + "id": "github/malonge/RagTag", + "title": "github/malonge/RagTag", + "url": " https://rseng.github.io/software/repository/github/malonge/RagTag", + "content": "Tools for fast and flexible genome assembly scaffolding and improvement" }, - "github/jameschapman19/cca_zoo": { - "id": "github/jameschapman19/cca_zoo", - "title": "github/jameschapman19/cca_zoo", - "url": " https://rseng.github.io/software/repository/github/jameschapman19/cca_zoo", - "content": "Canonical Correlation Analysis Zoo: A collection of Regularized, Deep Learning based, Kernel, and Probabilistic methods in a scikit-learn style framework" + "github/PeterKamphuis/FAT": { + "id": "github/PeterKamphuis/FAT", + "title": "github/PeterKamphuis/FAT", + "url": " https://rseng.github.io/software/repository/github/PeterKamphuis/FAT", + "content": "An IDL/GDL wrapper to automate TiRiFiC" }, - "github/KIT-MBS/pyREX": { - "id": "github/KIT-MBS/pyREX", - "title": "github/KIT-MBS/pyREX", - "url": " https://rseng.github.io/software/repository/github/KIT-MBS/pyREX", - "content": "Workflow-orientated python package for Replica Exchange Molecular Dynamics" + "github/mcsiple/mmrefpoints": { + "id": "github/mcsiple/mmrefpoints", + "title": "github/mcsiple/mmrefpoints", + "url": " https://rseng.github.io/software/repository/github/mcsiple/mmrefpoints", + "content": "A package for simulating marine mammal abundance and calculating reference points." }, - 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Spectrum visualization, manipulation, and fitting" }, - "github/FAIR-data-for-CAPACITY/FHIR-to-CAPACITY": { - "id": "github/FAIR-data-for-CAPACITY/FHIR-to-CAPACITY", - "title": "github/FAIR-data-for-CAPACITY/FHIR-to-CAPACITY", - "url": " https://rseng.github.io/software/repository/github/FAIR-data-for-CAPACITY/FHIR-to-CAPACITY", + "github/spacetelescope/pystortion": { + "id": "github/spacetelescope/pystortion", + "title": "github/spacetelescope/pystortion", + "url": " https://rseng.github.io/software/repository/github/spacetelescope/pystortion", "content": "None" }, - "github/GOMC-WSU/GOMC": { - "id": "github/GOMC-WSU/GOMC", - "title": "github/GOMC-WSU/GOMC", - "url": " https://rseng.github.io/software/repository/github/GOMC-WSU/GOMC", - "content": "GOMC - GPU Optimized Monte Carlo is a parallel molecular simulation code designed for high-performance simulation of large systems" + "github/spacetelescope/hst_cosmic_rays": { + "id": "github/spacetelescope/hst_cosmic_rays", + "title": "github/spacetelescope/hst_cosmic_rays", + "url": " https://rseng.github.io/software/repository/github/spacetelescope/hst_cosmic_rays", + "content": "None" }, - 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"github/AOtools/aotools": { - "id": "github/AOtools/aotools", - "title": "github/AOtools/aotools", - "url": " https://rseng.github.io/software/repository/github/AOtools/aotools", - "content": "A useful set of tools for Adaptive Optics in Python" + "github/spacetelescope/jdaviz": { + "id": "github/spacetelescope/jdaviz", + "title": "github/spacetelescope/jdaviz", + "url": " https://rseng.github.io/software/repository/github/spacetelescope/jdaviz", + "content": "JWST astronomical data analysis tools in the Jupyter platform" }, - "github/kimpenn/VERSE": { - "id": "github/kimpenn/VERSE", - "title": "github/kimpenn/VERSE", - "url": " https://rseng.github.io/software/repository/github/kimpenn/VERSE", - "content": "A versatile and efficient RNA-Seq read counting tool" + "github/bluesky/bluesky": { + "id": "github/bluesky/bluesky", + "title": "github/bluesky/bluesky", + "url": " https://rseng.github.io/software/repository/github/bluesky/bluesky", + "content": "experiment orchestration and data acquisition" }, - 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"url": " https://rseng.github.io/software/repository/github/BradhamLab/icat", - "content": "Identifying Cell-states Across Treatments" + "github/AMReX-Astro/wdmerger": { + "id": "github/AMReX-Astro/wdmerger", + "title": "github/AMReX-Astro/wdmerger", + "url": " https://rseng.github.io/software/repository/github/AMReX-Astro/wdmerger", + "content": "A software package for simulating white dwarf mergers with CASTRO" }, - "github/abeelen/powspec": { - "id": "github/abeelen/powspec", - "title": "github/abeelen/powspec", - "url": " https://rseng.github.io/software/repository/github/abeelen/powspec", - "content": "Power and cross spectral density of 2D arrays" + "github/AMReX-Astro/Castro": { + "id": "github/AMReX-Astro/Castro", + "title": "github/AMReX-Astro/Castro", + "url": " https://rseng.github.io/software/repository/github/AMReX-Astro/Castro", + "content": "Castro (Compressible Astrophysics): An adaptive mesh, astrophysical compressible (radiation-, magneto-) hydrodynamics simulation code for massively parallel CPU and GPU architectures." }, - "github/blackjax-devs/blackjax": { - "id": "github/blackjax-devs/blackjax", - "title": "github/blackjax-devs/blackjax", - "url": " https://rseng.github.io/software/repository/github/blackjax-devs/blackjax", - "content": "BlackJAX is a sampling library designed for ease of use, speed and modularity." + "github/AMReX-Astro/Nyx": { + "id": "github/AMReX-Astro/Nyx", + "title": "github/AMReX-Astro/Nyx", + "url": " https://rseng.github.io/software/repository/github/AMReX-Astro/Nyx", + "content": "An adaptive mesh, N-body hydro cosmological simulation code" }, - "github/TomKellyGenetics/graphsim": { - "id": "github/TomKellyGenetics/graphsim", - "title": "github/TomKellyGenetics/graphsim", - "url": " https://rseng.github.io/software/repository/github/TomKellyGenetics/graphsim", - "content": "R package: Simulate Expression data from igraph network using mvtnorm (multivariate normal)." + "github/bethgelab/foolbox": { + "id": "github/bethgelab/foolbox", + "title": "github/bethgelab/foolbox", + "url": " https://rseng.github.io/software/repository/github/bethgelab/foolbox", + "content": "A Python toolbox to create adversarial examples that fool neural networks in PyTorch, TensorFlow, and JAX" }, - "github/atomneb/AtomNeb-py": { - "id": "github/atomneb/AtomNeb-py", - "title": "github/atomneb/AtomNeb-py", - "url": " https://rseng.github.io/software/repository/github/atomneb/AtomNeb-py", - "content": "AtomNeb - Python Package for Atomic Data of Ionized Nebulae" + "github/meta-logic/sequoia": { + "id": "github/meta-logic/sequoia", + "title": "github/meta-logic/sequoia", + "url": " https://rseng.github.io/software/repository/github/meta-logic/sequoia", + "content": "Design, play with, and analyze sequent calculus proof systems." }, - "github/nikhilroxtomar/FANet": { - "id": "github/nikhilroxtomar/FANet", - "title": "github/nikhilroxtomar/FANet", - "url": " https://rseng.github.io/software/repository/github/nikhilroxtomar/FANet", - "content": "FANet: A Feedback Attention Network for Improved Biomedical Image Segmentation [IEEE Transactions on Neural Networks and Learning Systems]" + "github/dbosul/CWITools": { + "id": "github/dbosul/CWITools", + "title": "github/dbosul/CWITools", + "url": " https://rseng.github.io/software/repository/github/dbosul/CWITools", + "content": "Tools for Cosmic Web Imager Data" }, - "github/sheydenreich/threepoint": { - "id": "github/sheydenreich/threepoint", - "title": "github/sheydenreich/threepoint", - "url": " https://rseng.github.io/software/repository/github/sheydenreich/threepoint", - "content": "None" + "github/opengeos/segment-geospatial": { + "id": "github/opengeos/segment-geospatial", + "title": "github/opengeos/segment-geospatial", + "url": " https://rseng.github.io/software/repository/github/opengeos/segment-geospatial", + "content": "A Python package for segmenting geospatial data with the Segment Anything Model (SAM)" }, - "github/parmoo/parmoo": { - "id": "github/parmoo/parmoo", - "title": "github/parmoo/parmoo", - "url": " https://rseng.github.io/software/repository/github/parmoo/parmoo", - "content": "Python library for parallel multiobjective simulation optimization" + "github/sonoUnoTeam/sonoUno-desktop": { + "id": "github/sonoUnoTeam/sonoUno-desktop", + "title": "github/sonoUnoTeam/sonoUno-desktop", + "url": " https://rseng.github.io/software/repository/github/sonoUnoTeam/sonoUno-desktop", + "content": "SonoUno is a sonification software for astronomical data presented on a table (txt or csv files). The software is being developed based on the study of other software, standards of accessibility like the ISO 9241-171:2008 (Guidance on software accessibility) and theoretical framework based on literature review and end user tests." }, - "github/leirufeng/iEnhancer-DCSV": { - "id": "github/leirufeng/iEnhancer-DCSV", - "title": "github/leirufeng/iEnhancer-DCSV", - "url": " https://rseng.github.io/software/repository/github/leirufeng/iEnhancer-DCSV", - "content": "None" + "github/bretthandrews/flexCE": { + "id": "github/bretthandrews/flexCE", + "title": "github/bretthandrews/flexCE", + "url": " https://rseng.github.io/software/repository/github/bretthandrews/flexCE", + "content": "A flexible Chemical Evolution model in python" }, - "github/benmontet/f3": { - "id": "github/benmontet/f3", - "title": "github/benmontet/f3", - "url": " https://rseng.github.io/software/repository/github/benmontet/f3", - "content": "Full Frame Fotometry from the Kepler Full Frame Images" + "github/wangsiwei2010/FPMVS-CAG": { + "id": "github/wangsiwei2010/FPMVS-CAG", + "title": "github/wangsiwei2010/FPMVS-CAG", + "url": " https://rseng.github.io/software/repository/github/wangsiwei2010/FPMVS-CAG", + "content": "code of "Fast Parameter-free Multi-view Subspace Clustering with Consensus Anchor Guidance " published in IEEE TIP2022" }, - "github/savage13/sacio": { - "id": "github/savage13/sacio", - "title": "github/savage13/sacio", - "url": " https://rseng.github.io/software/repository/github/savage13/sacio", - "content": "sacio library" + "github/tony-travis/PIQUE": { + "id": "github/tony-travis/PIQUE", + "title": "github/tony-travis/PIQUE", + "url": " https://rseng.github.io/software/repository/github/tony-travis/PIQUE", + "content": "Parallel Identification of QTL's Using EMMAX" }, - "github/snad-space/coniferest": { - "id": "github/snad-space/coniferest", - "title": "github/snad-space/coniferest", - "url": " https://rseng.github.io/software/repository/github/snad-space/coniferest", + "github/ANTsX/ANTs": { + "id": "github/ANTsX/ANTs", + "title": "github/ANTsX/ANTs", + "url": " https://rseng.github.io/software/repository/github/ANTsX/ANTs", + "content": "Advanced Normalization Tools (ANTs) " + }, + "github/FrancesBW/bellamy": { + "id": "github/FrancesBW/bellamy", + "title": "github/FrancesBW/bellamy", + "url": " https://rseng.github.io/software/repository/github/FrancesBW/bellamy", "content": "None" }, - "github/snad-space/zwad": { - "id": "github/snad-space/zwad", - "title": "github/snad-space/zwad", - "url": " https://rseng.github.io/software/repository/github/snad-space/zwad", - "content": "ZTF anomaly detection" + "github/kuenzelab/ENDURE": { + "id": "github/kuenzelab/ENDURE", + "title": "github/kuenzelab/ENDURE", + "url": " https://rseng.github.io/software/repository/github/kuenzelab/ENDURE", + "content": "Tool for energy breakdown analysis of protein designs" }, - "github/snad-space/ztf-viewer": { - "id": "github/snad-space/ztf-viewer", - "title": "github/snad-space/ztf-viewer", - "url": " https://rseng.github.io/software/repository/github/snad-space/ztf-viewer", - "content": "ZTF data releases light curve viewer" + "github/gbernstein/pixmappy": { + "id": "github/gbernstein/pixmappy", + "title": "github/gbernstein/pixmappy", + "url": " https://rseng.github.io/software/repository/github/gbernstein/pixmappy", + "content": "Python interface to gbdes pixel map (astrometry) solutions" }, - "github/JungleComputing/rocket": { - "id": "github/JungleComputing/rocket", - "title": "github/JungleComputing/rocket", - "url": " https://rseng.github.io/software/repository/github/JungleComputing/rocket", - "content": "Rocket is a Constellation-based runtime system for efficient execution of all-pair compute problem on distributed heterogeneous platforms" + "github/gbernstein/gbdes": { + "id": "github/gbernstein/gbdes", + "title": "github/gbernstein/gbdes", + "url": " https://rseng.github.io/software/repository/github/gbernstein/gbdes", + "content": "Gary's DES instrumental signature removal / fitting programs" }, - "github/toshiyan/cmblensplus": { - "id": "github/toshiyan/cmblensplus", - "title": "github/toshiyan/cmblensplus", - "url": " https://rseng.github.io/software/repository/github/toshiyan/cmblensplus", + "github/ByrumLab/proteoDA": { + "id": "github/ByrumLab/proteoDA", + "title": "github/ByrumLab/proteoDA", + "url": " https://rseng.github.io/software/repository/github/ByrumLab/proteoDA", "content": "None" }, - 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"url": " https://rseng.github.io/software/repository/github/vatlab/sos-notebook", - "content": "Multi-language Jupyter Notebook" + "github/HoBeZwe/SphericalScattering.jl": { + "id": "github/HoBeZwe/SphericalScattering.jl", + "title": "github/HoBeZwe/SphericalScattering.jl", + "url": " https://rseng.github.io/software/repository/github/HoBeZwe/SphericalScattering.jl", + "content": "This package provides semi-analytical solutions to the scattering of time harmonic and static electromagnetic fields from spherical objects." }, - "github/mgieles/limepy": { - "id": "github/mgieles/limepy", - "title": "github/mgieles/limepy", - "url": " https://rseng.github.io/software/repository/github/mgieles/limepy", - "content": "Lowered Isothermal Model Explorer in Python" + "github/isakro/shoredate": { + "id": "github/isakro/shoredate", + "title": "github/isakro/shoredate", + "url": " https://rseng.github.io/software/repository/github/isakro/shoredate", + "content": "R package for shoreline dating coastal Stone Age sites" }, - "github/cns-iu/HRA-supporting-information": { - "id": "github/cns-iu/HRA-supporting-information", - "title": "github/cns-iu/HRA-supporting-information", - "url": " https://rseng.github.io/software/repository/github/cns-iu/HRA-supporting-information", - "content": "None" + "github/SysBioUAB/hpi_predictor": { + "id": "github/SysBioUAB/hpi_predictor", + "title": "github/SysBioUAB/hpi_predictor", + "url": " https://rseng.github.io/software/repository/github/SysBioUAB/hpi_predictor", + "content": "Bash+R tool to predict host-pathogen protein-protein interactions based on numerical encoding of physicochemical descriptors" }, - "github/davek44/Glimmer-MG": { - "id": "github/davek44/Glimmer-MG", - "title": "github/davek44/Glimmer-MG", - "url": " https://rseng.github.io/software/repository/github/davek44/Glimmer-MG", - "content": "Gene prediction in metagenomic sequences using Glimmer augmented by phylogenetic classification and clustering" + "github/cosmo-ethz/CosmoHammer": { + "id": "github/cosmo-ethz/CosmoHammer", + "title": "github/cosmo-ethz/CosmoHammer", + "url": " https://rseng.github.io/software/repository/github/cosmo-ethz/CosmoHammer", + "content": "Cosmological parameter estimation with the MCMC Hammer, please use https://cosmo-gitlab.phys.ethz.ch/cosmo/CosmoHammer, this repository is outdated ! Docs at http://cosmo-docs.phys.ethz.ch/cosmoHammer/" }, - "github/ryneches/SuchTree": { - "id": "github/ryneches/SuchTree", - "title": "github/ryneches/SuchTree", - "url": " https://rseng.github.io/software/repository/github/ryneches/SuchTree", - "content": "A Python library for fast, thread-safe computations on phylogenetic trees" + "github/cosmo-ethz/hide": { + "id": "github/cosmo-ethz/hide", + "title": "github/cosmo-ethz/hide", + "url": " https://rseng.github.io/software/repository/github/cosmo-ethz/hide", + "content": "A package for simulating of a single dish radio telescope survey" }, - "github/oleksulkowski/Syn-CpG-Spacer": { - "id": "github/oleksulkowski/Syn-CpG-Spacer", - "title": "github/oleksulkowski/Syn-CpG-Spacer", - "url": " https://rseng.github.io/software/repository/github/oleksulkowski/Syn-CpG-Spacer", - "content": "A Panel progressive web app for synonymous recoding of viral genomes with CpG dinucleotides" + "github/cosmo-ethz/seek": { + "id": "github/cosmo-ethz/seek", + "title": "github/cosmo-ethz/seek", + "url": " https://rseng.github.io/software/repository/github/cosmo-ethz/seek", + "content": "A flexible and easy-to-extend data processing pipeline for single dish radio telescopes" }, - "github/jrenaud90/TidalPy": { - "id": "github/jrenaud90/TidalPy", - "title": "github/jrenaud90/TidalPy", - "url": " https://rseng.github.io/software/repository/github/jrenaud90/TidalPy", - "content": "Software suite to perform solid-body tidal dissipation calculations for rocky and icy worlds" + "github/mgcooper/baseflow": { + "id": "github/mgcooper/baseflow", + "title": "github/mgcooper/baseflow", + "url": " https://rseng.github.io/software/repository/github/mgcooper/baseflow", + "content": "baseflow recession analysis toolbox" }, - "github/hdeeg/KvW": { - "id": "github/hdeeg/KvW", - "title": "github/hdeeg/KvW", - "url": " https://rseng.github.io/software/repository/github/hdeeg/KvW", - "content": "Kwee Van Woerden algorithm for eclipse or transit minimum timing, with improved error calculation" + "github/zhanglabtools/CASAVA": { + "id": "github/zhanglabtools/CASAVA", + "title": "github/zhanglabtools/CASAVA", + "url": " https://rseng.github.io/software/repository/github/zhanglabtools/CASAVA", + "content": "Resources of our paper CASAVA" }, - "github/sid-krish/Rhometa_Full_Genome": { - "id": "github/sid-krish/Rhometa_Full_Genome", - "title": "github/sid-krish/Rhometa_Full_Genome", - "url": " https://rseng.github.io/software/repository/github/sid-krish/Rhometa_Full_Genome", - "content": "None" + "github/SpaceOdyssey/Blobby3D": { + "id": "github/SpaceOdyssey/Blobby3D", + "title": "github/SpaceOdyssey/Blobby3D", + "url": " https://rseng.github.io/software/repository/github/SpaceOdyssey/Blobby3D", + "content": "Blobby3D is a tool to perform Bayesian inference for gas kinematics on emission line observations of galaxies using Integral Field Spectroscopy." }, - "github/tdaylan/pcat": { - "id": "github/tdaylan/pcat", - "title": "github/tdaylan/pcat", - "url": " https://rseng.github.io/software/repository/github/tdaylan/pcat", - "content": "A transdimensional, hierarchical, Bayesian framework to sample from a metamodel" + "github/hishamhm/htop": { + "id": "github/hishamhm/htop", + "title": "github/hishamhm/htop", + "url": " https://rseng.github.io/software/repository/github/hishamhm/htop", + "content": "htop is an interactive text-mode process viewer for Unix systems. It aims to be a better 'top'." }, - "github/li-yangyang/lotus": { - "id": "github/li-yangyang/lotus", - "title": "github/li-yangyang/lotus", - "url": " https://rseng.github.io/software/repository/github/li-yangyang/lotus", - "content": "Fast tool for 1D Non-LTE stellar parameter determination via Equivalent Width method" + "github/ulebreui/shark": { + "id": "github/ulebreui/shark", + "title": "github/ulebreui/shark", + "url": " https://rseng.github.io/software/repository/github/ulebreui/shark", + "content": "This is the public repository of the shark code (Lebreuilly et al., 2023)" }, - "github/bwoshea/ZEUS-MP_2": { - "id": "github/bwoshea/ZEUS-MP_2", - "title": "github/bwoshea/ZEUS-MP_2", - "url": " https://rseng.github.io/software/repository/github/bwoshea/ZEUS-MP_2", - "content": "This repository is the home of the ZEUS-MP 2.0 code, which was created by John Hayes and others at the Laboratory for Computational Astrophysics at UIUC and UCSD." + "github/epiforecasts/covidregionaldata": { + "id": "github/epiforecasts/covidregionaldata", + "title": "github/epiforecasts/covidregionaldata", + "url": " https://rseng.github.io/software/repository/github/epiforecasts/covidregionaldata", + "content": "An interface to subnational and national level COVID-19 data. For all countries supported, this includes a daily time-series of cases. Wherever available we also provide data on deaths, hospitalisations, and tests. National level data is also supported using a range of data sources as well as linelist data and links to intervention data sets." }, - "github/humanfactors/FIPS": { - "id": "github/humanfactors/FIPS", - "title": "github/humanfactors/FIPS", - "url": " https://rseng.github.io/software/repository/github/humanfactors/FIPS", - "content": "The Fatigue Impairment Prediction Suite (for R)" + "github/IMB-Computational-Genomics-Lab/scGPS": { + "id": "github/IMB-Computational-Genomics-Lab/scGPS", + "title": "github/IMB-Computational-Genomics-Lab/scGPS", + "url": " https://rseng.github.io/software/repository/github/IMB-Computational-Genomics-Lab/scGPS", + "content": "A framework for clustering (CORE) and estimation of relationship between pairs of clusters (scGPS) from single cell data " }, - "github/astrogilda/mirkwood": { - "id": "github/astrogilda/mirkwood", - "title": "github/astrogilda/mirkwood", - "url": " https://rseng.github.io/software/repository/github/astrogilda/mirkwood", - "content": "None" + "github/brandonckelly/carma_pack": { + "id": "github/brandonckelly/carma_pack", + "title": "github/brandonckelly/carma_pack", + "url": " https://rseng.github.io/software/repository/github/brandonckelly/carma_pack", + "content": "MCMC Sampler for Performing Bayesian Inference on Continuous Time Autoregressive Models." }, - "github/gperezs/StarcNet": { - "id": "github/gperezs/StarcNet", - "title": "github/gperezs/StarcNet", - "url": " https://rseng.github.io/software/repository/github/gperezs/StarcNet", - "content": "Machine learning for star cluster classification" + "github/jacobmerson/model-traits": { + "id": "github/jacobmerson/model-traits", + "title": "github/jacobmerson/model-traits", + "url": " https://rseng.github.io/software/repository/github/jacobmerson/model-traits", + "content": "simple library for dealing with simulation boundary conditions" }, - "github/sjbeckett/localcovid19now": { - "id": "github/sjbeckett/localcovid19now", - "title": "github/sjbeckett/localcovid19now", - "url": " https://rseng.github.io/software/repository/github/sjbeckett/localcovid19now", - "content": "processing and mapping COVID-19 case data at subnational scales" + "github/kgullikson88/Telluric-Fitter": { + "id": "github/kgullikson88/Telluric-Fitter", + "title": "github/kgullikson88/Telluric-Fitter", + "url": " https://rseng.github.io/software/repository/github/kgullikson88/Telluric-Fitter", + "content": "Telluric fitting made easy" }, - "github/dengzhuo-AI/Real-Fundus": { - "id": "github/dengzhuo-AI/Real-Fundus", - "title": "github/dengzhuo-AI/Real-Fundus", - "url": " https://rseng.github.io/software/repository/github/dengzhuo-AI/Real-Fundus", - "content": "None" + "github/kgullikson88/Companion-Finder": { + "id": "github/kgullikson88/Companion-Finder", + "title": "github/kgullikson88/Companion-Finder", + "url": " https://rseng.github.io/software/repository/github/kgullikson88/Companion-Finder", + "content": "A set of scripts for looking for planets and binary companions in time series spectra" }, - "github/malonge/RagTag": { - "id": "github/malonge/RagTag", - "title": "github/malonge/RagTag", - "url": " https://rseng.github.io/software/repository/github/malonge/RagTag", - "content": "Tools for fast and flexible genome assembly scaffolding and improvement" + "github/jumphone/inferloop": { + "id": "github/jumphone/inferloop", + "title": "github/jumphone/inferloop", + "url": " https://rseng.github.io/software/repository/github/jumphone/inferloop", + "content": "InferLoop: leveraging single-cell chromatin accessibility for the signal of chromatin loop" }, - "github/ocean-eddy-cpt/gcm-filters": { - "id": "github/ocean-eddy-cpt/gcm-filters", - "title": "github/ocean-eddy-cpt/gcm-filters", - "url": " https://rseng.github.io/software/repository/github/ocean-eddy-cpt/gcm-filters", - "content": "Diffusion-based Spatial Filtering of Gridded Data" + "github/SCM-NV/qmflows": { + "id": "github/SCM-NV/qmflows", + "title": "github/SCM-NV/qmflows", + "url": " https://rseng.github.io/software/repository/github/SCM-NV/qmflows", + "content": "This library tackles the construction and efficient execution of computational chemistry workflows" }, - "github/NBISweden/AGAT": { - "id": "github/NBISweden/AGAT", - "title": "github/NBISweden/AGAT", - "url": " https://rseng.github.io/software/repository/github/NBISweden/AGAT", - "content": "Another Gtf/Gff Analysis Toolkit" + "github/SCM-NV/qmflows-namd": { + "id": "github/SCM-NV/qmflows-namd", + "title": "github/SCM-NV/qmflows-namd", + "url": " https://rseng.github.io/software/repository/github/SCM-NV/qmflows-namd", + "content": "Package containing several workflows to compute molecular properties for nanomaterials" }, - "github/winni2k/abeona": { - "id": "github/winni2k/abeona", - "title": "github/winni2k/abeona", - "url": " https://rseng.github.io/software/repository/github/winni2k/abeona", - "content": "abeona -- Abeona is the goddess of outward graph traversal" + "github/SCM-NV/pyZacros": { + "id": "github/SCM-NV/pyZacros", + "title": "github/SCM-NV/pyZacros", + "url": " https://rseng.github.io/software/repository/github/SCM-NV/pyZacros", + "content": "Python library to handle KMC codes." }, - "github/nbellomo/Multi_CLASS": { - "id": "github/nbellomo/Multi_CLASS", - "title": "github/nbellomo/Multi_CLASS", - "url": " https://rseng.github.io/software/repository/github/nbellomo/Multi_CLASS", - "content": "Public repository of the Multi_CLASS code" + "github/andersdot/photoParallax": { + "id": "github/andersdot/photoParallax", + "title": "github/andersdot/photoParallax", + "url": " https://rseng.github.io/software/repository/github/andersdot/photoParallax", + "content": "data-driven photometric parallaxes, built with Gaia and 2MASS" }, - "github/Multiversario/satcand": { - "id": "github/Multiversario/satcand", - "title": "github/Multiversario/satcand", - "url": " https://rseng.github.io/software/repository/github/Multiversario/satcand", - "content": "Tools to apply theoretical constraints of orbital stability and tidal migration to KOI exomoon candidates. " + "github/ryansmcgee/seirsplus": { + "id": "github/ryansmcgee/seirsplus", + "title": "github/ryansmcgee/seirsplus", + "url": " https://rseng.github.io/software/repository/github/ryansmcgee/seirsplus", + "content": "Models of SEIRS epidemic dynamics with extensions, including network-structured populations, testing, contact tracing, and social distancing." }, - "github/egjergo/galcem": { - "id": "github/egjergo/galcem", - "title": "github/egjergo/galcem", - "url": " https://rseng.github.io/software/repository/github/egjergo/galcem", - "content": "Please email us to get a JupyterHub account, or for any other queries" + "github/SPARC-FAIR-Codeathon/aqua": { + "id": "github/SPARC-FAIR-Codeathon/aqua", + "title": "github/SPARC-FAIR-Codeathon/aqua", + "url": " https://rseng.github.io/software/repository/github/SPARC-FAIR-Codeathon/aqua", + "content": "Advanced Query Architecture for the SPARC Portal." }, - "github/RealTimeGenomics/rtg-tools": { - "id": "github/RealTimeGenomics/rtg-tools", - "title": "github/RealTimeGenomics/rtg-tools", - "url": " https://rseng.github.io/software/repository/github/RealTimeGenomics/rtg-tools", - "content": "RTG Tools: Utilities for accurate VCF comparison and manipulation" + "github/Kushaalkumar-pothula/FLARE": { + "id": "github/Kushaalkumar-pothula/FLARE", + "title": "github/Kushaalkumar-pothula/FLARE", + "url": " https://rseng.github.io/software/repository/github/Kushaalkumar-pothula/FLARE", + "content": "Generates a synthetic Fast Radio Burst catalog, using the Monte Carlo technique." }, - "github/li-shaochuan/SEDIM": { - "id": "github/li-shaochuan/SEDIM", - "title": "github/li-shaochuan/SEDIM", - "url": " https://rseng.github.io/software/repository/github/li-shaochuan/SEDIM", - "content": "None" + "github/MolMeDB/MolMeDB": { + "id": "github/MolMeDB/MolMeDB", + "title": "github/MolMeDB/MolMeDB", + "url": " https://rseng.github.io/software/repository/github/MolMeDB/MolMeDB", + "content": "MolMeDB is an open chemistry database about interactions of molecules with membranes." }, - "github/nvalimak/fsm-lite": { - "id": "github/nvalimak/fsm-lite", - "title": "github/nvalimak/fsm-lite", - "url": " https://rseng.github.io/software/repository/github/nvalimak/fsm-lite", - "content": "frequency-based string mining (lite)" + "github/bartongroup/RoSA": { + "id": "github/bartongroup/RoSA", + "title": "github/bartongroup/RoSA", + "url": " https://rseng.github.io/software/repository/github/bartongroup/RoSA", + "content": "Antisense analysis scripts" }, - "github/Shyentist/fish-r-man": { - "id": "github/Shyentist/fish-r-man", - "title": "github/Shyentist/fish-r-man", - "url": " https://rseng.github.io/software/repository/github/Shyentist/fish-r-man", - "content": "Open-Source Shiny R Dashboard to easily query, download, analyse and visualise Global Fishing Watch data on fishing effort." + "github/bartongroup/yanosim": { + "id": "github/bartongroup/yanosim", + "title": "github/bartongroup/yanosim", + "url": " https://rseng.github.io/software/repository/github/bartongroup/yanosim", + "content": "Nanopore DRS read simulator" }, - "github/jupyterlab/jupyterlab": { - "id": "github/jupyterlab/jupyterlab", - "title": "github/jupyterlab/jupyterlab", - "url": " https://rseng.github.io/software/repository/github/jupyterlab/jupyterlab", - "content": "JupyterLab computational environment." + "github/MLMI2-CSSI/foundry": { + "id": "github/MLMI2-CSSI/foundry", + "title": "github/MLMI2-CSSI/foundry", + "url": " https://rseng.github.io/software/repository/github/MLMI2-CSSI/foundry", + "content": "Simplifying the discovery and usage of machine-learning ready datasets in materials science and chemistry" }, - "github/Kaixhin/Rainbow": { - "id": "github/Kaixhin/Rainbow", - "title": "github/Kaixhin/Rainbow", - "url": " https://rseng.github.io/software/repository/github/Kaixhin/Rainbow", - "content": "Rainbow: Combining Improvements in Deep Reinforcement Learning" + "github/mbillingr/libgdf": { + "id": "github/mbillingr/libgdf", + "title": "github/mbillingr/libgdf", + "url": " https://rseng.github.io/software/repository/github/mbillingr/libgdf", + "content": "C++ implementation of GDF - "a general dataformat for biosignals" version V2.20." }, - "github/Kaixhin/PlaNet": { - "id": "github/Kaixhin/PlaNet", - "title": "github/Kaixhin/PlaNet", - "url": " https://rseng.github.io/software/repository/github/Kaixhin/PlaNet", - "content": "Deep Planning Network: Control from pixels by latent planning with learned dynamics" + "github/privong/pyMCspearman": { + "id": "github/privong/pyMCspearman", + "title": "github/privong/pyMCspearman", + "url": " https://rseng.github.io/software/repository/github/privong/pyMCspearman", + "content": "Monte carlo calculation of Spearman's rank correlation coefficient with uncertainties. Following Curran (2014)" }, - "github/Kaixhin/dockerfiles": { - "id": "github/Kaixhin/dockerfiles", - "title": "github/Kaixhin/dockerfiles", - "url": " https://rseng.github.io/software/repository/github/Kaixhin/dockerfiles", - "content": "Compilation of Dockerfiles with automated builds enabled on the Docker Registry" + "github/privong/pymccorrelation": { + "id": "github/privong/pymccorrelation", + "title": "github/privong/pymccorrelation", + "url": " https://rseng.github.io/software/repository/github/privong/pymccorrelation", + "content": "Correlation coefficients with uncertainties" }, - "github/Kaixhin/FGLab": { - "id": "github/Kaixhin/FGLab", - "title": "github/Kaixhin/FGLab", - "url": " https://rseng.github.io/software/repository/github/Kaixhin/FGLab", - "content": "Future Gadget Laboratory" + "github/netrias/rnassist": { + "id": "github/netrias/rnassist", + "title": "github/netrias/rnassist", + "url": " https://rseng.github.io/software/repository/github/netrias/rnassist", + "content": "None" }, - "github/Kaixhin/FGMachine": { - "id": "github/Kaixhin/FGMachine", - "title": "github/Kaixhin/FGMachine", - "url": " https://rseng.github.io/software/repository/github/Kaixhin/FGMachine", - "content": "Future Gadget Machine" + "github/copasi/COPASI": { + "id": "github/copasi/COPASI", + "title": "github/copasi/COPASI", + "url": " https://rseng.github.io/software/repository/github/copasi/COPASI", + "content": "COPASI is a software application for simulation and analysis of biochemical networks and their dynamics." }, - "github/Kaixhin/Atari": { - "id": "github/Kaixhin/Atari", - "title": "github/Kaixhin/Atari", - "url": " https://rseng.github.io/software/repository/github/Kaixhin/Atari", - "content": "Persistent advantage learning dueling double DQN for the Arcade Learning Environment" + "github/copasi/basico": { + "id": "github/copasi/basico", + "title": "github/copasi/basico", + "url": " https://rseng.github.io/software/repository/github/copasi/basico", + "content": "A simplified python interface to COPASI." }, - "github/Kaixhin/Autoencoders": { - "id": "github/Kaixhin/Autoencoders", - "title": "github/Kaixhin/Autoencoders", - "url": " https://rseng.github.io/software/repository/github/Kaixhin/Autoencoders", - "content": "Torch implementations of various types of autoencoders" + "github/ExoplanetML/Nigraha": { + "id": "github/ExoplanetML/Nigraha", + "title": "github/ExoplanetML/Nigraha", + "url": " https://rseng.github.io/software/repository/github/ExoplanetML/Nigraha", + "content": "A neural network based pipeline to identify and evaluate planet candidates from TESS light curves." }, - "github/Kaixhin/spinning-up-basic": { - "id": "github/Kaixhin/spinning-up-basic", - "title": "github/Kaixhin/spinning-up-basic", - "url": " https://rseng.github.io/software/repository/github/Kaixhin/spinning-up-basic", - "content": "Basic versions of agents from Spinning Up in Deep RL written in PyTorch" + "github/hetalang/heta-compiler": { + "id": "github/hetalang/heta-compiler", + "title": "github/hetalang/heta-compiler", + "url": " https://rseng.github.io/software/repository/github/hetalang/heta-compiler", + "content": "Software tool for the compilation of Heta-based QSP modeling platform" }, - "github/azizka/IUCNN": { - "id": "github/azizka/IUCNN", - "title": "github/azizka/IUCNN", - "url": " https://rseng.github.io/software/repository/github/azizka/IUCNN", - "content": " Train neural networks based on geographic species occurrences, environmental data and existing IUCN Red List assessments to predict the conservation status of "Not Evaluated" or "Data Deficient" species, for any taxon or geographic region of interest. https://iucnn.github.io/IUCNN/" + "github/PeterBartram/TES": { + "id": "github/PeterBartram/TES", + "title": "github/PeterBartram/TES", + "url": " https://rseng.github.io/software/repository/github/PeterBartram/TES", + "content": "Terrestrial Exoplanet Simulator public repository" }, - "github/zhwm/SparsePro_Paper": { - "id": "github/zhwm/SparsePro_Paper", - "title": "github/zhwm/SparsePro_Paper", - "url": " https://rseng.github.io/software/repository/github/zhwm/SparsePro_Paper", - "content": "Code repo for SparsePro Paper" + "github/vbaliga/gaussplotR": { + "id": "github/vbaliga/gaussplotR", + "title": "github/vbaliga/gaussplotR", + "url": " https://rseng.github.io/software/repository/github/vbaliga/gaussplotR", + "content": "🔔 Fit, predict, and plot 2D Gaussians in R" }, - 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(visitors via old url will be redirected to the website with new url)" }, - "github/tidymodels/stacks": { - "id": "github/tidymodels/stacks", - "title": "github/tidymodels/stacks", - "url": " https://rseng.github.io/software/repository/github/tidymodels/stacks", - "content": "An R package for tidy stacked ensemble modeling" + "github/eucp-project/atlas": { + "id": "github/eucp-project/atlas", + "title": "github/eucp-project/atlas", + "url": " https://rseng.github.io/software/repository/github/eucp-project/atlas", + "content": "prototype result browser" }, - "github/tidymodels/infer": { - "id": "github/tidymodels/infer", - "title": "github/tidymodels/infer", - "url": " https://rseng.github.io/software/repository/github/tidymodels/infer", - "content": "An R package for tidyverse-friendly statistical inference" + "github/DeepRank/iScore": { + "id": "github/DeepRank/iScore", + "title": "github/DeepRank/iScore", + "url": " https://rseng.github.io/software/repository/github/DeepRank/iScore", + "content": "iScore: an MPI supported software for ranking protein-protein docking models based on a random walk graph kernel and support vector machines" }, - "github/dlakaplan/pulsarsurveyscraper": { - "id": "github/dlakaplan/pulsarsurveyscraper", - "title": "github/dlakaplan/pulsarsurveyscraper", - "url": " https://rseng.github.io/software/repository/github/dlakaplan/pulsarsurveyscraper", + "github/DeepRank/deeprank-core": { + "id": "github/DeepRank/deeprank-core", + "title": "github/DeepRank/deeprank-core", + "url": " https://rseng.github.io/software/repository/github/DeepRank/deeprank-core", "content": "None" }, - "github/candYgene/pbg-ld": { - "id": "github/candYgene/pbg-ld", - "title": "github/candYgene/pbg-ld", - "url": " https://rseng.github.io/software/repository/github/candYgene/pbg-ld", - "content": "Linked Data Platform for Plant Breeding & Genomics" + "github/DeepRank/deeprank": { + "id": "github/DeepRank/deeprank", + "title": "github/DeepRank/deeprank", + "url": " https://rseng.github.io/software/repository/github/DeepRank/deeprank", + "content": "Deep learning framework for data mining protein-protein interactions using CNN" }, - "github/candYgene/abg-ld": { - "id": "github/candYgene/abg-ld", - "title": "github/candYgene/abg-ld", - "url": " https://rseng.github.io/software/repository/github/candYgene/abg-ld", - "content": "Linked Data Platform for Animal Breeding & Genomics" + "github/DeepRank/pssmgen": { + "id": "github/DeepRank/pssmgen", + "title": "github/DeepRank/pssmgen", + "url": " https://rseng.github.io/software/repository/github/DeepRank/pssmgen", + "content": "Generates consistent PSSM and/or PDB files for protein-protein complexes" }, - "github/candYgene/siga": { - "id": "github/candYgene/siga", - "title": "github/candYgene/siga", - "url": " https://rseng.github.io/software/repository/github/candYgene/siga", - "content": "Semantically Interoperable Genome Annotations" + "github/DeepRank/pdb2sql": { + "id": "github/DeepRank/pdb2sql", + "title": "github/DeepRank/pdb2sql", + "url": " https://rseng.github.io/software/repository/github/DeepRank/pdb2sql", + "content": "Fast and versatile biomolecular structure PDB file parser using SQL queries" }, - "github/candYgene/QTM": { - "id": "github/candYgene/QTM", - "title": "github/candYgene/QTM", - "url": " https://rseng.github.io/software/repository/github/candYgene/QTM", - "content": "QTLTableMiner++ tool for mining tables in scientific articles" + "github/DeepRank/DeepRank-GNN": { + "id": "github/DeepRank/DeepRank-GNN", + "title": "github/DeepRank/DeepRank-GNN", + "url": " https://rseng.github.io/software/repository/github/DeepRank/DeepRank-GNN", + "content": "Graph Network for protein-protein interface" }, - "github/jeffzhen/omnical": { - "id": "github/jeffzhen/omnical", - "title": "github/jeffzhen/omnical", - "url": " https://rseng.github.io/software/repository/github/jeffzhen/omnical", - "content": "Redundant calibration code for low frequency radio interferometers, managed by Jeff Zheng" + "github/nextgenusfs/funannotate": { + "id": "github/nextgenusfs/funannotate", + "title": "github/nextgenusfs/funannotate", + "url": " https://rseng.github.io/software/repository/github/nextgenusfs/funannotate", + "content": "Eukaryotic Genome Annotation Pipeline" }, - 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"github/elliohow/fMRI_ROI_Analysis_Tool": { - "id": "github/elliohow/fMRI_ROI_Analysis_Tool", - "title": "github/elliohow/fMRI_ROI_Analysis_Tool", - "url": " https://rseng.github.io/software/repository/github/elliohow/fMRI_ROI_Analysis_Tool", - "content": "An analysis tool that uses per-voxel statistical maps in conjunction with FSL atlases to create per-region statistical maps. Current usage includes the creation of regional maps of temporal signal to noise ratio." + "github/ColemanRHarris/mxnorm": { + "id": "github/ColemanRHarris/mxnorm", + "title": "github/ColemanRHarris/mxnorm", + "url": " https://rseng.github.io/software/repository/github/ColemanRHarris/mxnorm", + "content": "R package to normalize multiplexed imaging data." }, - "github/JamesPaynter/PyGRB": { - "id": "github/JamesPaynter/PyGRB", - "title": "github/JamesPaynter/PyGRB", - "url": " https://rseng.github.io/software/repository/github/JamesPaynter/PyGRB", - "content": "Gamma-ray burst analysis library" + "github/TravisWheelerLab/NINJA": { + "id": "github/TravisWheelerLab/NINJA", + "title": "github/TravisWheelerLab/NINJA", + "url": " https://rseng.github.io/software/repository/github/TravisWheelerLab/NINJA", + "content": "Nearly Infinite Neighbor Joining Application" }, - "github/halomod/halomod": { - "id": "github/halomod/halomod", - "title": "github/halomod/halomod", - "url": " https://rseng.github.io/software/repository/github/halomod/halomod", - "content": "Python package for dealing with the Halo Model" + "github/TravisWheelerLab/VIBES": { + "id": "github/TravisWheelerLab/VIBES", + "title": "github/TravisWheelerLab/VIBES", + "url": " https://rseng.github.io/software/repository/github/TravisWheelerLab/VIBES", + "content": "Viral Integrations in Bacterial genomES" }, - "github/halomod/hmf": { - "id": "github/halomod/hmf", - "title": "github/halomod/hmf", - "url": " https://rseng.github.io/software/repository/github/halomod/hmf", - "content": "Python halo mass function calculator" + "github/TinkerTools/tinker9": { + "id": "github/TinkerTools/tinker9", + "title": "github/TinkerTools/tinker9", + "url": " https://rseng.github.io/software/repository/github/TinkerTools/tinker9", + "content": "Tinker9: Next Generation of Tinker with GPU Support" }, - "github/masadcv/FastGeodis": { - "id": "github/masadcv/FastGeodis", - "title": "github/masadcv/FastGeodis", - "url": " https://rseng.github.io/software/repository/github/masadcv/FastGeodis", - "content": "Fast Implementation of Generalised Geodesic Distance Transform for CPU (OpenMP) and GPU (CUDA)" + "github/TinkerTools/Tinker-HP": { + "id": "github/TinkerTools/Tinker-HP", + "title": "github/TinkerTools/Tinker-HP", + "url": " https://rseng.github.io/software/repository/github/TinkerTools/Tinker-HP", + "content": "Tinker-HP: High-Performance Massively Parallel Evolution of Tinker on CPUs & GPUs" }, - "github/hamers/tpi": { - "id": "github/hamers/tpi", - "title": "github/hamers/tpi", - "url": " https://rseng.github.io/software/repository/github/hamers/tpi", - "content": "Test Particle Integrator: integrate test particles around a massive black hole" + "github/alexfields/ORF-RATER": { + "id": "github/alexfields/ORF-RATER", + "title": "github/alexfields/ORF-RATER", + "url": " https://rseng.github.io/software/repository/github/alexfields/ORF-RATER", + "content": "Regression-based annotation of protein-coding sequences from ribosome profiling data" }, - "github/hamers/secularmultiple": { - "id": "github/hamers/secularmultiple", - "title": "github/hamers/secularmultiple", - "url": " https://rseng.github.io/software/repository/github/hamers/secularmultiple", - "content": "Code to model the secular evolution of a hierarchical multiple system" + "github/hasindu2008/slow5tools": { + "id": "github/hasindu2008/slow5tools", + "title": "github/hasindu2008/slow5tools", + "url": " https://rseng.github.io/software/repository/github/hasindu2008/slow5tools", + "content": "Slow5tools is a toolkit for converting (FAST5 <-> SLOW5), compressing, viewing, indexing and manipulating data in SLOW5 format." }, - "github/jdeast/EXOFASTv2": { - "id": "github/jdeast/EXOFASTv2", - "title": "github/jdeast/EXOFASTv2", - "url": " https://rseng.github.io/software/repository/github/jdeast/EXOFASTv2", - "content": "An exoplanet transit, radial velocity, astrometry, and stellar fitting software package in IDL" + "github/MonashSmartStructures/ospgrillage": { + "id": "github/MonashSmartStructures/ospgrillage", + "title": "github/MonashSmartStructures/ospgrillage", + "url": " https://rseng.github.io/software/repository/github/MonashSmartStructures/ospgrillage", + "content": "`ospgrillage` is a package that wraps `OpenSeesPy` with an interface dedicated to the development and analysis of regular bridge deck grillage models." }, - 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PyRice design is modular and implements a smart query system which fits the computing resources to optimize the query speed." + "github/PGB-LIV/MHCVision": { + "id": "github/PGB-LIV/MHCVision", + "title": "github/PGB-LIV/MHCVision", + "url": " https://rseng.github.io/software/repository/github/PGB-LIV/MHCVision", + "content": "FDR/PEP estimation for MHC-peptide binding prediction" }, - "github/lucianolorenti/ceruleo": { - "id": "github/lucianolorenti/ceruleo", - "title": "github/lucianolorenti/ceruleo", - "url": " https://rseng.github.io/software/repository/github/lucianolorenti/ceruleo", - "content": "CeRULEo: Comprehensive utilitiEs for Remaining Useful Life Estimation methOds" + "github/jrkerns/pylinac": { + "id": "github/jrkerns/pylinac", + "title": "github/jrkerns/pylinac", + "url": " https://rseng.github.io/software/repository/github/jrkerns/pylinac", + "content": "A TG-142 toolkit for doing routine linear accelerator quality assurance" + }, + "github/abeelen/powspec": { + "id": "github/abeelen/powspec", + "title": "github/abeelen/powspec", + "url": " https://rseng.github.io/software/repository/github/abeelen/powspec", + "content": "Power and cross spectral density of 2D arrays" + }, + "github/lgbouma/gyro-interp": { + "id": "github/lgbouma/gyro-interp", + "title": "github/lgbouma/gyro-interp", + "url": " https://rseng.github.io/software/repository/github/lgbouma/gyro-interp", + "content": "Gyrochronology via interpolation of open cluster rotation sequences." }, "github/dutilh/CAT": { "id": "github/dutilh/CAT", @@ -3111,1967 +2073,2105 @@ "url": " https://rseng.github.io/software/repository/github/dutilh/CAT", "content": "CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)" }, - "github/tbep-tech/tbeptools": { - "id": "github/tbep-tech/tbeptools", - "title": "github/tbep-tech/tbeptools", - "url": " https://rseng.github.io/software/repository/github/tbep-tech/tbeptools", - "content": "R package for Tampa Bay Estuary Program functions" + "github/linsalrob/PhiSpy": { + "id": "github/linsalrob/PhiSpy", + "title": "github/linsalrob/PhiSpy", + "url": " https://rseng.github.io/software/repository/github/linsalrob/PhiSpy", + "content": "Prediction of prophages from bacterial genomes" + }, + "github/fulcrumgenomics/fgbio": { + "id": "github/fulcrumgenomics/fgbio", + "title": "github/fulcrumgenomics/fgbio", + "url": " https://rseng.github.io/software/repository/github/fulcrumgenomics/fgbio", + "content": "Tools for working with genomic and high throughput sequencing data." + }, + "github/sbebo/joypy": { + "id": "github/sbebo/joypy", + "title": "github/sbebo/joypy", + "url": " https://rseng.github.io/software/repository/github/sbebo/joypy", + "content": "Joyplots in Python with matplotlib & pandas :chart_with_upwards_trend:" + }, + "github/ccsosa/GOCompare": { + "id": "github/ccsosa/GOCompare", + "title": "github/ccsosa/GOCompare", + "url": " https://rseng.github.io/software/repository/github/ccsosa/GOCompare", + "content": "This is an R package designed to analyze functional enrichment results between two species (A list of genes and their orthologues)" + }, + "github/ekaterinailin/AltaiPony": { + "id": "github/ekaterinailin/AltaiPony", + "title": "github/ekaterinailin/AltaiPony", + "url": " https://rseng.github.io/software/repository/github/ekaterinailin/AltaiPony", + "content": "Find flares in Kepler, K2, and TESS light curves. Notebooks for quickstart inside." + }, + "github/kyleaoman/martini": { + "id": "github/kyleaoman/martini", + "title": "github/kyleaoman/martini", + "url": " https://rseng.github.io/software/repository/github/kyleaoman/martini", + "content": "Mock spatially resolved spectral line observations of simulated galaxies. 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"github/lwang-astro/SDAR": { - "id": "github/lwang-astro/SDAR", - "title": "github/lwang-astro/SDAR", - "url": " https://rseng.github.io/software/repository/github/lwang-astro/SDAR", - "content": "Slow-down Algorithmic regularization (SDAR) code for solving few-body problems" + "github/vaexio/vaex": { + "id": "github/vaexio/vaex", + "title": "github/vaexio/vaex", + "url": " https://rseng.github.io/software/repository/github/vaexio/vaex", + "content": "Out-of-Core hybrid Apache Arrow/NumPy DataFrame for Python, ML, visualization and exploration of big tabular data at a billion rows per second 🚀" }, - "github/insilicomedicine/GENTRL": { - "id": "github/insilicomedicine/GENTRL", - "title": "github/insilicomedicine/GENTRL", - "url": " https://rseng.github.io/software/repository/github/insilicomedicine/GENTRL", - "content": "Generative Tensorial Reinforcement Learning (GENTRL) model" + "github/vocalpy/crowsetta": { + "id": "github/vocalpy/crowsetta", + "title": "github/vocalpy/crowsetta", + "url": " https://rseng.github.io/software/repository/github/vocalpy/crowsetta", + "content": "A tool to work with any format for annotating vocalizations" }, - "github/sevimcengiz/Oryx-MRSI": { - "id": "github/sevimcengiz/Oryx-MRSI", - "title": "github/sevimcengiz/Oryx-MRSI", - "url": " https://rseng.github.io/software/repository/github/sevimcengiz/Oryx-MRSI", + "github/VarStarDetect/varstardetect": { + "id": "github/VarStarDetect/varstardetect", + "title": "github/VarStarDetect/varstardetect", + "url": " https://rseng.github.io/software/repository/github/VarStarDetect/varstardetect", "content": "None" }, - "github/nanograv/PINT": { - "id": "github/nanograv/PINT", - "title": "github/nanograv/PINT", - "url": " https://rseng.github.io/software/repository/github/nanograv/PINT", - "content": "PINT is not TEMPO3 -- Software for high-precision pulsar timing" + "github/vdemichev/DiaNN": { + "id": "github/vdemichev/DiaNN", + "title": "github/vdemichev/DiaNN", + "url": " https://rseng.github.io/software/repository/github/vdemichev/DiaNN", + "content": "DIA-NN - a universal automated software suite for DIA proteomics data analysis. " }, - "github/nanograv/enterprise": { - "id": "github/nanograv/enterprise", - "title": "github/nanograv/enterprise", - "url": " https://rseng.github.io/software/repository/github/nanograv/enterprise", - "content": "ENTERPRISE (Enhanced Numerical Toolbox Enabling a Robust PulsaR Inference SuitE) is a pulsar timing analysis code, aimed at noise analysis, gravitational-wave searches, and timing model analysis." + "github/zkdtc/MLC_ELGs": { + "id": "github/zkdtc/MLC_ELGs", + "title": "github/zkdtc/MLC_ELGs", + "url": " https://rseng.github.io/software/repository/github/zkdtc/MLC_ELGs", + "content": "Machine Learning Classifiers for intermediate redshift Emission Line Galaxies" }, - "github/alexfields/ORF-RATER": { - "id": "github/alexfields/ORF-RATER", - "title": "github/alexfields/ORF-RATER", - "url": " https://rseng.github.io/software/repository/github/alexfields/ORF-RATER", - "content": "Regression-based annotation of protein-coding sequences from ribosome profiling data" + "github/tholoien/empiriciSN": { + "id": "github/tholoien/empiriciSN", + "title": "github/tholoien/empiriciSN", + "url": " https://rseng.github.io/software/repository/github/tholoien/empiriciSN", + "content": "Generate realistic parameters for a SN given host galaxy observations based on empirical correlations from SN datasets" }, - "github/snugel/cas-offinder": { - "id": "github/snugel/cas-offinder", - "title": "github/snugel/cas-offinder", - "url": " https://rseng.github.io/software/repository/github/snugel/cas-offinder", - "content": "An ultrafast and versatile algorithm that searches for potential off-target sites of CRISPR/Cas-derived RNA-guided endonucleases." + "github/tholoien/XDGMM": { + "id": "github/tholoien/XDGMM", + "title": "github/tholoien/XDGMM", + "url": " https://rseng.github.io/software/repository/github/tholoien/XDGMM", + "content": "A wrapper class for the scikit-learn BaseEstimator class that implements both the astroML and Bovy et al. (2011) XDGMM methods." }, - "github/danielkoll/tidally-locked-coordinates": { - "id": "github/danielkoll/tidally-locked-coordinates", - "title": "github/danielkoll/tidally-locked-coordinates", - "url": " https://rseng.github.io/software/repository/github/danielkoll/tidally-locked-coordinates", - "content": "Scripts for transforming GCM output into a tidally locked coordinate system." + "github/nickelnine37/pykronecker": { + "id": "github/nickelnine37/pykronecker", + "title": "github/nickelnine37/pykronecker", + "url": " https://rseng.github.io/software/repository/github/nickelnine37/pykronecker", + "content": "A python library for creating Kronecker Product operators with efficient lazy computation" }, - "github/danielkoll/PyRADS": { - "id": "github/danielkoll/PyRADS", - "title": "github/danielkoll/PyRADS", - "url": " https://rseng.github.io/software/repository/github/danielkoll/PyRADS", - "content": "A line-by-line longwave radiation code for planetary atmospheres." + "github/sblunt/orbitize": { + "id": "github/sblunt/orbitize", + "title": "github/sblunt/orbitize", + "url": " https://rseng.github.io/software/repository/github/sblunt/orbitize", + "content": "Orbit-fitting for directly imaged objects" }, - 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"id": "github/hongli-ma/RNANetMotif", - "title": "github/hongli-ma/RNANetMotif", - "url": " https://rseng.github.io/software/repository/github/hongli-ma/RNANetMotif", - "content": "RNA structural motif finder" + "github/jobovy/apogee": { + "id": "github/jobovy/apogee", + "title": "github/jobovy/apogee", + "url": " https://rseng.github.io/software/repository/github/jobovy/apogee", + "content": "Tools for dealing with APOGEE data" }, - "github/TrackerControl/tracker-control-android": { - "id": "github/TrackerControl/tracker-control-android", - "title": "github/TrackerControl/tracker-control-android", - "url": " https://rseng.github.io/software/repository/github/TrackerControl/tracker-control-android", - "content": "TrackerControl: monitor and control trackers and ads." + "github/jobovy/segueSelect": { + "id": "github/jobovy/segueSelect", + "title": "github/jobovy/segueSelect", + "url": " https://rseng.github.io/software/repository/github/jobovy/segueSelect", + "content": "Selection function for the SDSS/SEGUE survey (G and K star samples)" + }, + "github/jobovy/extreme-deconvolution": { + "id": "github/jobovy/extreme-deconvolution", + "title": "github/jobovy/extreme-deconvolution", + "url": " https://rseng.github.io/software/repository/github/jobovy/extreme-deconvolution", + "content": "Density estimation using Gaussian mixtures in the presence of noisy, heterogeneous and incomplete data" }, - 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"id": "github/michaelhb/superplot", - "title": "github/michaelhb/superplot", - "url": " https://rseng.github.io/software/repository/github/michaelhb/superplot", - "content": "GUI for making high-quality plots from data from MultiNest or BAYES-X" + "github/ugovaretto/molekel": { + "id": "github/ugovaretto/molekel", + "title": "github/ugovaretto/molekel", + "url": " https://rseng.github.io/software/repository/github/ugovaretto/molekel", + "content": "molekel" }, - "github/thomasorb/orbs": { - "id": "github/thomasorb/orbs", - "title": "github/thomasorb/orbs", - "url": " https://rseng.github.io/software/repository/github/thomasorb/orbs", - "content": "ORBS is the data reduction pipeline for SITELLE" + "github/MrOlm/drep": { + "id": "github/MrOlm/drep", + "title": "github/MrOlm/drep", + "url": " https://rseng.github.io/software/repository/github/MrOlm/drep", + "content": "a python program for rapidly comparing large numbers of genomes, dRep can also "de-replicate" a genome set by identifying groups of highly similar genomes and choosing the best representative genome for each genome set." }, - 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For fitting straight line models to data with one or more breakpoints where the gradient changes. 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It implements two alternative methods for identification of essential genes and provides additional tools to investigate the Tn-seq data. The primary goal of the data analysis is to study fitness by identifying genes that are essential or beneficial under specific growth conditions." + "github/climate-machine/Oceananigans.jl": { + "id": "github/climate-machine/Oceananigans.jl", + "title": "github/climate-machine/Oceananigans.jl", + "url": " https://rseng.github.io/software/repository/github/climate-machine/Oceananigans.jl", + "content": "🌊 Fast and friendly fluid dynamics on CPUs and GPUs" }, - "github/PaulKuin/uvotpy": { - "id": "github/PaulKuin/uvotpy", - "title": "github/PaulKuin/uvotpy", - "url": " https://rseng.github.io/software/repository/github/PaulKuin/uvotpy", - "content": "Swift UVOT grisms - spectral extraction" + "github/widdowquinn/pyani": { + "id": "github/widdowquinn/pyani", + "title": "github/widdowquinn/pyani", + "url": " https://rseng.github.io/software/repository/github/widdowquinn/pyani", + "content": "Application and Python module for average nucleotide identity analyses of microbes." }, - "github/bthorne93/PySM_public": { - "id": "github/bthorne93/PySM_public", - "title": "github/bthorne93/PySM_public", - "url": " https://rseng.github.io/software/repository/github/bthorne93/PySM_public", - "content": "PySM: Software for simulating the Galactic microwave sky" + "github/annehutter/polyspectrum": { + "id": "github/annehutter/polyspectrum", + "title": "github/annehutter/polyspectrum", + "url": " https://rseng.github.io/software/repository/github/annehutter/polyspectrum", + "content": "MPI-parallelised code to compute polyspectrum (including bispectrum) from a 3D grid" }, - "github/MrShoenel/metrics-as-scores": { - "id": "github/MrShoenel/metrics-as-scores", - "title": "github/MrShoenel/metrics-as-scores", - "url": " https://rseng.github.io/software/repository/github/MrShoenel/metrics-as-scores", - "content": "Contains the data and scripts needed for the application Metrics as Scores" + "github/annehutter/astraeus": { + "id": "github/annehutter/astraeus", + "title": "github/annehutter/astraeus", + "url": " https://rseng.github.io/software/repository/github/annehutter/astraeus", + "content": "Home of the semi-analytical / semi-numerical galaxy evolution and reionization code ASTRAEUS" }, - 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Generate, analyze and export complex 2D space partitions like metallic grain structures" }, - "github/arq5x/grabix": { - "id": "github/arq5x/grabix", - "title": "github/arq5x/grabix", - "url": " https://rseng.github.io/software/repository/github/arq5x/grabix", - "content": " a wee tool for random access into BGZF files." + "github/davek44/Glimmer-MG": { + "id": "github/davek44/Glimmer-MG", + "title": "github/davek44/Glimmer-MG", + "url": " https://rseng.github.io/software/repository/github/davek44/Glimmer-MG", + "content": "Gene prediction in metagenomic sequences using Glimmer augmented by phylogenetic classification and clustering" }, - "github/Dailer/RCausticMass": { - "id": "github/Dailer/RCausticMass", - "title": "github/Dailer/RCausticMass", - "url": " https://rseng.github.io/software/repository/github/Dailer/RCausticMass", - "content": "Caustic Mass Estimator for Galaxy Clusters" + "github/neuralhydrology/neuralhydrology": { + "id": "github/neuralhydrology/neuralhydrology", + "title": "github/neuralhydrology/neuralhydrology", + "url": " https://rseng.github.io/software/repository/github/neuralhydrology/neuralhydrology", + "content": "Python library to train neural networks with a strong focus on hydrological applications." }, - 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"url": " https://rseng.github.io/software/repository/github/vmmunoza/nuHawkHunter", - "content": "Repository with forecast of PBH neutrinos" + "github/krober10nd/SeismicMesh": { + "id": "github/krober10nd/SeismicMesh", + "title": "github/krober10nd/SeismicMesh", + "url": " https://rseng.github.io/software/repository/github/krober10nd/SeismicMesh", + "content": "2D/3D serial and parallel triangular mesh generation tool for Finite Element Methods." }, - "github/dunnkers/fseval": { - "id": "github/dunnkers/fseval", - "title": "github/dunnkers/fseval", - "url": " https://rseng.github.io/software/repository/github/dunnkers/fseval", - "content": "Benchmarking framework for Feature Selection and Feature Ranking algorithms 🚀" + "github/ericsteinbring/Special-Blurring": { + "id": "github/ericsteinbring/Special-Blurring", + "title": "github/ericsteinbring/Special-Blurring", + "url": " https://rseng.github.io/software/repository/github/ericsteinbring/Special-Blurring", + "content": "Calculates the effect of quantum-foam blurring, appropriate for the special gamma-ray burst GRB221009A." }, - 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"github/danhey/maelstrom": { - "id": "github/danhey/maelstrom", - "title": "github/danhey/maelstrom", - "url": " https://rseng.github.io/software/repository/github/danhey/maelstrom", - "content": "Forward modelling of pulsating stars in binaries" + "github/tjlcbakx/redshift-search-graphs": { + "id": "github/tjlcbakx/redshift-search-graphs", + "title": "github/tjlcbakx/redshift-search-graphs", + "url": " https://rseng.github.io/software/repository/github/tjlcbakx/redshift-search-graphs", + "content": "Efficient analysis of bandwidth coverage and spectral lines for finding z-specs" }, - "github/danhey/echelle": { - "id": "github/danhey/echelle", - "title": "github/danhey/echelle", - "url": " https://rseng.github.io/software/repository/github/danhey/echelle", - "content": "Dynamic echelle diagrams for asteroseismology" + "github/biswajitmb/DarpanX": { + "id": "github/biswajitmb/DarpanX", + "title": "github/biswajitmb/DarpanX", + "url": " https://rseng.github.io/software/repository/github/biswajitmb/DarpanX", + "content": "DarpanX is a Python 3 package that provides functionality to compute reflectivity and other specular optical functions of a multilayer or single layer mirror for different energy and angles as well as to fit the XRR measurements of the mirrors." }, - "github/COSMIC-PopSynth/COSMIC": { - "id": "github/COSMIC-PopSynth/COSMIC", - "title": "github/COSMIC-PopSynth/COSMIC", - "url": " https://rseng.github.io/software/repository/github/COSMIC-PopSynth/COSMIC", - "content": "COSMIC (Compact Object Synthesis and Monte Carlo Investigation Code)" + "github/JuliaArrays/InfiniteArrays.jl": { + "id": "github/JuliaArrays/InfiniteArrays.jl", + "title": "github/JuliaArrays/InfiniteArrays.jl", + "url": " https://rseng.github.io/software/repository/github/JuliaArrays/InfiniteArrays.jl", + "content": "A Julia package for representing infinite-dimensional arrays" }, - "github/SYalouz/QuantNBody": { - "id": "github/SYalouz/QuantNBody", - "title": "github/SYalouz/QuantNBody", - "url": " https://rseng.github.io/software/repository/github/SYalouz/QuantNBody", - "content": "QuantNBody : a python package for quantum chemistry/physics to manipulate many-body operators and wave functions." + "github/JuliaArrays/LazyArrays.jl": { + "id": "github/JuliaArrays/LazyArrays.jl", + "title": "github/JuliaArrays/LazyArrays.jl", + "url": " https://rseng.github.io/software/repository/github/JuliaArrays/LazyArrays.jl", + "content": "Lazy arrays and linear algebra in Julia" }, - 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"github/matthiaslee/Xmatch": { - "id": "github/matthiaslee/Xmatch", - "title": "github/matthiaslee/Xmatch", - "url": " https://rseng.github.io/software/repository/github/matthiaslee/Xmatch", - "content": "a GPU accelerated astronomic catalog cross-matching tool" + "github/parkus/ffd": { + "id": "github/parkus/ffd", + "title": "github/parkus/ffd", + "url": " https://rseng.github.io/software/repository/github/parkus/ffd", + "content": "Tools for the analysis of flare frequency distributions for flares detected in heterogenous datasets." }, - "github/TheMillerLab/genetex": { - "id": "github/TheMillerLab/genetex", - "title": "github/TheMillerLab/genetex", - "url": " https://rseng.github.io/software/repository/github/TheMillerLab/genetex", - "content": "None" + "github/gbouras13/plassembler": { + "id": "github/gbouras13/plassembler", + "title": "github/gbouras13/plassembler", + "url": " https://rseng.github.io/software/repository/github/gbouras13/plassembler", + "content": "Program to quickly and accurately assemble plasmids in hybrid sequenced bacterial isolates" }, - "github/caselawanalytics/CaseLawAnalytics": { - "id": "github/caselawanalytics/CaseLawAnalytics", - "title": "github/caselawanalytics/CaseLawAnalytics", - "url": " https://rseng.github.io/software/repository/github/caselawanalytics/CaseLawAnalytics", - "content": "None" + "github/DavidT3/XGA": { + "id": "github/DavidT3/XGA", + "title": "github/DavidT3/XGA", + "url": " https://rseng.github.io/software/repository/github/DavidT3/XGA", + "content": "X-ray: Generate and Analyse is a module designed to make the analysis of XMM observations simple and efficient. It provides an interface with SAS for the creation of XMM data products, as well as a way to easily perform fits (scalable for multiple observations) and retrieve information about an object, all within a Python package. " }, - "github/Huang-CL/Magrathea": { - "id": "github/Huang-CL/Magrathea", - "title": "github/Huang-CL/Magrathea", - "url": " https://rseng.github.io/software/repository/github/Huang-CL/Magrathea", - "content": "None" + "github/fred3m/toyz": { + "id": "github/fred3m/toyz", + "title": "github/fred3m/toyz", + "url": " https://rseng.github.io/software/repository/github/fred3m/toyz", + "content": "Toyz for Data Analysis and Reduction" }, - "github/pysersic/pysersic": { - "id": "github/pysersic/pysersic", - "title": "github/pysersic/pysersic", - "url": " https://rseng.github.io/software/repository/github/pysersic/pysersic", - "content": "Bayesian fitting of Sersic profiles to galaxy images accelerated with jax" + "github/LuisScoccola/persistable": { + "id": "github/LuisScoccola/persistable", + "title": "github/LuisScoccola/persistable", + "url": " https://rseng.github.io/software/repository/github/LuisScoccola/persistable", + "content": "density-based clustering for exploratory data analysis based on multi-parameter persistence" }, - "github/openscm/openscm-twolayermodel": { - "id": "github/openscm/openscm-twolayermodel", - "title": "github/openscm/openscm-twolayermodel", - "url": " https://rseng.github.io/software/repository/github/openscm/openscm-twolayermodel", - "content": "Implementations of two-layer models by Held et al. and Geoffroy et al." + "github/ImproPhoto/pymicmac": { + "id": "github/ImproPhoto/pymicmac", + "title": "github/ImproPhoto/pymicmac", + "url": " https://rseng.github.io/software/repository/github/ImproPhoto/pymicmac", + "content": "Python tools for the MicMac FOSS photogrammetric "suite"" }, - "github/mzemp/halogen": { - "id": "github/mzemp/halogen", - "title": "github/mzemp/halogen", - "url": " https://rseng.github.io/software/repository/github/mzemp/halogen", - "content": "Tool to generate spherically symmetric initial conditions for N-body simulations." + "github/tobias-dv-lnu/s4rdm3x": { + "id": "github/tobias-dv-lnu/s4rdm3x", + "title": "github/tobias-dv-lnu/s4rdm3x", + "url": " https://rseng.github.io/software/repository/github/tobias-dv-lnu/s4rdm3x", + "content": "None" }, - 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"github/igvteam/igv-reports": { - "id": "github/igvteam/igv-reports", - "title": "github/igvteam/igv-reports", - "url": " https://rseng.github.io/software/repository/github/igvteam/igv-reports", - "content": "Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files." + "github/PMBio/peer": { + "id": "github/PMBio/peer", + "title": "github/PMBio/peer", + "url": " https://rseng.github.io/software/repository/github/PMBio/peer", + "content": "A factor analysis package" }, - "github/monarch-initiative/loinc2hpo": { - "id": "github/monarch-initiative/loinc2hpo", - "title": "github/monarch-initiative/loinc2hpo", - "url": " https://rseng.github.io/software/repository/github/monarch-initiative/loinc2hpo", - "content": "Java library to map LOINC-encoded test results to Human Phenotype Ontology" + "github/chervias/DustFilaments": { + "id": "github/chervias/DustFilaments", + "title": "github/chervias/DustFilaments", + "url": " https://rseng.github.io/software/repository/github/chervias/DustFilaments", + "content": "Paint filaments to produce a thermal dust full sky map at mm frequencies" }, - 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"github/Planet-AI-GmbH/tfaip": { - "id": "github/Planet-AI-GmbH/tfaip", - "title": "github/Planet-AI-GmbH/tfaip", - "url": " https://rseng.github.io/software/repository/github/Planet-AI-GmbH/tfaip", - "content": "Python-based research framework for developing, organizing, and deploying Deep Learning models powered by Tensorflow." + "github/prioritizr/wdpar": { + "id": "github/prioritizr/wdpar", + "title": "github/prioritizr/wdpar", + "url": " https://rseng.github.io/software/repository/github/prioritizr/wdpar", + "content": "Interface to the World Database on Protected Areas" }, - "github/pypeit/PypeIt": { - "id": "github/pypeit/PypeIt", - "title": "github/pypeit/PypeIt", - "url": " https://rseng.github.io/software/repository/github/pypeit/PypeIt", - "content": "The Python Spectroscopic Data Reduction Pipeline" + "github/cvbuchem/LavAtmos": { + "id": "github/cvbuchem/LavAtmos", + "title": "github/cvbuchem/LavAtmos", + "url": " https://rseng.github.io/software/repository/github/cvbuchem/LavAtmos", + "content": "This code performs gas-melt equilibrium calculations for a given temperature and melt composition." }, - "github/smandal97/Sprout": { - "id": "github/smandal97/Sprout", - "title": "github/smandal97/Sprout", - "url": " https://rseng.github.io/software/repository/github/smandal97/Sprout", - "content": "Sprout is a finite volume hydro code based on the moving mesh approach. It uses a simple expanding Cartesian grid to track outflows for several orders of magnitudes in expansion." + "github/MIC-DKFZ/TractSeg": { + "id": "github/MIC-DKFZ/TractSeg", + "title": "github/MIC-DKFZ/TractSeg", + "url": " https://rseng.github.io/software/repository/github/MIC-DKFZ/TractSeg", + "content": "Automatic White Matter Bundle Segmentation" }, - "github/dstansby/pfsspy": { - "id": "github/dstansby/pfsspy", - "title": "github/dstansby/pfsspy", - "url": " https://rseng.github.io/software/repository/github/dstansby/pfsspy", - "content": "Potential Field Source Surface model package for Python" + "github/MIC-DKFZ/HD-BET": { + "id": "github/MIC-DKFZ/HD-BET", + "title": "github/MIC-DKFZ/HD-BET", + "url": " https://rseng.github.io/software/repository/github/MIC-DKFZ/HD-BET", + "content": "MRI brain extraction tool" }, - "github/ACCarnall/bagpipes": { - "id": "github/ACCarnall/bagpipes", - "title": "github/ACCarnall/bagpipes", - "url": " https://rseng.github.io/software/repository/github/ACCarnall/bagpipes", - "content": "Bagpipes is a state of the art code for generating realistic model galaxy spectra and fitting these to spectroscopic and photometric observations. Users should install with pip, not by cloning the repository." + "github/taehoryu/TDEmass": { + "id": "github/taehoryu/TDEmass", + "title": "github/taehoryu/TDEmass", + "url": " https://rseng.github.io/software/repository/github/taehoryu/TDEmass", + "content": "None" }, - "github/ACCarnall/SpectRes": { - "id": "github/ACCarnall/SpectRes", - "title": "github/ACCarnall/SpectRes", - "url": " https://rseng.github.io/software/repository/github/ACCarnall/SpectRes", - "content": "SpectRes is a Python module which efficiently resamples spectra and their associated uncertainties onto an arbitrary wavelength grid. Read the documentation at" + "github/HinLeung622/pipes_vis": { + "id": "github/HinLeung622/pipes_vis", + "title": "github/HinLeung622/pipes_vis", + "url": " https://rseng.github.io/software/repository/github/HinLeung622/pipes_vis", + "content": "A small, interactive GUI/visualizer tool for SPS spectra, powered by bagpipes" }, - "github/kostergroup/SIMsalabim": { - "id": "github/kostergroup/SIMsalabim", - "title": "github/kostergroup/SIMsalabim", - "url": " https://rseng.github.io/software/repository/github/kostergroup/SIMsalabim", - "content": "A 1D drift-diffusion simulator for semiconductor devices (LEDs, solar cells, diodes, organics, perovskites)" + "github/symmy596/Polypy": { + "id": "github/symmy596/Polypy", + "title": "github/symmy596/Polypy", + "url": " https://rseng.github.io/software/repository/github/symmy596/Polypy", + "content": "polypy - Analysis Tools for Solid State Molecular Dynamics and Monte Carlo Trajectories" }, - "github/exobssim/rapoc-public": { - "id": "github/exobssim/rapoc-public", - "title": "github/exobssim/rapoc-public", - "url": " https://rseng.github.io/software/repository/github/exobssim/rapoc-public", - "content": "Rapoc uses molecular absorption measurements (i.e. wavelength-dependent opacities) to calculate Rosseland and Planck mean opacities that are commonly used in atmospheric modelling." + "github/symmy596/SurfinPy": { + "id": "github/symmy596/SurfinPy", + "title": "github/symmy596/SurfinPy", + "url": " https://rseng.github.io/software/repository/github/symmy596/SurfinPy", + "content": "Thermodynamic Phase Diagram Generator" }, - "github/galkintool/galkin": { - "id": "github/galkintool/galkin", - "title": "github/galkintool/galkin", - "url": " https://rseng.github.io/software/repository/github/galkintool/galkin", - "content": "None" + "github/geoelements/gns": { + "id": "github/geoelements/gns", + "title": "github/geoelements/gns", + "url": " https://rseng.github.io/software/repository/github/geoelements/gns", + "content": "Graph Network Simulator" }, - "github/Krona/wiki": { - "id": "github/Krona/wiki", - "title": "github/Krona/wiki", - "url": " https://rseng.github.io/software/repository/github/Krona/wiki", - "content": "is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files." + "github/msolpera/pyUPMASK": { + "id": "github/msolpera/pyUPMASK", + "title": "github/msolpera/pyUPMASK", + "url": " https://rseng.github.io/software/repository/github/msolpera/pyUPMASK", + "content": "Unsupervised clustering method for stellar clusters." }, - "github/popgenmethods/smcpp": { - "id": "github/popgenmethods/smcpp", - "title": "github/popgenmethods/smcpp", - "url": " https://rseng.github.io/software/repository/github/popgenmethods/smcpp", - "content": "SMC++ infers population history from whole-genome sequence data." + "github/mavrix93/LightCurvesClassifier": { + "id": "github/mavrix93/LightCurvesClassifier", + "title": "github/mavrix93/LightCurvesClassifier", + "url": " https://rseng.github.io/software/repository/github/mavrix93/LightCurvesClassifier", + "content": "Package for machine learning of astronomical objects such as light curves" }, - 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"id": "github/EC-Earth/ece2cmor3", - "title": "github/EC-Earth/ece2cmor3", - "url": " https://rseng.github.io/software/repository/github/EC-Earth/ece2cmor3", - "content": "Post-processing and cmorization of ec-earth output" + "github/bregaldo/pywst": { + "id": "github/bregaldo/pywst", + "title": "github/bregaldo/pywst", + "url": " https://rseng.github.io/software/repository/github/bregaldo/pywst", + "content": "Python package for WST and RWST analyses of astrophysical data." }, - "github/GeoffDuniam/FITS-Code-Examples": { - "id": "github/GeoffDuniam/FITS-Code-Examples", - "title": "github/GeoffDuniam/FITS-Code-Examples", - "url": " https://rseng.github.io/software/repository/github/GeoffDuniam/FITS-Code-Examples", - "content": "Jupyter notes books and code examples for the FITS data modelling paper" + "github/ZhaiLab-SUSTech/FLEPSeq": { + "id": "github/ZhaiLab-SUSTech/FLEPSeq", + "title": "github/ZhaiLab-SUSTech/FLEPSeq", + "url": " https://rseng.github.io/software/repository/github/ZhaiLab-SUSTech/FLEPSeq", + "content": "The analysis pipeline for FLEP-seq" }, - 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"id": "github/redcap-tools/PyCap", - "title": "github/redcap-tools/PyCap", - "url": " https://rseng.github.io/software/repository/github/redcap-tools/PyCap", - "content": "REDCap in Python" + "github/andreyshabalin/TwinEQTL": { + "id": "github/andreyshabalin/TwinEQTL", + "title": "github/andreyshabalin/TwinEQTL", + "url": " https://rseng.github.io/software/repository/github/andreyshabalin/TwinEQTL", + "content": "TwinMeta: Fast and Powerful Association Analysis for eQTL and GWAS in Twin Studies" }, - "github/LalResearchGroup/CNV-clinviewer": { - "id": "github/LalResearchGroup/CNV-clinviewer", - "title": "github/LalResearchGroup/CNV-clinviewer", - "url": " https://rseng.github.io/software/repository/github/LalResearchGroup/CNV-clinviewer", - "content": "None" + "github/xpsi-group/xpsi": { + "id": "github/xpsi-group/xpsi", + "title": "github/xpsi-group/xpsi", + "url": " https://rseng.github.io/software/repository/github/xpsi-group/xpsi", + "content": "X-PSI: X-ray Pulse Simulation and Inference" }, - "github/Nextomics/nextsv": { - "id": "github/Nextomics/nextsv", - "title": "github/Nextomics/nextsv", - "url": " https://rseng.github.io/software/repository/github/Nextomics/nextsv", - "content": "automated structural variation detection for long-read sequencing" + "github/cullanhowlett/l-picola": { + "id": "github/cullanhowlett/l-picola", + "title": "github/cullanhowlett/l-picola", + "url": " https://rseng.github.io/software/repository/github/cullanhowlett/l-picola", + "content": "A public repository for the code L-PICOLA" }, - "github/KeplerGO/kadenza": { - "id": "github/KeplerGO/kadenza", - "title": "github/KeplerGO/kadenza", - "url": " https://rseng.github.io/software/repository/github/KeplerGO/kadenza", - "content": "Converts raw cadence target data from the Kepler space telescope into astronomer-friendly FITS files." + "github/DTsuna/CHIPS": { + "id": "github/DTsuna/CHIPS", + "title": "github/DTsuna/CHIPS", + "url": " https://rseng.github.io/software/repository/github/DTsuna/CHIPS", + "content": "Open source code to unveil the Complete History of Interaction-Powered Supernovae" + }, + "github/OnroerendErfgoed/atramhasis": { + "id": "github/OnroerendErfgoed/atramhasis", + "title": "github/OnroerendErfgoed/atramhasis", + "url": " https://rseng.github.io/software/repository/github/OnroerendErfgoed/atramhasis", + "content": "An online SKOS editor" }, - "github/KeplerGO/PyKE": { - "id": "github/KeplerGO/PyKE", - "title": "github/KeplerGO/PyKE", - "url": " https://rseng.github.io/software/repository/github/KeplerGO/PyKE", - "content": "Easy command line tools for Kepler, K2 & TESS data analysis." + "github/sisl/POMDPStressTesting.jl": { + "id": "github/sisl/POMDPStressTesting.jl", + "title": "github/sisl/POMDPStressTesting.jl", + "url": " https://rseng.github.io/software/repository/github/sisl/POMDPStressTesting.jl", + "content": "Adaptive stress testing of black-box systems within POMDPs.jl" }, - "github/KeplerGO/k2mosaic": { - "id": "github/KeplerGO/k2mosaic", - "title": "github/KeplerGO/k2mosaic", - "url": " https://rseng.github.io/software/repository/github/KeplerGO/k2mosaic", - "content": "Mosaic Target Pixel Files (TPFs) obtained by NASA's Kepler/K2 missions into CCD-sized images and movies." + "github/Peppags/CNN-SVR": { + "id": "github/Peppags/CNN-SVR", + "title": "github/Peppags/CNN-SVR", + "url": " https://rseng.github.io/software/repository/github/Peppags/CNN-SVR", + "content": "CNN-SVR: A deep learning approach for predicting CRISPR/Cas9 guide RNA on-target activity" }, - 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Given the results of a Bayesian model (possibly based on MCMC) in the form of simulations from the posterior distributions of suitable variables of costs and clinical benefits for two or more interventions, produces a health economic evaluation. Compares one of the interventions (the "reference") to the others ("comparators"). Produces many summary and plots to analyse the results" }, - "github/sPaMFouR/RedPipe": { - "id": "github/sPaMFouR/RedPipe", - "title": "github/sPaMFouR/RedPipe", - "url": " https://rseng.github.io/software/repository/github/sPaMFouR/RedPipe", - "content": "Python Scripts for Data Reduction and Analysis" + "github/q1cui/discourseGT": { + "id": "github/q1cui/discourseGT", + "title": "github/q1cui/discourseGT", + "url": " https://rseng.github.io/software/repository/github/q1cui/discourseGT", + "content": "discourseGT — Analyze Group Patterns using Graph Theory in Educational Settings" }, - "github/UFParLab/aces4": { - "id": "github/UFParLab/aces4", - "title": "github/UFParLab/aces4", - "url": " https://rseng.github.io/software/repository/github/UFParLab/aces4", - "content": "Parallel Computational Chemistry Application" + "github/atzberg/mlmod": { + "id": "github/atzberg/mlmod", + "title": "github/atzberg/mlmod", + "url": " https://rseng.github.io/software/repository/github/atzberg/mlmod", + "content": "Machine learning package for data-driven modeling and simulation in LAMMPs." }, - 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The linking parameters, both transverse and along the line-of-sight, change as a function of redshift to account for selection effects. The code is written in C++ and implements OMP to loop through the photometric redshift bins." }, - "github/ComputationalRegulatoryGenomicsICL/TFBS": { - "id": "github/ComputationalRegulatoryGenomicsICL/TFBS", - "title": "github/ComputationalRegulatoryGenomicsICL/TFBS", - "url": " https://rseng.github.io/software/repository/github/ComputationalRegulatoryGenomicsICL/TFBS", - "content": "TFBS perl module" + "github/sfarrens/sf_deconvolve": { + "id": "github/sfarrens/sf_deconvolve", + "title": "github/sfarrens/sf_deconvolve", + "url": " https://rseng.github.io/software/repository/github/sfarrens/sf_deconvolve", + "content": "A Python code designed for PSF deconvolution using a low-rank approximation and sparsity. The code can handle a fixed PSF for the entire field or a stack of PSFs for each galaxy position." }, - "github/Qiskit/qiskit-experiments": { - "id": "github/Qiskit/qiskit-experiments", - "title": "github/Qiskit/qiskit-experiments", - "url": " https://rseng.github.io/software/repository/github/Qiskit/qiskit-experiments", - "content": "Qiskit Experiments" + "github/willvousden/ptemcee": { + "id": "github/willvousden/ptemcee", + "title": "github/willvousden/ptemcee", + "url": " https://rseng.github.io/software/repository/github/willvousden/ptemcee", + "content": "A parallel-tempered version of emcee." }, - "github/Qiskit/rustworkx": { - "id": "github/Qiskit/rustworkx", - "title": "github/Qiskit/rustworkx", - "url": " https://rseng.github.io/software/repository/github/Qiskit/rustworkx", - "content": "A high performance Python graph library implemented in Rust." + "github/cabb99/open3spn2": { + "id": "github/cabb99/open3spn2", + "title": "github/cabb99/open3spn2", + "url": " https://rseng.github.io/software/repository/github/cabb99/open3spn2", + "content": "An implementation of the 3SPN2 and 3SPN2.C coarse-grained DNA forcefields in OpenMM" + }, + "github/el2718/FastQSL": { + "id": "github/el2718/FastQSL", + "title": "github/el2718/FastQSL", + "url": " https://rseng.github.io/software/repository/github/el2718/FastQSL", + "content": "None" + }, + "github/michalychforever/CLASS-PT": { + "id": "github/michalychforever/CLASS-PT", + "title": "github/michalychforever/CLASS-PT", + "url": " https://rseng.github.io/software/repository/github/michalychforever/CLASS-PT", + "content": "Nonlinear perturbation theory extension of the Boltzmann code CLASS" + }, + "github/anuradhawick/LRBinner": { + "id": "github/anuradhawick/LRBinner", + "title": "github/anuradhawick/LRBinner", + "url": " https://rseng.github.io/software/repository/github/anuradhawick/LRBinner", + "content": "LRBinner is a long-read binning tool published in WABI 2021 proceedings and AMB." }, - 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"github/eltevo/steps": { - "id": "github/eltevo/steps", - "title": "github/eltevo/steps", - "url": " https://rseng.github.io/software/repository/github/eltevo/steps", - "content": "Stereographically Projected Cosmological Simulations" + "github/fcs-analysis/PyCorrFit": { + "id": "github/fcs-analysis/PyCorrFit", + "title": "github/fcs-analysis/PyCorrFit", + "url": " https://rseng.github.io/software/repository/github/fcs-analysis/PyCorrFit", + "content": "data analysis and fitting software for fluorescence correlation spectroscopy (FCS)" }, - "github/darioizzo/dcgp": { - "id": "github/darioizzo/dcgp", - "title": "github/darioizzo/dcgp", - "url": " https://rseng.github.io/software/repository/github/darioizzo/dcgp", - "content": "Implementation of a differentiable CGP (Cartesian Genetic Programming)" + "github/fcs-analysis/PyScanFCS": { + "id": "github/fcs-analysis/PyScanFCS", + "title": "github/fcs-analysis/PyScanFCS", + "url": " https://rseng.github.io/software/repository/github/fcs-analysis/PyScanFCS", + "content": "data evaluation in perpendicular line scanning FCS" }, - "github/trichter/yam": { - "id": "github/trichter/yam", - "title": "github/trichter/yam", - "url": " https://rseng.github.io/software/repository/github/trichter/yam", - "content": "Yet another monitoring tool using correlations of ambient noise" + "github/maserlib/ExPRES": { + "id": "github/maserlib/ExPRES", + "title": "github/maserlib/ExPRES", + "url": " https://rseng.github.io/software/repository/github/maserlib/ExPRES", + "content": "Exoplanetary and Planetary Radio Emission Simulator" }, - "github/TearsWaiting/MIMML": { - "id": "github/TearsWaiting/MIMML", - "title": "github/TearsWaiting/MIMML", - "url": " https://rseng.github.io/software/repository/github/TearsWaiting/MIMML", - "content": "The implement of MIMML in paper: Accelerating Bioactive Peptides Discovery via Mutual Information based Meta-learning" + "github/Materials-Consortia/optimade-python-tools": { + "id": "github/Materials-Consortia/optimade-python-tools", + "title": "github/Materials-Consortia/optimade-python-tools", + "url": " https://rseng.github.io/software/repository/github/Materials-Consortia/optimade-python-tools", + "content": "Tools for implementing and consuming OPTIMADE APIs in Python" }, - "github/sandmanns/CopyDetective": { - "id": "github/sandmanns/CopyDetective", - "title": "github/sandmanns/CopyDetective", - "url": " https://rseng.github.io/software/repository/github/sandmanns/CopyDetective", - "content": "Detection threshold aware CNV Calling in NGS data" + "github/Materials-Consortia/OPTIMADE-Filter": { + "id": "github/Materials-Consortia/OPTIMADE-Filter", + "title": "github/Materials-Consortia/OPTIMADE-Filter", + "url": " https://rseng.github.io/software/repository/github/Materials-Consortia/OPTIMADE-Filter", + "content": "OPTIMADE filter language parser in Perl" }, - "github/lutteropp/NetRAX": { - "id": "github/lutteropp/NetRAX", - "title": "github/lutteropp/NetRAX", - "url": " https://rseng.github.io/software/repository/github/lutteropp/NetRAX", - "content": "Phylogenetic Network Inference without ILS" + "github/ezer/PAFway": { + "id": "github/ezer/PAFway", + "title": "github/ezer/PAFway", + "url": " https://rseng.github.io/software/repository/github/ezer/PAFway", + "content": "functional associations in networks" }, - 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"github/avigan/pyZELDA": { - "id": "github/avigan/pyZELDA", - "title": "github/avigan/pyZELDA", - "url": " https://rseng.github.io/software/repository/github/avigan/pyZELDA", - "content": "Zernike wavefront sensor analysis and simulation tools" + "github/RTIInternational/gobbli": { + "id": "github/RTIInternational/gobbli", + "title": "github/RTIInternational/gobbli", + "url": " https://rseng.github.io/software/repository/github/RTIInternational/gobbli", + "content": "Deep learning with text doesn't have to be scary." }, - "github/avigan/SPHERE": { - "id": "github/avigan/SPHERE", - "title": "github/avigan/SPHERE", - "url": " https://rseng.github.io/software/repository/github/avigan/SPHERE", - "content": "Reduction and analysis code for the VLT/SPHERE instrument" + "github/dhubber/seren": { + "id": "github/dhubber/seren", + "title": "github/dhubber/seren", + "url": " https://rseng.github.io/software/repository/github/dhubber/seren", + "content": "SEREN SPH code (Hubber et al. 2011) for astrophysical hydrodynamics simulations" }, - "github/Smith42/pix2prof": { - "id": "github/Smith42/pix2prof", - "title": "github/Smith42/pix2prof", - "url": " https://rseng.github.io/software/repository/github/Smith42/pix2prof", - "content": "Pix2Prof: extracting sequential galaxy data with a language model" + "github/nhcrisp/ADBSat": { + "id": "github/nhcrisp/ADBSat", + "title": "github/nhcrisp/ADBSat", + "url": " https://rseng.github.io/software/repository/github/nhcrisp/ADBSat", + "content": "Aerodynamic Database for Satellites" }, - "github/Smith42/astroddpm": { - "id": "github/Smith42/astroddpm", - "title": "github/Smith42/astroddpm", - "url": " https://rseng.github.io/software/repository/github/Smith42/astroddpm", - "content": "A denoising diffusion probabilistic model synthesises galaxies that are qualitatively and physically indistinguishable from the real thing." + "github/raghuastro/GRIZZLY": { + "id": "github/raghuastro/GRIZZLY", + "title": "github/raghuastro/GRIZZLY", + "url": " https://rseng.github.io/software/repository/github/raghuastro/GRIZZLY", + "content": "None" }, - "github/Smith42/XDF-GAN": { - "id": "github/Smith42/XDF-GAN", - "title": "github/Smith42/XDF-GAN", - "url": " https://rseng.github.io/software/repository/github/Smith42/XDF-GAN", - "content": "A GAN for the generation of mock astronomical surveys" + "github/wathela/FIRST-CLASSIFIER": { + "id": "github/wathela/FIRST-CLASSIFIER", + "title": "github/wathela/FIRST-CLASSIFIER", + "url": " https://rseng.github.io/software/repository/github/wathela/FIRST-CLASSIFIER", + "content": "FIRST Classifier: Compact and Extended Radio Galaxies Classification using Deep Convolutional Neural Networks" }, - "github/CGAL/cgal": { - "id": "github/CGAL/cgal", - "title": "github/CGAL/cgal", - "url": " https://rseng.github.io/software/repository/github/CGAL/cgal", - "content": "The public CGAL repository, see the README below" + "github/BIC-MNI/libminc": { + "id": "github/BIC-MNI/libminc", + "title": "github/BIC-MNI/libminc", + "url": " https://rseng.github.io/software/repository/github/BIC-MNI/libminc", + "content": "libminc is the core library and API of the MINC toolkit" }, - "github/dpthorngren/PlanetSlicer": { - "id": "github/dpthorngren/PlanetSlicer", - "title": "github/dpthorngren/PlanetSlicer", - "url": " https://rseng.github.io/software/repository/github/dpthorngren/PlanetSlicer", - "content": "A simple implementation of the orange-slice algorithm for fitting brightness maps to phase curves (from Cowan and Agol 2008) extended to also handle reflected light (Mayorga et al. 2020)." + "github/linnarsson-lab/loompy": { + "id": "github/linnarsson-lab/loompy", + "title": "github/linnarsson-lab/loompy", + "url": " https://rseng.github.io/software/repository/github/linnarsson-lab/loompy", + "content": "Python implementation of the Loom file format - http://loompy.org" }, - "github/aewallin/allantools": { - "id": "github/aewallin/allantools", - "title": "github/aewallin/allantools", - "url": " https://rseng.github.io/software/repository/github/aewallin/allantools", - "content": "Allan deviation and related time & frequency statistics library in Python" + "github/TeamCOMPAS/COMPAS": { + "id": "github/TeamCOMPAS/COMPAS", + "title": "github/TeamCOMPAS/COMPAS", + "url": " https://rseng.github.io/software/repository/github/TeamCOMPAS/COMPAS", + "content": "COMPAS rapid binary population synthesis code" }, - 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It decomposes a multi-objective optimization problem into a number of single-objective optimization sub-problems and then uses a search heuristic to optimize these sub-problems simultaneously and cooperatively." }, - "github/pierfied/karmma": { - "id": "github/pierfied/karmma", - "title": "github/pierfied/karmma", - "url": " https://rseng.github.io/software/repository/github/pierfied/karmma", - "content": "KaRMMa - Kappa Reconstruction for Mass Mapping" + "github/Multiversario/satcand": { + "id": "github/Multiversario/satcand", + "title": "github/Multiversario/satcand", + "url": " https://rseng.github.io/software/repository/github/Multiversario/satcand", + "content": "Tools to apply theoretical constraints of orbital stability and tidal migration to KOI exomoon candidates. 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This contains code for reading and writing a variety of Bioinformatics / DNA Sequence formats." }, - "github/sverhoeven/docker-cartodb": { - "id": "github/sverhoeven/docker-cartodb", - "title": "github/sverhoeven/docker-cartodb", - "url": " https://rseng.github.io/software/repository/github/sverhoeven/docker-cartodb", - "content": "Dockerized CartoDB" + "github/jkbonfield/htscodecs": { + "id": "github/jkbonfield/htscodecs", + "title": "github/jkbonfield/htscodecs", + "url": " https://rseng.github.io/software/repository/github/jkbonfield/htscodecs", + "content": "Custom compression for CRAM and others." }, - "github/tresoldi/ngesh": { - "id": "github/tresoldi/ngesh", - "title": "github/tresoldi/ngesh", - "url": " https://rseng.github.io/software/repository/github/tresoldi/ngesh", - "content": "A Python library for generating random phylogenetic trees and related data" + "github/jkbonfield/crumble": { + "id": "github/jkbonfield/crumble", + "title": "github/jkbonfield/crumble", + "url": " https://rseng.github.io/software/repository/github/jkbonfield/crumble", + "content": "controllable lossy compression of BAM/CRAM files." }, - "github/bancaditalia/black-it": { - "id": "github/bancaditalia/black-it", - "title": "github/bancaditalia/black-it", - "url": " https://rseng.github.io/software/repository/github/bancaditalia/black-it", - "content": "Black-box abm calibration kit by the Bank of Italy" + "github/altjerue/paramo": { + "id": "github/altjerue/paramo", + "title": "github/altjerue/paramo", + "url": " https://rseng.github.io/software/repository/github/altjerue/paramo", + "content": "Vine a Comala porque me dijeron que acá vivía mi padre, un tal Pedro Páramo." }, - "github/desihub/desitarget": { - "id": "github/desihub/desitarget", - "title": "github/desihub/desitarget", - "url": " https://rseng.github.io/software/repository/github/desihub/desitarget", - "content": "DESI Targeting" + "github/jsobeck/MOOG_SCAT": { + "id": "github/jsobeck/MOOG_SCAT", + "title": "github/jsobeck/MOOG_SCAT", + "url": " https://rseng.github.io/software/repository/github/jsobeck/MOOG_SCAT", + "content": "Repository for the latest version of the MOOG_SCAT code" }, - "github/desihub/fastspecfit": { - "id": "github/desihub/fastspecfit", - "title": "github/desihub/fastspecfit", - "url": " https://rseng.github.io/software/repository/github/desihub/fastspecfit", - "content": "Fast (simple) spectral synthesis and emission-line fitting of DESI spectra." + "github/lczech/gappa": { + "id": "github/lczech/gappa", + "title": "github/lczech/gappa", + "url": " https://rseng.github.io/software/repository/github/lczech/gappa", + "content": "A toolkit for analyzing and visualizing phylogenetic (placement) data" }, - "github/anwarbio/bioassays": { - "id": "github/anwarbio/bioassays", - "title": "github/anwarbio/bioassays", - "url": " https://rseng.github.io/software/repository/github/anwarbio/bioassays", - "content": "None" + "github/ishinder/EASTR": { + "id": "github/ishinder/EASTR", + "title": "github/ishinder/EASTR", + "url": " https://rseng.github.io/software/repository/github/ishinder/EASTR", + "content": "Emending Alignment of Spliced Transcript Reads" + }, + "github/yatisht/usher": { + "id": "github/yatisht/usher", + "title": "github/yatisht/usher", + "url": " https://rseng.github.io/software/repository/github/yatisht/usher", + "content": "Ultrafast Sample Placement on Existing Trees" }, - "github/rferdman/afr": { - "id": "github/rferdman/afr", - "title": "github/rferdman/afr", - "url": " https://rseng.github.io/software/repository/github/rferdman/afr", - "content": "Software package that includes various routines and tools allowing the user to reduce, process, and manipulate pulsar data, and create times-of-arrival compatible with tempo and tempo2 timing software. 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"url": " https://rseng.github.io/software/repository/github/jveitchmichaelis/pygadgetreader", - "content": "A mirror of pygadgetreader because BItbucket stopped hosting Mercurial repos (and we needed it now!)" + "github/shaelebrown/TDApplied": { + "id": "github/shaelebrown/TDApplied", + "title": "github/shaelebrown/TDApplied", + "url": " https://rseng.github.io/software/repository/github/shaelebrown/TDApplied", + "content": "An R package for statistics and machine learning with persistence diagrams" }, - "github/SpaceML/GalaxyGAN": { - "id": "github/SpaceML/GalaxyGAN", - "title": "github/SpaceML/GalaxyGAN", - "url": " https://rseng.github.io/software/repository/github/SpaceML/GalaxyGAN", + "github/yiwenstat/MCPCA_PopGen": { + "id": "github/yiwenstat/MCPCA_PopGen", + "title": "github/yiwenstat/MCPCA_PopGen", + "url": " https://rseng.github.io/software/repository/github/yiwenstat/MCPCA_PopGen", "content": "None" }, - "github/rhdtownsend/gyre": { - "id": "github/rhdtownsend/gyre", - "title": "github/rhdtownsend/gyre", - 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Used to calculate a set of scores that reflect the probability that input sequence fragments are prokaryotic and eukaryotic viral sequences." }, - "github/icecube/TauRunner": { - "id": "github/icecube/TauRunner", - "title": "github/icecube/TauRunner", - "url": " https://rseng.github.io/software/repository/github/icecube/TauRunner", - "content": "Code to propagate tau neutrinos at very high energies" + "github/scikit-tda/DREiMac": { + "id": "github/scikit-tda/DREiMac", + "title": "github/scikit-tda/DREiMac", + "url": " https://rseng.github.io/software/repository/github/scikit-tda/DREiMac", + "content": "Dimensionality Reduction with Eilenberg-MacLane Coordinates" }, - "github/wf4ever/astrotaverna": { - "id": "github/wf4ever/astrotaverna", - "title": "github/wf4ever/astrotaverna", - "url": " https://rseng.github.io/software/repository/github/wf4ever/astrotaverna", - "content": "Astronomy plugins for Taverna Workbench" + "github/pkestene/xsmurf": { + "id": "github/pkestene/xsmurf", + "title": "github/pkestene/xsmurf", + "url": " https://rseng.github.io/software/repository/github/pkestene/xsmurf", + "content": "a wavelet-based multifractal image analysis tool implementing the WTMM (Wavelet Transform Modulus Maxima) method." }, - "github/ogotoh/spaln": { - "id": "github/ogotoh/spaln", - "title": "github/ogotoh/spaln", - "url": " https://rseng.github.io/software/repository/github/ogotoh/spaln", - "content": "Genome mapping and spliced alignment of cDNA or amino acid sequences" + "github/pkestene/ramsesGPU": { + "id": "github/pkestene/ramsesGPU", + "title": "github/pkestene/ramsesGPU", + "url": " https://rseng.github.io/software/repository/github/pkestene/ramsesGPU", + "content": "Astrophysics MHD simulation code optimized for large cluster of GPU" }, - "github/AndrewAnnex/SpiceyPy": { - "id": "github/AndrewAnnex/SpiceyPy", - "title": "github/AndrewAnnex/SpiceyPy", - "url": " https://rseng.github.io/software/repository/github/AndrewAnnex/SpiceyPy", - "content": "SpiceyPy: a Pythonic Wrapper for the SPICE Toolkit." + "github/jeschaef/Graph4Med": { + "id": "github/jeschaef/Graph4Med", + "title": "github/jeschaef/Graph4Med", + "url": " https://rseng.github.io/software/repository/github/jeschaef/Graph4Med", + "content": "None" }, - "github/dpseidel/stmove": { - "id": "github/dpseidel/stmove", - "title": "github/dpseidel/stmove", - "url": " https://rseng.github.io/software/repository/github/dpseidel/stmove", - "content": "Build reproducible reports for spatial-temporal animal movement analysis" + "github/DynaSlum/satsense": { + "id": "github/DynaSlum/satsense", + "title": "github/DynaSlum/satsense", + "url": " https://rseng.github.io/software/repository/github/DynaSlum/satsense", + "content": "Satsense is a Python library for land use/cover classification using satellite imagery" }, - "github/JorenSix/Olaf": { - "id": "github/JorenSix/Olaf", - "title": "github/JorenSix/Olaf", - "url": " https://rseng.github.io/software/repository/github/JorenSix/Olaf", - "content": "Olaf: Overly Lightweight Acoustic Fingerprinting is a portable acoustic fingerprinting system." + "github/gmbrandt/xwavecal": { + "id": "github/gmbrandt/xwavecal", + "title": "github/gmbrandt/xwavecal", + "url": " https://rseng.github.io/software/repository/github/gmbrandt/xwavecal", + "content": "A library of routines for wavelength calibrating echelle spectrographs for high precision radial velocity work. A limited data-reduction pipeline is included." }, - "github/JorenSix/Panako": { - "id": "github/JorenSix/Panako", - "title": "github/JorenSix/Panako", - "url": " https://rseng.github.io/software/repository/github/JorenSix/Panako", - "content": "The Panako acoustic fingerprinting system." + "github/gmbrandt/HTOF": { + "id": "github/gmbrandt/HTOF", + "title": "github/gmbrandt/HTOF", + "url": " https://rseng.github.io/software/repository/github/gmbrandt/HTOF", + "content": "HTOF: Code which parses the intermediate data from Hipparcos and Gaia and fits astrometric solutions to those data. Capable of computing likelyhoods and parameter errors in line with the catalog." }, - "github/pyamg/pyamg": { - "id": "github/pyamg/pyamg", - "title": "github/pyamg/pyamg", - "url": " https://rseng.github.io/software/repository/github/pyamg/pyamg", - "content": "Algebraic Multigrid Solvers in Python" + "github/cobilab/RFSC": { + "id": "github/cobilab/RFSC", + "title": "github/cobilab/RFSC", + "url": " https://rseng.github.io/software/repository/github/cobilab/RFSC", + "content": "Reference-Free Sequence Classification Tool for DNA sequences in metagenomic samples" + }, + "github/cobilab/altair": { + "id": "github/cobilab/altair", + "title": "github/cobilab/altair", + "url": " https://rseng.github.io/software/repository/github/cobilab/altair", + "content": "AltaiR: a C toolkit for alignment-free and spatial-temporal analysis of multi-FASTA data" }, - "github/polca/unfold": { - "id": "github/polca/unfold", - "title": "github/polca/unfold", - "url": " https://rseng.github.io/software/repository/github/polca/unfold", - "content": "UNpacking For scenariO-based Lca Databases" + "github/codemeleon/seqPanther": { + "id": "github/codemeleon/seqPanther", + "title": "github/codemeleon/seqPanther", + "url": " https://rseng.github.io/software/repository/github/codemeleon/seqPanther", + "content": "Variant Caller and Patcher" }, - "github/jakobherpich/pyICs": { - "id": "github/jakobherpich/pyICs", - "title": "github/jakobherpich/pyICs", - "url": " https://rseng.github.io/software/repository/github/jakobherpich/pyICs", - "content": "An initial conditions creator for isolated galaxy formation simulations." + "github/healytwin1/HISS": { + "id": "github/healytwin1/HISS", + "title": "github/healytwin1/HISS", + "url": " https://rseng.github.io/software/repository/github/healytwin1/HISS", + "content": "HI Stacking Software" }, "github/johnpaulett/python-hl7": { "id": "github/johnpaulett/python-hl7", @@ -5079,191 +4179,245 @@ "url": " https://rseng.github.io/software/repository/github/johnpaulett/python-hl7", "content": "A simple library for parsing messages of Health Level 7 (HL7) version 2.x into Python objects." }, - 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"title": "github/copasi/COPASI", - "url": " https://rseng.github.io/software/repository/github/copasi/COPASI", - "content": "COPASI is a software application for simulation and analysis of biochemical networks and their dynamics." + "github/luxsrc/gray": { + "id": "github/luxsrc/gray", + "title": "github/luxsrc/gray", + "url": " https://rseng.github.io/software/repository/github/luxsrc/gray", + "content": "A general relativistic ray tracing code based on lux" }, - "github/copasi/basico": { - "id": "github/copasi/basico", - "title": "github/copasi/basico", - "url": " https://rseng.github.io/software/repository/github/copasi/basico", - "content": "A simplified python interface to COPASI." + "github/bioinform/somaticseq": { + "id": "github/bioinform/somaticseq", + "title": "github/bioinform/somaticseq", + "url": " https://rseng.github.io/software/repository/github/bioinform/somaticseq", + "content": "An ensemble approach to accurately detect somatic mutations using SomaticSeq" }, - "github/desmid/mview": { - "id": "github/desmid/mview", - "title": "github/desmid/mview", - "url": " https://rseng.github.io/software/repository/github/desmid/mview", - "content": "MView extracts and reformats the results of a sequence database search or multiple alignment." + "github/ruanjue/wtdbg2": { + "id": "github/ruanjue/wtdbg2", + "title": "github/ruanjue/wtdbg2", + "url": " https://rseng.github.io/software/repository/github/ruanjue/wtdbg2", + "content": "Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly" }, - "github/FluidityProject/fluidity": { - "id": "github/FluidityProject/fluidity", - "title": "github/FluidityProject/fluidity", - "url": " https://rseng.github.io/software/repository/github/FluidityProject/fluidity", - "content": "Fluidity" + "github/katholt/srst2": { + "id": "github/katholt/srst2", + "title": "github/katholt/srst2", + "url": " https://rseng.github.io/software/repository/github/katholt/srst2", + "content": "Short Read Sequence Typing for Bacterial Pathogens" }, - "github/gmzsebastian/FLEET": { - "id": "github/gmzsebastian/FLEET", - "title": "github/gmzsebastian/FLEET", - "url": " https://rseng.github.io/software/repository/github/gmzsebastian/FLEET", - "content": "Finding Luminous and Exotic Extragalactic Transients" + "github/katholt/Kaptive": { + "id": "github/katholt/Kaptive", + "title": "github/katholt/Kaptive", + "url": " https://rseng.github.io/software/repository/github/katholt/Kaptive", + "content": "obtain information about K and O types for Klebsiella genome assemblies" }, - "github/kerkelae/disimpy": { - "id": "github/kerkelae/disimpy", - "title": "github/kerkelae/disimpy", - "url": " https://rseng.github.io/software/repository/github/kerkelae/disimpy", - "content": "Massively parallelized Monte Carlo diffusion MRI simulator written in Python." + "github/katholt/Kleborate": { + "id": "github/katholt/Kleborate", + "title": "github/katholt/Kleborate", + "url": " https://rseng.github.io/software/repository/github/katholt/Kleborate", + "content": "tool to screen Klebsiella genome assemblies" }, - 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Currently targeting REST APIs." + "github/abelson-lab/smMIP-tools": { + "id": "github/abelson-lab/smMIP-tools", + "title": "github/abelson-lab/smMIP-tools", + "url": " https://rseng.github.io/software/repository/github/abelson-lab/smMIP-tools", + "content": "None" }, - "github/dingshandeng/diskmint": { - "id": "github/dingshandeng/diskmint", - "title": "github/dingshandeng/diskmint", - "url": " https://rseng.github.io/software/repository/github/dingshandeng/diskmint", - "content": "DiskMINT (Disk Model For INdividual Targets): a tool to estimate disk masses with CO isotopologues" + "github/jonas/tig": { + "id": "github/jonas/tig", + "title": "github/jonas/tig", + "url": " https://rseng.github.io/software/repository/github/jonas/tig", + "content": "Text-mode interface for git" }, - "github/vijayvarma392/binaryBHexp": { - "id": "github/vijayvarma392/binaryBHexp", - "title": "github/vijayvarma392/binaryBHexp", - "url": " https://rseng.github.io/software/repository/github/vijayvarma392/binaryBHexp", - "content": "The binary Black Hole explorer (visualizations)" + "github/ClusterMonteCarlo/CMC-COSMIC": { + "id": "github/ClusterMonteCarlo/CMC-COSMIC", + "title": "github/ClusterMonteCarlo/CMC-COSMIC", + "url": " https://rseng.github.io/software/repository/github/ClusterMonteCarlo/CMC-COSMIC", + "content": "None" }, - "github/python-hydro/pyro2": { - "id": "github/python-hydro/pyro2", - "title": "github/python-hydro/pyro2", - "url": " https://rseng.github.io/software/repository/github/python-hydro/pyro2", - "content": "A framework for hydrodynamics explorations and prototyping" + "github/jmackereth/orbit-estimation": { + "id": "github/jmackereth/orbit-estimation", + "title": "github/jmackereth/orbit-estimation", + "url": " https://rseng.github.io/software/repository/github/jmackereth/orbit-estimation", + "content": "calculating fast orbital parameters using the Stäckel approximation" }, - "github/PieterjanRobbe/GaussianRandomFields.jl": { - "id": "github/PieterjanRobbe/GaussianRandomFields.jl", - "title": "github/PieterjanRobbe/GaussianRandomFields.jl", - "url": " https://rseng.github.io/software/repository/github/PieterjanRobbe/GaussianRandomFields.jl", - "content": "A package for Gaussian random field generation in Julia" + "github/wcoulton/CompressedFisher": { + "id": "github/wcoulton/CompressedFisher", + "title": "github/wcoulton/CompressedFisher", + "url": " https://rseng.github.io/software/repository/github/wcoulton/CompressedFisher", + "content": "None" }, - "github/the-rccg/hw2d": { - "id": "github/the-rccg/hw2d", - "title": "github/the-rccg/hw2d", - "url": " https://rseng.github.io/software/repository/github/the-rccg/hw2d", - "content": "Reference implementation for the Hasegawa-Wakatani model of plasma turbulence inside nuclear fusion reactors in two dimensions" + "github/morisUtokyo/uTR": { + "id": "github/morisUtokyo/uTR", + "title": "github/morisUtokyo/uTR", + "url": " https://rseng.github.io/software/repository/github/morisUtokyo/uTR", + "content": "Detect key Units in mosaic Tandem Repeats from representative reads from the same locus " }, - 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union, intersection and complement - on k-mer lists." + }, + "github/kernsuite-debian/parseltongue": { + "id": "github/kernsuite-debian/parseltongue", + "title": "github/kernsuite-debian/parseltongue", + "url": " https://rseng.github.io/software/repository/github/kernsuite-debian/parseltongue", + "content": "None" + }, + "github/lorenzo-rovigatti/oxDNA": { + "id": "github/lorenzo-rovigatti/oxDNA", + "title": "github/lorenzo-rovigatti/oxDNA", + "url": " https://rseng.github.io/software/repository/github/lorenzo-rovigatti/oxDNA", + "content": "A new version of the code to simulate the oxDNA/oxRNA models, now equipped with Python bindings" }, - "github/sylvainprigent/napari-tracks-reader": { - "id": "github/sylvainprigent/napari-tracks-reader", - "title": "github/sylvainprigent/napari-tracks-reader", - "url": " https://rseng.github.io/software/repository/github/sylvainprigent/napari-tracks-reader", - "content": "napari reader plugin for tracking" + "github/itpplasma/GORILLA": { + "id": "github/itpplasma/GORILLA", + "title": "github/itpplasma/GORILLA", + "url": " https://rseng.github.io/software/repository/github/itpplasma/GORILLA", + "content": "GORILLA: Guiding-center ORbit Integration with Local Linearization Approach" }, - 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Never be embarrassed again to say that you have a small data situation!" }, "github/Julian/jsonschema": { "id": "github/Julian/jsonschema", @@ -5271,311 +4425,347 @@ "url": " https://rseng.github.io/software/repository/github/Julian/jsonschema", "content": "An(other) implementation of JSON Schema for Python" }, - "github/jakeret/abcpmc": { - "id": "github/jakeret/abcpmc", - "title": "github/jakeret/abcpmc", - "url": " https://rseng.github.io/software/repository/github/jakeret/abcpmc", - "content": "Approximate Bayesian Computation Population Monte Carlo" + "github/bshoshany/OGRe": { + "id": "github/bshoshany/OGRe", + "title": "github/bshoshany/OGRe", + "url": " https://rseng.github.io/software/repository/github/bshoshany/OGRe", + "content": "An object-oriented general relativity package for Mathematica." }, - "github/jakeret/tf_unet": { - "id": "github/jakeret/tf_unet", - "title": "github/jakeret/tf_unet", - "url": " https://rseng.github.io/software/repository/github/jakeret/tf_unet", - "content": "Generic U-Net Tensorflow implementation for image segmentation" + "github/samb8s/PsrPopPy": { + "id": "github/samb8s/PsrPopPy", + "title": "github/samb8s/PsrPopPy", + "url": " https://rseng.github.io/software/repository/github/samb8s/PsrPopPy", + "content": "Python implementation of PSRPOP, designed to be run from the command line or from Python scripts/interpreter" }, - "github/difuture-lmu/dsBinVal": { - "id": "github/difuture-lmu/dsBinVal", - "title": "github/difuture-lmu/dsBinVal", - "url": " https://rseng.github.io/software/repository/github/difuture-lmu/dsBinVal", - "content": "ROC-GLM and calibration analysis for DataSHIELD" + "github/linuxscout/pyarabic": { + "id": "github/linuxscout/pyarabic", + "title": "github/linuxscout/pyarabic", + "url": " https://rseng.github.io/software/repository/github/linuxscout/pyarabic", + "content": "pyarabic" }, - "github/NickSwainston/pulsar_spectra": { - "id": "github/NickSwainston/pulsar_spectra", - "title": "github/NickSwainston/pulsar_spectra", - "url": " https://rseng.github.io/software/repository/github/NickSwainston/pulsar_spectra", - "content": "A simple interface to record pulsar's flux density measurements for a large number of papers and perform fitting of spectral models." + "github/AnthonyOfSeattle/pyAscoreValidation": { + "id": "github/AnthonyOfSeattle/pyAscoreValidation", + "title": "github/AnthonyOfSeattle/pyAscoreValidation", + "url": " https://rseng.github.io/software/repository/github/AnthonyOfSeattle/pyAscoreValidation", + "content": "Validation experiments for the pyAscore python package." }, - "github/raredd/kmdata": { - "id": "github/raredd/kmdata", - "title": "github/raredd/kmdata", - "url": " https://rseng.github.io/software/repository/github/raredd/kmdata", - "content": "kmdata: A Database of Reconstructed Individual Patient Level Data from 153 Oncology Clinical trials" + "github/pyFFTW/pyFFTW": { + "id": "github/pyFFTW/pyFFTW", + "title": "github/pyFFTW/pyFFTW", + "url": " https://rseng.github.io/software/repository/github/pyFFTW/pyFFTW", + "content": "A pythonic python wrapper around FFTW" }, - 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K2CE was designed to work with standard Kepler or K2 data products: long-cadence (30 min) and short-cadence (1 min) light curve files and long-cadence and short-cadence target pixel files. The tool has been modified to work with light curve files and target pixel files from the TESS mission." + }, + "github/nasa/prog_models": { + "id": "github/nasa/prog_models", + "title": "github/nasa/prog_models", + "url": " https://rseng.github.io/software/repository/github/nasa/prog_models", + "content": "The NASA Prognostic Model Package is a Python framework focused on defining and building models for prognostics (computation of remaining useful life) of engineering systems, and provides a set of prognostics models for select components developed within this framework, suitable for use in prognostics applications for these components." + }, + "github/nasa/KeplerPORTs": { + "id": "github/nasa/KeplerPORTs", + "title": "github/nasa/KeplerPORTs", + "url": " https://rseng.github.io/software/repository/github/nasa/KeplerPORTs", "content": "None" }, - "github/matteozennaro/reps": { - "id": "github/matteozennaro/reps", - "title": "github/matteozennaro/reps", - "url": " https://rseng.github.io/software/repository/github/matteozennaro/reps", - "content": "REPS - rescaled power spectra for initial conditions with massive neutrinos" + "github/nasa/kepler-robovetter": { + "id": "github/nasa/kepler-robovetter", + "title": "github/nasa/kepler-robovetter", + "url": " https://rseng.github.io/software/repository/github/nasa/kepler-robovetter", + "content": "None" + }, + "github/luizfelippesr/magnetizer": { + "id": "github/luizfelippesr/magnetizer", + "title": "github/luizfelippesr/magnetizer", + "url": " https://rseng.github.io/software/repository/github/luizfelippesr/magnetizer", + "content": "Magnetizer - A Fortran code that post-processes the output of a semi-analytic model of galaxy formation and produces a catalogue of galaxies with detailed radial dependent ISM properties, including magnetic fields" + }, + "github/luizfelippesr/galmag": { + "id": "github/luizfelippesr/galmag", + "title": "github/luizfelippesr/galmag", + "url": " https://rseng.github.io/software/repository/github/luizfelippesr/galmag", + "content": "GalMag - A Python tool for computing realistic galactic magnetic fields" + }, + "github/EnricoCorsaro/FAMED": { + "id": "github/EnricoCorsaro/FAMED", + "title": "github/EnricoCorsaro/FAMED", + "url": " https://rseng.github.io/software/repository/github/EnricoCorsaro/FAMED", + "content": "FAMED (Fast and AutoMated pEak bagging with DIAMONDS) - 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" + "github/chapmanb/bcbio.prioritize": { + "id": "github/chapmanb/bcbio.prioritize", + "title": "github/chapmanb/bcbio.prioritize", + "url": " https://rseng.github.io/software/repository/github/chapmanb/bcbio.prioritize", + "content": "Prioritize small variants, structural variants and coverage based on biological inputs" }, - "github/ZJUFanLab/scTITANS": { - "id": "github/ZJUFanLab/scTITANS", - "title": "github/ZJUFanLab/scTITANS", - "url": " https://rseng.github.io/software/repository/github/ZJUFanLab/scTITANS", - "content": "Identifying key genes and cell subclusters for time-series single cell sequencing data" + "github/chapmanb/bcbio.variation": { + "id": "github/chapmanb/bcbio.variation", + "title": "github/chapmanb/bcbio.variation", + "url": " https://rseng.github.io/software/repository/github/chapmanb/bcbio.variation", + "content": "Toolkit to analyze genomic variation data, built on the GATK with Clojure" }, - "github/ZJUFanLab/bulk2space": { - "id": "github/ZJUFanLab/bulk2space", - "title": "github/ZJUFanLab/bulk2space", - "url": " https://rseng.github.io/software/repository/github/ZJUFanLab/bulk2space", - "content": "a spatial deconvolution method based on deep learning frameworks, which converts bulk transcriptomes into spatially resolved single-cell expression profiles" + "github/chapmanb/bcbb": { + "id": "github/chapmanb/bcbb", + "title": "github/chapmanb/bcbb", + "url": " https://rseng.github.io/software/repository/github/chapmanb/bcbb", + "content": "Incubator for useful bioinformatics code, primarily in Python and R" }, - "github/pmlmodelling/nctoolkit": { - "id": "github/pmlmodelling/nctoolkit", - "title": "github/pmlmodelling/nctoolkit", - "url": " https://rseng.github.io/software/repository/github/pmlmodelling/nctoolkit", - "content": "A Python package for netCDF analysis and post-processing" + "github/algo-cancer/CAMMiQ": { + "id": "github/algo-cancer/CAMMiQ", + "title": "github/algo-cancer/CAMMiQ", + "url": " https://rseng.github.io/software/repository/github/algo-cancer/CAMMiQ", + "content": "Metagenomics microbial abundance quantification" }, - 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" + "github/sidmohite/nimbus-astro": { + "id": "github/sidmohite/nimbus-astro", + "title": "github/sidmohite/nimbus-astro", + "url": " https://rseng.github.io/software/repository/github/sidmohite/nimbus-astro", + "content": "A Bayesian inference framework to constrain kilonova models." }, - "github/saeyslab/PeacoQC": { - "id": "github/saeyslab/PeacoQC", - "title": "github/saeyslab/PeacoQC", - "url": " https://rseng.github.io/software/repository/github/saeyslab/PeacoQC", - "content": "Peak-based selection of high quality cytometry data" + "github/esandford/EightBitTransit": { + "id": "github/esandford/EightBitTransit", + "title": "github/esandford/EightBitTransit", + "url": " https://rseng.github.io/software/repository/github/esandford/EightBitTransit", + "content": "Calculate light curves from pixel grids, and recover shadow images from light curves." }, - "github/isovic/graphmap": { - "id": "github/isovic/graphmap", - "title": "github/isovic/graphmap", - "url": " https://rseng.github.io/software/repository/github/isovic/graphmap", - "content": "GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:" + "github/xoopR/set6": { + "id": "github/xoopR/set6", + "title": "github/xoopR/set6", + "url": " https://rseng.github.io/software/repository/github/xoopR/set6", + "content": "R6 object-oriented interface for mathematical sets." }, - "github/FlowModelingControl/flowtorch": { - "id": "github/FlowModelingControl/flowtorch", - "title": "github/FlowModelingControl/flowtorch", - "url": " https://rseng.github.io/software/repository/github/FlowModelingControl/flowtorch", - "content": "flowTorch - a Python library for analysis and reduced-order modeling of fluid flows" + "github/Crick-CancerGenomics/ascat": { + "id": "github/Crick-CancerGenomics/ascat", + "title": "github/Crick-CancerGenomics/ascat", + "url": " https://rseng.github.io/software/repository/github/Crick-CancerGenomics/ascat", + "content": "ASCAT copy number R package" }, - "github/Quantum-Dynamics-Hub/libra-code": { - "id": "github/Quantum-Dynamics-Hub/libra-code", - "title": "github/Quantum-Dynamics-Hub/libra-code", - 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"title": "github/HLasse/TextDescriptives", - "url": " https://rseng.github.io/software/repository/github/HLasse/TextDescriptives", - "content": "A Python library for calculating a large variety of metrics from text" - }, - "github/vaexio/vaex": { - "id": "github/vaexio/vaex", - "title": "github/vaexio/vaex", - "url": " https://rseng.github.io/software/repository/github/vaexio/vaex", - "content": "Out-of-Core hybrid Apache Arrow/NumPy DataFrame for Python, ML, visualization and exploration of big tabular data at a billion rows per second 🚀" - }, - "github/cmillion/gPhoton": { - "id": "github/cmillion/gPhoton", - "title": "github/cmillion/gPhoton", - "url": " https://rseng.github.io/software/repository/github/cmillion/gPhoton", - "content": "The GALEX photon database and tools project." - }, - "github/astromb/PICsar2D": { - "id": "github/astromb/PICsar2D", - "title": "github/astromb/PICsar2D", - "url": " https://rseng.github.io/software/repository/github/astromb/PICsar2D", - "content": "Particle In Cell pulSAR code" - 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JavaScript module built with Svelte and Snowpack." + "github/idruglab/hignn": { + "id": "github/idruglab/hignn", + "title": "github/idruglab/hignn", + "url": " https://rseng.github.io/software/repository/github/idruglab/hignn", + "content": "Code for "HiGNN: A Hierarchical Informative Graph Neural Network for Molecular Property Prediction Equipped with Feature-Wise Attention"" }, - "github/dparkins/CosmoNest": { - "id": "github/dparkins/CosmoNest", - "title": "github/dparkins/CosmoNest", - "url": " https://rseng.github.io/software/repository/github/dparkins/CosmoNest", - "content": "Cosmological Nested Sampling (to be used with cosmomc)" + "github/YesselmanLab/rna_map": { + "id": "github/YesselmanLab/rna_map", + "title": "github/YesselmanLab/rna_map", + "url": " https://rseng.github.io/software/repository/github/YesselmanLab/rna_map", + "content": "tools to do mutational profiling (MaP) analysis for RNA chemical mapping experiments." }, - "github/florisvb/PyNumDiff": { - "id": "github/florisvb/PyNumDiff", - "title": "github/florisvb/PyNumDiff", - "url": " https://rseng.github.io/software/repository/github/florisvb/PyNumDiff", - "content": "Methods for numerical differentiation of noisy data in python" + "github/aspuru-guzik-group/funsies": { + "id": "github/aspuru-guzik-group/funsies", + "title": "github/aspuru-guzik-group/funsies", + "url": " https://rseng.github.io/software/repository/github/aspuru-guzik-group/funsies", + "content": "funsies is a lightweight workflow engine 🔧" }, - "github/SolavLab/DuoDIC": { - "id": "github/SolavLab/DuoDIC", - "title": "github/SolavLab/DuoDIC", - "url": " https://rseng.github.io/software/repository/github/SolavLab/DuoDIC", - "content": "Stereo 3D Digital Image Correlation (3D-DIC) MATLAB toolbox" + "github/ec363/fpcountr": { + "id": "github/ec363/fpcountr", + "title": "github/ec363/fpcountr", + "url": " https://rseng.github.io/software/repository/github/ec363/fpcountr", + "content": "Fluorescent protein calibration for plate readers" }, - "github/czbiohub/cerebra": { - "id": "github/czbiohub/cerebra", - "title": "github/czbiohub/cerebra", - "url": " https://rseng.github.io/software/repository/github/czbiohub/cerebra", - "content": "A tool for fast and accurate summarizing of variant calling format (VCF) files" + "github/hiddenSymmetries/simsopt": { + "id": "github/hiddenSymmetries/simsopt", + "title": "github/hiddenSymmetries/simsopt", + "url": " https://rseng.github.io/software/repository/github/hiddenSymmetries/simsopt", + "content": "Simons Stellarator Optimizer Code" }, - "github/JieZheng-ShanghaiTech/PiLSL": { - "id": "github/JieZheng-ShanghaiTech/PiLSL", - "title": "github/JieZheng-ShanghaiTech/PiLSL", - "url": " https://rseng.github.io/software/repository/github/JieZheng-ShanghaiTech/PiLSL", - "content": "PiLSL is a pairwise interaction learning-based graph neural network (GNN) model for prediction of synthetic lethality (SL) as anti-cancer drug targets. It learns the representation of pairwise interaction between two genes from a knowledge graph (KG)." + "github/noraeisner/LATTE": { + "id": "github/noraeisner/LATTE", + "title": "github/noraeisner/LATTE", + "url": " https://rseng.github.io/software/repository/github/noraeisner/LATTE", + "content": "Lightcurve Analysis Tool for Transiting Exoplanet" }, - "github/UUDigitalHumanitieslab/texcavator": { - "id": "github/UUDigitalHumanitieslab/texcavator", - "title": "github/UUDigitalHumanitieslab/texcavator", - "url": " https://rseng.github.io/software/repository/github/UUDigitalHumanitieslab/texcavator", - "content": "Text mining on the Royal Library newspaper corpus" + "github/dolfin-adjoint/pyadjoint": { + "id": "github/dolfin-adjoint/pyadjoint", + "title": "github/dolfin-adjoint/pyadjoint", + "url": " https://rseng.github.io/software/repository/github/dolfin-adjoint/pyadjoint", + "content": "The algorithmic differentation tool pyadjoint and add-ons." }, - "github/bempp/bempp-cl": { - "id": "github/bempp/bempp-cl", - "title": "github/bempp/bempp-cl", - "url": " https://rseng.github.io/software/repository/github/bempp/bempp-cl", - "content": "A fast Python based just-in-time compiling boundary element library" + "github/kno10/python-kmedoids": { + "id": "github/kno10/python-kmedoids", + "title": "github/kno10/python-kmedoids", + "url": " https://rseng.github.io/software/repository/github/kno10/python-kmedoids", + "content": "Fast K-Medoids clustering in Python with FasterPAM" }, - "github/COINtoolbox/ActSNClass": { - "id": "github/COINtoolbox/ActSNClass", - "title": "github/COINtoolbox/ActSNClass", - "url": " https://rseng.github.io/software/repository/github/COINtoolbox/ActSNClass", - "content": "Active Learning for SN photometric classification" + "github/xmuyulab/DreamDIA-XMBD": { + "id": "github/xmuyulab/DreamDIA-XMBD", + "title": "github/xmuyulab/DreamDIA-XMBD", + "url": " https://rseng.github.io/software/repository/github/xmuyulab/DreamDIA-XMBD", + "content": "Software for data-independent acquisition (DIA) proteomic data processing with deep representation features." }, - "github/COINtoolbox/DRACULA": { - "id": "github/COINtoolbox/DRACULA", - "title": "github/COINtoolbox/DRACULA", - "url": " https://rseng.github.io/software/repository/github/COINtoolbox/DRACULA", - "content": "None" + "github/nlesc-dirac/sagecal": { + "id": "github/nlesc-dirac/sagecal", + "title": "github/nlesc-dirac/sagecal", + "url": " https://rseng.github.io/software/repository/github/nlesc-dirac/sagecal", + "content": "SAGECal is a very fast, memory efficient and GPU accelerated radio interferometric calibration program. It supports all source models including points, Gaussians and Shapelets. Distributed calibration using MPI and consensus optimization is enabled. Tools to build/restore sky models are included." }, - "github/COINtoolbox/CosmoPhotoz": { - "id": "github/COINtoolbox/CosmoPhotoz", - "title": "github/COINtoolbox/CosmoPhotoz", - "url": " https://rseng.github.io/software/repository/github/COINtoolbox/CosmoPhotoz", - "content": "Photometric redshift estimator utilising Generalized Linear Models." + "github/jupyterlab/jupyterlab": { + "id": "github/jupyterlab/jupyterlab", + "title": "github/jupyterlab/jupyterlab", + "url": " https://rseng.github.io/software/repository/github/jupyterlab/jupyterlab", + "content": "JupyterLab computational environment." }, - "github/bbfrederick/stabilitycalc": { - "id": "github/bbfrederick/stabilitycalc", - "title": "github/bbfrederick/stabilitycalc", - "url": " https://rseng.github.io/software/repository/github/bbfrederick/stabilitycalc", - "content": "Automatic QC processing for fMRI data" + "github/andresGranadosC/GalRotpy": { + "id": "github/andresGranadosC/GalRotpy", + "title": "github/andresGranadosC/GalRotpy", + "url": " https://rseng.github.io/software/repository/github/andresGranadosC/GalRotpy", + "content": "A Python-based tool to parametrize the rotation curve and the gravitational potential of disk-like galaxies" }, - "github/jonas/tig": { - "id": "github/jonas/tig", - "title": "github/jonas/tig", - "url": " https://rseng.github.io/software/repository/github/jonas/tig", - "content": "Text-mode interface for git" + "github/artis-mcrt/artis": { + "id": "github/artis-mcrt/artis", + "title": "github/artis-mcrt/artis", + "url": " https://rseng.github.io/software/repository/github/artis-mcrt/artis", + "content": "3D Monte Carlo radiative transfer code for supernovae" }, - "github/ArtRand/signalAlign": { - "id": "github/ArtRand/signalAlign", - "title": "github/ArtRand/signalAlign", - "url": " https://rseng.github.io/software/repository/github/ArtRand/signalAlign", - "content": "HMM-HDP models for MinION signal alignments" + "github/nabeelre/BTSbot": { + "id": "github/nabeelre/BTSbot", + "title": "github/nabeelre/BTSbot", + "url": " https://rseng.github.io/software/repository/github/nabeelre/BTSbot", + "content": "Automated identification of supernovae with multi-modal deep learning" }, - "github/morriscb/The-wiZZ": { - "id": "github/morriscb/The-wiZZ", - "title": "github/morriscb/The-wiZZ", - "url": " https://rseng.github.io/software/repository/github/morriscb/The-wiZZ", - "content": "A clustering redshift estimation code for us folks. For information on the method see Schmidt et al. 2013, Menard et al. 2013, and Rahman et al. 2015, 2016b. 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It is specially designed for processing next-generation sequencing (NGS) paired-end sequences." + "github/pavanvidem/chira": { + "id": "github/pavanvidem/chira", + "title": "github/pavanvidem/chira", + "url": " https://rseng.github.io/software/repository/github/pavanvidem/chira", + "content": "Chimeric Read Annotator" }, - "github/mikegrudic/MakeCloud": { - "id": "github/mikegrudic/MakeCloud", - "title": "github/mikegrudic/MakeCloud", - "url": " https://rseng.github.io/software/repository/github/mikegrudic/MakeCloud", - "content": "MakeCloud: Make turbulent GMC initial conditions for GIZMO" + "github/nluetts/NoisySignalIntegration.jl": { + "id": "github/nluetts/NoisySignalIntegration.jl", + "title": "github/nluetts/NoisySignalIntegration.jl", + "url": " https://rseng.github.io/software/repository/github/nluetts/NoisySignalIntegration.jl", + "content": "None" }, - "github/mikegrudic/pytreegrav": { - "id": "github/mikegrudic/pytreegrav", - "title": "github/mikegrudic/pytreegrav", - "url": " https://rseng.github.io/software/repository/github/mikegrudic/pytreegrav", - "content": "Fast N-body gravitational force and potential in Python" + "github/miguelcarcamov/csromer": { + "id": "github/miguelcarcamov/csromer", + "title": "github/miguelcarcamov/csromer", + "url": " https://rseng.github.io/software/repository/github/miguelcarcamov/csromer", + "content": "Compressive Sensing and Optimization Framework to reconstruct Faraday Depth signals" }, - "github/mes5k/amap-align": { - "id": "github/mes5k/amap-align", - "title": "github/mes5k/amap-align", - "url": " https://rseng.github.io/software/repository/github/mes5k/amap-align", - "content": "Automatically exported from code.google.com/p/amap-align" + "github/miguelcarcamov/gpuvmem": { + "id": "github/miguelcarcamov/gpuvmem", + "title": "github/miguelcarcamov/gpuvmem", + "url": " https://rseng.github.io/software/repository/github/miguelcarcamov/gpuvmem", + "content": "GPU Framework for Radio Astronomical Image Synthesis" }, - "github/mpokorny/vysmaw": { - "id": "github/mpokorny/vysmaw", - "title": "github/mpokorny/vysmaw", - "url": " https://rseng.github.io/software/repository/github/mpokorny/vysmaw", - "content": "Fast visibility stream muncher" + "github/Ajstros/pyripherals": { + "id": "github/Ajstros/pyripherals", + "title": "github/Ajstros/pyripherals", + "url": " https://rseng.github.io/software/repository/github/Ajstros/pyripherals", + "content": "Python solution for communicating with peripheral ICs" }, - "github/cole-trapnell-lab/cufflinks": { - "id": "github/cole-trapnell-lab/cufflinks", - "title": "github/cole-trapnell-lab/cufflinks", - "url": " https://rseng.github.io/software/repository/github/cole-trapnell-lab/cufflinks", - "content": "a reference-guided assembler that assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples." + "github/smsharma/fermi-gce-flows": { + "id": "github/smsharma/fermi-gce-flows", + "title": "github/smsharma/fermi-gce-flows", + "url": " https://rseng.github.io/software/repository/github/smsharma/fermi-gce-flows", + "content": "Simulation-based inference for the Galactic Center gamma-ray excess. 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The main feature is a workflow that helps guide auditors through the sampling process. Additionally, there are stand-alone analyses for planning, selecting, and evaluating a sample. 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"title": "github/SarveshVGharat/Plages-Identification", - "url": " https://rseng.github.io/software/repository/github/SarveshVGharat/Plages-Identification", - "content": "None" + "github/ropensci/magick": { + "id": "github/ropensci/magick", + "title": "github/ropensci/magick", + "url": " https://rseng.github.io/software/repository/github/ropensci/magick", + "content": "Magic, madness, heaven, sin" }, - "github/alphapsa/PIPE": { - "id": "github/alphapsa/PIPE", - "title": "github/alphapsa/PIPE", - "url": " https://rseng.github.io/software/repository/github/alphapsa/PIPE", - "content": "PSF Imagette Photometric Extraction - PSF photometry for CHEOPS data" + "github/ropensci/hoardr": { + "id": "github/ropensci/hoardr", + "title": "github/ropensci/hoardr", + "url": " https://rseng.github.io/software/repository/github/ropensci/hoardr", + "content": "manage cached files" }, - "github/easybuilders/easybuild": { - "id": "github/easybuilders/easybuild", - "title": "github/easybuilders/easybuild", - 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"title": "github/lofar-astron/RMextract", - "url": " https://rseng.github.io/software/repository/github/lofar-astron/RMextract", - "content": "extract TEC, vTEC, Earthmagnetic field and Rotation Measures from GPS and WMM data for radio interferometry observations " + "github/ropensci/graphql": { + "id": "github/ropensci/graphql", + "title": "github/ropensci/graphql", + "url": " https://rseng.github.io/software/repository/github/ropensci/graphql", + "content": "Bindings to libgraphqlparser for R" }, - "github/lofar-astron/DP3": { - "id": "github/lofar-astron/DP3", - "title": "github/lofar-astron/DP3", - "url": " https://rseng.github.io/software/repository/github/lofar-astron/DP3", - "content": "DP3: streaming processing pipeline for radio interferometric data" + "github/ropensci/wateRinfo": { + "id": "github/ropensci/wateRinfo", + "title": "github/ropensci/wateRinfo", + "url": " https://rseng.github.io/software/repository/github/ropensci/wateRinfo", + "content": "R package to download time series data from waterinfo.be" }, - 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"github/ekg/freebayes": { - "id": "github/ekg/freebayes", - "title": "github/ekg/freebayes", - "url": " https://rseng.github.io/software/repository/github/ekg/freebayes", - "content": "Bayesian haplotype-based genetic polymorphism discovery and genotyping." + "github/ropensci/rfema": { + "id": "github/ropensci/rfema", + "title": "github/ropensci/rfema", + "url": " https://rseng.github.io/software/repository/github/ropensci/rfema", + "content": " rfema allows users to access The Federal Emergency Management Agency's (FEMA) publicly available data through their API. The package provides a set of functions to easily navigate and access data from the National Flood Insurance Program along and FEMA's various disaster aid programs." }, - "github/ekg/tabixpp": { - "id": "github/ekg/tabixpp", - "title": "github/ekg/tabixpp", - "url": " https://rseng.github.io/software/repository/github/ekg/tabixpp", - "content": "C++ wrapper to tabix indexer" + "github/ropensci/targets": { + "id": "github/ropensci/targets", + "title": "github/ropensci/targets", + "url": " https://rseng.github.io/software/repository/github/ropensci/targets", + "content": "Function-oriented Make-like declarative workflows for R" }, - "github/ekg/seqwish": { - "id": "github/ekg/seqwish", - "title": "github/ekg/seqwish", - "url": " https://rseng.github.io/software/repository/github/ekg/seqwish", - "content": "alignment to variation graph inducer" + "github/ropensci/jsonvalidate": { + "id": "github/ropensci/jsonvalidate", + "title": "github/ropensci/jsonvalidate", + "url": " https://rseng.github.io/software/repository/github/ropensci/jsonvalidate", + "content": ":heavy_check_mark::interrobang: Validate JSON" }, - "github/NCAR/NCAR-Classic-Libraries-for-Geophysics": { - "id": "github/NCAR/NCAR-Classic-Libraries-for-Geophysics", - "title": "github/NCAR/NCAR-Classic-Libraries-for-Geophysics", - "url": " https://rseng.github.io/software/repository/github/NCAR/NCAR-Classic-Libraries-for-Geophysics", - "content": "None" + "github/ropensci/lingtypology": { + "id": "github/ropensci/lingtypology", + "title": "github/ropensci/lingtypology", + "url": " https://rseng.github.io/software/repository/github/ropensci/lingtypology", + "content": "R package for linguistic cartography and typological databases search" }, - "github/twopin/CAMP": { - "id": "github/twopin/CAMP", - "title": "github/twopin/CAMP", - "url": " https://rseng.github.io/software/repository/github/twopin/CAMP", - "content": "predicting peptide-protein interactions" + "github/ropensci/rgpdd": { + "id": "github/ropensci/rgpdd", + "title": "github/ropensci/rgpdd", + "url": " https://rseng.github.io/software/repository/github/ropensci/rgpdd", + "content": "Interface to the Global Population Dynamics Database, http://www3.imperial.ac.uk/cpb/databases/gpdd" }, - "github/lgrcia/prose": { - "id": "github/lgrcia/prose", - "title": "github/lgrcia/prose", - "url": " https://rseng.github.io/software/repository/github/lgrcia/prose", - "content": "A python framework to process FITS images. Built for Astronomy." + "github/ropensci/rerddap": { + "id": "github/ropensci/rerddap", + "title": "github/ropensci/rerddap", + "url": " https://rseng.github.io/software/repository/github/ropensci/rerddap", + "content": "R client for working with ERDDAP servers" }, - "github/bluefoxr/COINr": { - "id": "github/bluefoxr/COINr", - "title": "github/bluefoxr/COINr", - "url": " https://rseng.github.io/software/repository/github/bluefoxr/COINr", - "content": "COINr" + "github/ropensci/cld2": { + "id": "github/ropensci/cld2", + "title": "github/ropensci/cld2", + "url": " https://rseng.github.io/software/repository/github/ropensci/cld2", + "content": "R Wrapper for Google's Compact Language Detector 2" }, - "github/hz1010/FIPRESCI_data_analysis": { - "id": "github/hz1010/FIPRESCI_data_analysis", - "title": "github/hz1010/FIPRESCI_data_analysis", - "url": " https://rseng.github.io/software/repository/github/hz1010/FIPRESCI_data_analysis", - "content": "Code for FIPERSCI data" + "github/ropensci/treebase": { + "id": "github/ropensci/treebase", + "title": "github/ropensci/treebase", + "url": " https://rseng.github.io/software/repository/github/ropensci/treebase", + "content": "An R interface to the treeBASE API (now on CRAN)" }, - "github/ssadedin/bazam": { - "id": "github/ssadedin/bazam", - "title": "github/ssadedin/bazam", - "url": " https://rseng.github.io/software/repository/github/ssadedin/bazam", - "content": "A read extraction and realignment tool for next generation sequencing data" + "github/ropensci/chromer": { + "id": "github/ropensci/chromer", + "title": "github/ropensci/chromer", + "url": " https://rseng.github.io/software/repository/github/ropensci/chromer", + "content": "package for interacting with the chromosome counts database (CCDB) at http://ccdb.tau.ac.il" }, - "github/valerio-marra/CalPriorSNIa": { - "id": "github/valerio-marra/CalPriorSNIa", - "title": "github/valerio-marra/CalPriorSNIa", - "url": " https://rseng.github.io/software/repository/github/valerio-marra/CalPriorSNIa", - "content": "Effective calibration prior on the absolute magnitude of Type Ia supernovae" + "github/ropensci/spatsoc": { + "id": "github/ropensci/spatsoc", + "title": "github/ropensci/spatsoc", + "url": " https://rseng.github.io/software/repository/github/ropensci/spatsoc", + "content": ":package: spatsoc is an R package for detecting spatial and temporal groups in GPS relocations. " }, - "github/parkus/ffd": { - "id": "github/parkus/ffd", - "title": "github/parkus/ffd", - "url": " https://rseng.github.io/software/repository/github/parkus/ffd", - "content": "Tools for the analysis of flare frequency distributions for flares detected in heterogenous datasets." + "github/ropensci/wdman": { + "id": "github/ropensci/wdman", + "title": "github/ropensci/wdman", + "url": " https://rseng.github.io/software/repository/github/ropensci/wdman", + "content": "Webdriver/Selenium Binary Manager" }, - "github/parkus/fiducial_flare": { - "id": "github/parkus/fiducial_flare", - "title": "github/parkus/fiducial_flare", - "url": " https://rseng.github.io/software/repository/github/parkus/fiducial_flare", - "content": "Generate spectra and lightcurves of a standardized far ultraviolet flare." + "github/ropensci/chirps": { + "id": "github/ropensci/chirps", + "title": "github/ropensci/chirps", + "url": " https://rseng.github.io/software/repository/github/ropensci/chirps", + "content": "API Client for CHIRPS" }, - "github/parkus/scicatalog": { - "id": "github/parkus/scicatalog", - "title": "github/parkus/scicatalog", - "url": " https://rseng.github.io/software/repository/github/parkus/scicatalog", - "content": "None" + "github/ropensci/rentrez": { + "id": "github/ropensci/rentrez", + "title": "github/ropensci/rentrez", + "url": " https://rseng.github.io/software/repository/github/ropensci/rentrez", + "content": "talk with NCBI entrez using R" }, - "github/MaceKuailv/seaduck": { - "id": "github/MaceKuailv/seaduck", - "title": "github/MaceKuailv/seaduck", - "url": " https://rseng.github.io/software/repository/github/MaceKuailv/seaduck", - "content": "A python package that interpolates data from ocean dataset from both Eulerian and Lagrangian perspective." + "github/ropensci/tinkr": { + "id": "github/ropensci/tinkr", + "title": "github/ropensci/tinkr", + "url": " https://rseng.github.io/software/repository/github/ropensci/tinkr", + "content": "Convert (R)Markdown files to XML, edit them, write them back as (R)Markdown" }, - 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"id": "github/uedaLabR/nanoDoc", - "title": "github/uedaLabR/nanoDoc", - "url": " https://rseng.github.io/software/repository/github/uedaLabR/nanoDoc", - "content": "RNA modification detection using Nanopore raw reads with Deep One Class classification" + "github/ropensci/rrricanes": { + "id": "github/ropensci/rrricanes", + "title": "github/ropensci/rrricanes", + "url": " https://rseng.github.io/software/repository/github/ropensci/rrricanes", + "content": "Web scraper for Atlantic and east Pacific hurricanes and tropical storms" }, - "github/LQYoLH/CnnCrispr": { - "id": "github/LQYoLH/CnnCrispr", - "title": "github/LQYoLH/CnnCrispr", - "url": " https://rseng.github.io/software/repository/github/LQYoLH/CnnCrispr", - "content": "A deep learning method for sgRNA off-target propensity prediction." + "github/ropensci/rbace": { + "id": "github/ropensci/rbace", + "title": "github/ropensci/rbace", + "url": " https://rseng.github.io/software/repository/github/ropensci/rbace", + "content": "BASE R client" }, - 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"id": "github/atmos-cloud-sim-uj/PyMPDATA", - "title": "github/atmos-cloud-sim-uj/PyMPDATA", - "url": " https://rseng.github.io/software/repository/github/atmos-cloud-sim-uj/PyMPDATA", - "content": "Numba-accelerated Pythonic implementation of MPDATA with examples in Python, Julia and Matlab" + "github/ropensci/smapr": { + "id": "github/ropensci/smapr", + "title": "github/ropensci/smapr", + "url": " https://rseng.github.io/software/repository/github/ropensci/smapr", + "content": "An R package for acquisition and processing of NASA SMAP data" }, - "github/atmos-cloud-sim-uj/PySDM": { - "id": "github/atmos-cloud-sim-uj/PySDM", - "title": "github/atmos-cloud-sim-uj/PySDM", - "url": " https://rseng.github.io/software/repository/github/atmos-cloud-sim-uj/PySDM", - "content": "Pythonic particle-based (super-droplet) warm-rain/aqueous-chemistry cloud microphysics package with box, parcel & 1D/2D prescribed-flow examples in Python, Julia and Matlab" + "github/ropensci/tracerer": { + "id": "github/ropensci/tracerer", + "title": "github/ropensci/tracerer", + "url": " https://rseng.github.io/software/repository/github/ropensci/tracerer", + "content": "tracerer, 'Tracer for R', is an R package to work with the output of BEAST2" }, - 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Provides a more pythonic and intuitive way to interact with the ZOS-API through python using a .NET connection. 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Analysis and Visualization of Mutation Enrichments for Selected Genomic Regions and Cancer Types" }, - "github/javicarron/pynkowski": { - "id": "github/javicarron/pynkowski", - "title": "github/javicarron/pynkowski", - "url": " https://rseng.github.io/software/repository/github/javicarron/pynkowski", - "content": "Pynkowski is a Python package to compute Minkowski Functionals, as well as their expected values for different fields." + "github/DEIB-GECO/VarSum": { + "id": "github/DEIB-GECO/VarSum", + "title": "github/DEIB-GECO/VarSum", + "url": " https://rseng.github.io/software/repository/github/DEIB-GECO/VarSum", + "content": "Data summarization tool for 1000 Genomes Project data" }, - "github/tumcms/Open-Infra-Platform": { - "id": "github/tumcms/Open-Infra-Platform", - "title": "github/tumcms/Open-Infra-Platform", - "url": " https://rseng.github.io/software/repository/github/tumcms/Open-Infra-Platform", - "content": "This is the official repository of the open-source Open Infra Platform software (as of April 2020)." + "github/DEIB-GECO/GeneNetFusion": { + "id": "github/DEIB-GECO/GeneNetFusion", + "title": "github/DEIB-GECO/GeneNetFusion", + "url": " https://rseng.github.io/software/repository/github/DEIB-GECO/GeneNetFusion", + "content": "None" }, - 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We welcome bug fixes and improvements. Note that most of the active developments are hosted on our https://gitlab.abinit.org/ server. Before embarking on making significant changes, please contact the Abinit group." + }, + "github/pavanvyn/triple-stability": { + "id": "github/pavanvyn/triple-stability", + "title": "github/pavanvyn/triple-stability", + "url": " https://rseng.github.io/software/repository/github/pavanvyn/triple-stability", + "content": "Code to check if a given configuration of a triple-star system is dynamically stable" }, - "github/veg/tn93": { - "id": "github/veg/tn93", - "title": "github/veg/tn93", - "url": " https://rseng.github.io/software/repository/github/veg/tn93", - "content": "TN93 fast distance calculator" + "github/mc-imperial/jfs": { + "id": "github/mc-imperial/jfs", + "title": "github/mc-imperial/jfs", + "url": " https://rseng.github.io/software/repository/github/mc-imperial/jfs", + "content": "Constraint solver based on coverage-guided fuzzing" }, - "github/wilkelab/Opfi": { - "id": "github/wilkelab/Opfi", - "title": "github/wilkelab/Opfi", - "url": " https://rseng.github.io/software/repository/github/wilkelab/Opfi", - "content": "A Python package for discovery, annotation, and analysis of gene clusters in genomics or metagenomics data sets." + "github/mc-imperial/gpuverify": { + "id": "github/mc-imperial/gpuverify", + "title": "github/mc-imperial/gpuverify", + "url": " https://rseng.github.io/software/repository/github/mc-imperial/gpuverify", + "content": "GPUVerify: a Verifier for GPU Kernels" }, - "github/XGI-MSU/WDMWaveletTransforms": { - "id": "github/XGI-MSU/WDMWaveletTransforms", - "title": "github/XGI-MSU/WDMWaveletTransforms", - "url": " https://rseng.github.io/software/repository/github/XGI-MSU/WDMWaveletTransforms", - "content": "None" + "github/mc-imperial/multicore-test-harness": { + "id": "github/mc-imperial/multicore-test-harness", + "title": "github/mc-imperial/multicore-test-harness", + "url": " https://rseng.github.io/software/repository/github/mc-imperial/multicore-test-harness", + "content": "A multicore microprocessor test harness for measuring interference" }, - "github/XGI-MSU/PyIMRPhenomD": { - "id": "github/XGI-MSU/PyIMRPhenomD", - "title": "github/XGI-MSU/PyIMRPhenomD", - "url": " https://rseng.github.io/software/repository/github/XGI-MSU/PyIMRPhenomD", - "content": "None" + "github/radis/radis": { + "id": "github/radis/radis", + "title": "github/radis/radis", + "url": " https://rseng.github.io/software/repository/github/radis/radis", + "content": "🌱 A fast line-by-line code for high-resolution infrared molecular spectra" }, - "github/FofanovLab/mtsv_tools": { - "id": "github/FofanovLab/mtsv_tools", - "title": "github/FofanovLab/mtsv_tools", - "url": " https://rseng.github.io/software/repository/github/FofanovLab/mtsv_tools", - "content": "Core metagenomic binning tools for mtsv" + "github/exobssim/rapoc-public": { + "id": "github/exobssim/rapoc-public", + "title": "github/exobssim/rapoc-public", + "url": " https://rseng.github.io/software/repository/github/exobssim/rapoc-public", + "content": "Rapoc uses molecular absorption measurements (i.e. wavelength-dependent opacities) to calculate Rosseland and Planck mean opacities that are commonly used in atmospheric modelling." }, - "github/klevis-a/kinematics-vis": { - "id": "github/klevis-a/kinematics-vis", - "title": "github/klevis-a/kinematics-vis", - "url": " https://rseng.github.io/software/repository/github/klevis-a/kinematics-vis", - "content": "JavaScript application for visualizing and analyzing shoulder joint kinematics" + "github/ryokbys/nap": { + "id": "github/ryokbys/nap", + "title": "github/ryokbys/nap", + "url": " https://rseng.github.io/software/repository/github/ryokbys/nap", + "content": "Nagoya Atomistic-simulation Package (NAP). Why don't you take a NAP? ;)" }, - "github/SysBioUAB/hpi_predictor": { - "id": "github/SysBioUAB/hpi_predictor", - "title": "github/SysBioUAB/hpi_predictor", - "url": " https://rseng.github.io/software/repository/github/SysBioUAB/hpi_predictor", - "content": "Bash+R tool to predict host-pathogen protein-protein interactions based on numerical encoding of physicochemical descriptors" + "github/XuhanLiu/DrugEx": { + "id": "github/XuhanLiu/DrugEx", + "title": "github/XuhanLiu/DrugEx", + "url": " https://rseng.github.io/software/repository/github/XuhanLiu/DrugEx", + "content": "Deep learning toolkit for Drug Design with Pareto-based Multi-Objective optimization in Polypharmacology" }, - "github/tidymess-code/tidymess": { - "id": "github/tidymess-code/tidymess", - "title": "github/tidymess-code/tidymess", - "url": " https://rseng.github.io/software/repository/github/tidymess-code/tidymess", - "content": "Tidal Dynamics of Multi-body ExtraSolar Systems" + "github/CRG-CNAG/anubis": { + "id": "github/CRG-CNAG/anubis", + "title": "github/CRG-CNAG/anubis", + "url": " https://rseng.github.io/software/repository/github/CRG-CNAG/anubis", + "content": "Python package for the analysis of tn-seq data" }, - "github/HaowenZhang/TRINITY": { - "id": "github/HaowenZhang/TRINITY", - "title": "github/HaowenZhang/TRINITY", - "url": " https://rseng.github.io/software/repository/github/HaowenZhang/TRINITY", - "content": "An empirical model that statistically connects dark matter halos, galaxies and supermassive black holes from z=0-10." + "github/jonas-fuchs/varVAMP": { + "id": "github/jonas-fuchs/varVAMP", + "title": "github/jonas-fuchs/varVAMP", + "url": " https://rseng.github.io/software/repository/github/jonas-fuchs/varVAMP", + "content": "Design degenerated primers on highly variable alignments for full genome sequencing or qPCR. Specifically developed for viruses." }, - "github/eldariont/svim": { - "id": "github/eldariont/svim", - "title": "github/eldariont/svim", - "url": " https://rseng.github.io/software/repository/github/eldariont/svim", - "content": "Structural Variant Identification Method using Long Reads" + "github/hpgem/nanomesh": { + "id": "github/hpgem/nanomesh", + "title": "github/hpgem/nanomesh", + "url": " https://rseng.github.io/software/repository/github/hpgem/nanomesh", + "content": "Python workflow tool for generating meshes from 2D and 3D microscopy image data" }, - "github/BasilioRuiz/SIR-code": { - "id": "github/BasilioRuiz/SIR-code", - "title": "github/BasilioRuiz/SIR-code", - "url": " https://rseng.github.io/software/repository/github/BasilioRuiz/SIR-code", - "content": "None" + "github/simonsobs/nemo": { + "id": "github/simonsobs/nemo", + "title": "github/simonsobs/nemo", + "url": " https://rseng.github.io/software/repository/github/simonsobs/nemo", + "content": "Millimeter-wave map filtering and Sunyaev-Zel'dovich galaxy cluster/source detection package. 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Supports computation on CPU and GPU." + "github/siavashk/pycpd": { + "id": "github/siavashk/pycpd", + "title": "github/siavashk/pycpd", + "url": " https://rseng.github.io/software/repository/github/siavashk/pycpd", + "content": "Pure Numpy Implementation of the Coherent Point Drift Algorithm" }, - "github/JuliaHCI/ADI.jl": { - "id": "github/JuliaHCI/ADI.jl", - "title": "github/JuliaHCI/ADI.jl", - "url": " https://rseng.github.io/software/repository/github/JuliaHCI/ADI.jl", - "content": "Algorithms for performing angular differential imaging (ADI)" + "github/0xCoto/Virgo": { + "id": "github/0xCoto/Virgo", + "title": "github/0xCoto/Virgo", + "url": " https://rseng.github.io/software/repository/github/0xCoto/Virgo", + "content": "📡 Virgo: A Versatile Spectrometer for Radio Astronomy" }, - "github/raufs/skDER": { - "id": "github/raufs/skDER", - "title": "github/raufs/skDER", - "url": " https://rseng.github.io/software/repository/github/raufs/skDER", - "content": "skDER: efficient & high-resolution dereplication of microbial genomes to select representatives for comparative genomics and metagenomics. 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It is built around the PyTorch machine learning framework, and uses automatic differentiation and (optional) GPU support to perform lightning fast optimisations of image models." }, - "github/liulizhi1996/HPODNets": { - "id": "github/liulizhi1996/HPODNets", - "title": "github/liulizhi1996/HPODNets", - "url": " https://rseng.github.io/software/repository/github/liulizhi1996/HPODNets", - "content": "HPODNets: deep graph convolutional networks for predicting human protein-phenotype associations" + "github/jtschindler/sculptor": { + "id": "github/jtschindler/sculptor", + "title": "github/jtschindler/sculptor", + "url": " https://rseng.github.io/software/repository/github/jtschindler/sculptor", + "content": "Sculptor - Interactive modeling of (electromagnetic) astronomical spectra." }, - "github/mcsiple/mmrefpoints": { - "id": "github/mcsiple/mmrefpoints", - "title": "github/mcsiple/mmrefpoints", - "url": " https://rseng.github.io/software/repository/github/mcsiple/mmrefpoints", - "content": "A package for simulating marine mammal abundance and calculating reference points." + "github/lmwalkowicz/Cheetah": { + "id": "github/lmwalkowicz/Cheetah", + "title": "github/lmwalkowicz/Cheetah", + "url": " https://rseng.github.io/software/repository/github/lmwalkowicz/Cheetah", + "content": "None" }, - "github/jean-pierreBoth/gsearch": { - "id": "github/jean-pierreBoth/gsearch", - "title": "github/jean-pierreBoth/gsearch", - "url": " https://rseng.github.io/software/repository/github/jean-pierreBoth/gsearch", - "content": "Approximate nearest neighbour search for microbial genomes based on hash metric" + "github/HAWinther/FML": { + "id": "github/HAWinther/FML", + "title": "github/HAWinther/FML", + "url": " https://rseng.github.io/software/repository/github/HAWinther/FML", + "content": "A C++ library for working with particles and grids in a parallel setting." }, - "github/MADHATdm/MADHAT": { - "id": "github/MADHATdm/MADHAT", - "title": "github/MADHATdm/MADHAT", - "url": " https://rseng.github.io/software/repository/github/MADHATdm/MADHAT", - "content": "Model-Agnostic Dark Halo Analysis Tool" + "github/HAWinther/MG-PICOLA-PUBLIC": { + "id": "github/HAWinther/MG-PICOLA-PUBLIC", + "title": "github/HAWinther/MG-PICOLA-PUBLIC", + "url": " https://rseng.github.io/software/repository/github/HAWinther/MG-PICOLA-PUBLIC", + "content": "This is a modified version of the L-PICOLA code extending the COLA approach for simulating cosmological structure formation to theories that exhibit scale-dependent growth. It can compute matter power-spectra (CDM and total), redshift-space multipole power-spectra P0,P2,P4 and do halofinding on the fly. 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A collection of code used to perform calculations use in Cosmology studies and written for GPUs. 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Extension packages are hosted by the MIRTK GitHub group at" + "github/scipy/scipy": { + "id": "github/scipy/scipy", + "title": "github/scipy/scipy", + "url": " https://rseng.github.io/software/repository/github/scipy/scipy", + "content": "Scipy library main repository" }, - "github/morispi/LRez": { - "id": "github/morispi/LRez", - "title": "github/morispi/LRez", - "url": " https://rseng.github.io/software/repository/github/morispi/LRez", - "content": "Standalone tool and library allowing to work with barcoded linked-reads" + "github/asancpt/caffsim": { + "id": "github/asancpt/caffsim", + "title": "github/asancpt/caffsim", + "url": " https://rseng.github.io/software/repository/github/asancpt/caffsim", + "content": "R package for simulation of caffeine concentration <doi:10.12793/tcp.2017.25.3.141>. https://asancpt.github.io/caffsim" }, - "github/egonw/bacting": { - "id": "github/egonw/bacting", - "title": "github/egonw/bacting", - "url": " https://rseng.github.io/software/repository/github/egonw/bacting", - "content": "Bacting := acting as the Bioclipse TNG" + "github/ahwkuepper/mcluster": { + "id": "github/ahwkuepper/mcluster", + "title": "github/ahwkuepper/mcluster", + "url": " https://rseng.github.io/software/repository/github/ahwkuepper/mcluster", + "content": "McLuster - a tool to make a star cluster" }, - "github/flyaflya/causact": { - "id": "github/flyaflya/causact", - "title": "github/flyaflya/causact", - "url": " https://rseng.github.io/software/repository/github/flyaflya/causact", - "content": "causact: R package to accelerate Bayesian analytics workflows." + "github/chakrah/sage": { + "id": "github/chakrah/sage", + "title": "github/chakrah/sage", + "url": " https://rseng.github.io/software/repository/github/chakrah/sage", + "content": "This code creates the stellar activity grid for exoplanets" }, - "github/a-griffiths/AutoSpec": { - "id": "github/a-griffiths/AutoSpec", - "title": "github/a-griffiths/AutoSpec", - "url": " https://rseng.github.io/software/repository/github/a-griffiths/AutoSpec", - "content": "Fast Automated Spectral Extraction Software for IFU Datacubes" + "github/vmmunoza/nuHawkHunter": { + "id": "github/vmmunoza/nuHawkHunter", + "title": "github/vmmunoza/nuHawkHunter", + "url": " https://rseng.github.io/software/repository/github/vmmunoza/nuHawkHunter", + "content": "Repository with forecast of PBH neutrinos" }, - "github/Zafiirah13/meercrab": { - "id": "github/Zafiirah13/meercrab", - "title": "github/Zafiirah13/meercrab", - "url": " https://rseng.github.io/software/repository/github/Zafiirah13/meercrab", - "content": "MeerLICHT Classification of Real And Bogus using deep learning" + "github/engyasin/Offline_MOT": { + "id": "github/engyasin/Offline_MOT", + "title": "github/engyasin/Offline_MOT", + "url": " https://rseng.github.io/software/repository/github/engyasin/Offline_MOT", + "content": "Multiple traffic entities detection and tracking from bird-view drone stationary videos https://engyasin.github.io/Offline_MOT/" + }, + "github/TRIQS/solid_dmft": { + "id": "github/TRIQS/solid_dmft", + "title": "github/TRIQS/solid_dmft", + "url": " https://rseng.github.io/software/repository/github/TRIQS/solid_dmft", + "content": "solid_dmft is a versatile python wrapper to perform DFT+DMFT calculations utilizing the TRIQS software library." }, - "github/single-cell-genetics/cellsnp-lite": { - "id": "github/single-cell-genetics/cellsnp-lite", - "title": "github/single-cell-genetics/cellsnp-lite", - "url": " https://rseng.github.io/software/repository/github/single-cell-genetics/cellsnp-lite", - "content": "Efficient genotyping bi-allelic SNPs on single cells" + "github/scotthgn/AGNvar": { + "id": "github/scotthgn/AGNvar", + "title": "github/scotthgn/AGNvar", + "url": " https://rseng.github.io/software/repository/github/scotthgn/AGNvar", + "content": "Python code for modelling spectral timing properties in AGN. Performs calculations of fully time-dependent SEDs following an input variable X-ray light-curve (See Hagen & Done (2023a)" }, - "github/shandley/hecatomb": { - "id": "github/shandley/hecatomb", - "title": "github/shandley/hecatomb", - "url": " https://rseng.github.io/software/repository/github/shandley/hecatomb", - "content": "hecatomb is a virome analysis pipeline for analysis of Illumina sequence data" + "github/scotthgn/relagn": { + "id": "github/scotthgn/relagn", + "title": "github/scotthgn/relagn", + "url": " https://rseng.github.io/software/repository/github/scotthgn/relagn", + "content": "AGN SED model based off AGNSED (Kubota & Done 2018), but taking into account full GR ray tracing. These relativistic correction are calculated by doing the convolution with the relativistic transfer code KYCONV (Dovciak, Karas & Yaqoob 2004) at each radial annulus" }, - "github/LTLA/basilisk": { - "id": "github/LTLA/basilisk", - "title": "github/LTLA/basilisk", - "url": " https://rseng.github.io/software/repository/github/LTLA/basilisk", - "content": "Clone of the Bioconductor repository for the basilisk package." + "github/mtazzari/binary": { + "id": "github/mtazzari/binary", + "title": "github/mtazzari/binary", + "url": " https://rseng.github.io/software/repository/github/mtazzari/binary", + "content": "This program computes the evolution of an accretion disc interacting with a binary system. Used in Tazzari, Lodato (2015)." }, - "github/LTLA/gesel.js": { - "id": "github/LTLA/gesel.js", - "title": "github/LTLA/gesel.js", - "url": " https://rseng.github.io/software/repository/github/LTLA/gesel.js", - "content": "Client-side gene set queries." + "github/mtazzari/uvplot": { + "id": "github/mtazzari/uvplot", + "title": "github/mtazzari/uvplot", + "url": " https://rseng.github.io/software/repository/github/mtazzari/uvplot", + "content": "A simple package to make nice visibility plots and to export visibilites from MS tables" }, - "github/a-renzini/pygwb": { - "id": "github/a-renzini/pygwb", - "title": "github/a-renzini/pygwb", - "url": " https://rseng.github.io/software/repository/github/a-renzini/pygwb", - "content": "None" + "github/mtazzari/galario": { + "id": "github/mtazzari/galario", + "title": "github/mtazzari/galario", + "url": " https://rseng.github.io/software/repository/github/mtazzari/galario", + "content": "Gpu Accelerated Library for Analysing Radio Interferometer Observations" }, - 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"github/garrelt/C2-Ray1D": { - "id": "github/garrelt/C2-Ray1D", - "title": "github/garrelt/C2-Ray1D", - "url": " https://rseng.github.io/software/repository/github/garrelt/C2-Ray1D", - "content": "1D version of C2-Ray" + "github/johnh2o2/cuvarbase": { + "id": "github/johnh2o2/cuvarbase", + "title": "github/johnh2o2/cuvarbase", + "url": " https://rseng.github.io/software/repository/github/johnh2o2/cuvarbase", + "content": "Python library for fast time-series analysis on CUDA GPUs" }, - "github/garrelt/C2-Ray3Dm1D_Helium": { - "id": "github/garrelt/C2-Ray3Dm1D_Helium", - "title": "github/garrelt/C2-Ray3Dm1D_Helium", - "url": " https://rseng.github.io/software/repository/github/garrelt/C2-Ray3Dm1D_Helium", - "content": "C2-Ray radiative transfer / photo-ionziation code, version with helium, combining 1D and 3D" + "github/IanHeywood/oxkat": { + "id": "github/IanHeywood/oxkat", + "title": "github/IanHeywood/oxkat", + "url": " https://rseng.github.io/software/repository/github/IanHeywood/oxkat", + "content": "MeerKAT calibration and imaging scripts" }, - "github/matthiasdemuzere/w2w": { - "id": "github/matthiasdemuzere/w2w", - "title": "github/matthiasdemuzere/w2w", - "url": " https://rseng.github.io/software/repository/github/matthiasdemuzere/w2w", - "content": "A python tool that ingests WUDAPT information into WRF." + "github/bruce-chappell/SunnyNet": { + "id": "github/bruce-chappell/SunnyNet", + "title": "github/bruce-chappell/SunnyNet", + "url": " https://rseng.github.io/software/repository/github/bruce-chappell/SunnyNet", + "content": "Repository for SunnyNet network" }, - "github/ranieremenezes/easyFermi": { - "id": "github/ranieremenezes/easyFermi", - "title": "github/ranieremenezes/easyFermi", - "url": " https://rseng.github.io/software/repository/github/ranieremenezes/easyFermi", - "content": "The easiest way to analyze Fermi-LAT data" + "github/optuna/optuna": { + "id": "github/optuna/optuna", + "title": "github/optuna/optuna", + "url": " https://rseng.github.io/software/repository/github/optuna/optuna", + "content": "A hyperparameter optimization framework" }, - "github/PrincetonUniversity/FastTemplatePeriodogram": { - "id": "github/PrincetonUniversity/FastTemplatePeriodogram", - "title": "github/PrincetonUniversity/FastTemplatePeriodogram", - "url": " https://rseng.github.io/software/repository/github/PrincetonUniversity/FastTemplatePeriodogram", - "content": "NlogN algorithm for least-squares fitting of periodic templates to noisy, non-equispaced time-series data." + "github/jluastro/PopSyCLE": { + "id": "github/jluastro/PopSyCLE", + "title": "github/jluastro/PopSyCLE", + "url": " https://rseng.github.io/software/repository/github/jluastro/PopSyCLE", + "content": "Population Synthesis for Compact-object Lensing Events" }, - "github/PrincetonUniversity/Athena-Cversion": { - "id": "github/PrincetonUniversity/Athena-Cversion", - "title": "github/PrincetonUniversity/Athena-Cversion", - "url": " https://rseng.github.io/software/repository/github/PrincetonUniversity/Athena-Cversion", - "content": "None" + "github/MiguelEA/nudec_BSM": { + "id": "github/MiguelEA/nudec_BSM", + "title": "github/MiguelEA/nudec_BSM", + "url": " https://rseng.github.io/software/repository/github/MiguelEA/nudec_BSM", + "content": "Neutrino Decoupling Beyond the Standard Model" }, - "github/PrincetonUniversity/athena": { - "id": "github/PrincetonUniversity/athena", - "title": "github/PrincetonUniversity/athena", - "url": " https://rseng.github.io/software/repository/github/PrincetonUniversity/athena", - "content": "Athena++ GRMHD code and adaptive mesh refinement (AMR) framework" + "github/lammps/lammps": { + "id": "github/lammps/lammps", + "title": "github/lammps/lammps", + "url": " https://rseng.github.io/software/repository/github/lammps/lammps", + "content": "Public development project of the LAMMPS MD software package " }, - "github/leprojetcastor/castor": { - "id": "github/leprojetcastor/castor", - "title": "github/leprojetcastor/castor", - "url": " https://rseng.github.io/software/repository/github/leprojetcastor/castor", - "content": "None" + "github/rust-bio/rust-bio-tools": { + "id": "github/rust-bio/rust-bio-tools", + "title": "github/rust-bio/rust-bio-tools", + "url": " https://rseng.github.io/software/repository/github/rust-bio/rust-bio-tools", + "content": "A set of command line utilities based on Rust-Bio." }, - "github/openmopac/MOPAC": { - "id": "github/openmopac/MOPAC", - "title": "github/openmopac/MOPAC", - "url": " https://rseng.github.io/software/repository/github/openmopac/MOPAC", - "content": "Molecular Orbital PACkage" + "github/rvaser/sword": { + "id": "github/rvaser/sword", + "title": "github/rvaser/sword", + "url": " https://rseng.github.io/software/repository/github/rvaser/sword", + "content": "SWORD - a highly efficient protein database search" }, - "github/nh13/DWGSIM": { - "id": "github/nh13/DWGSIM", - "title": "github/nh13/DWGSIM", - "url": " https://rseng.github.io/software/repository/github/nh13/DWGSIM", - "content": "a whole genome simulator for next-generation sequencing based off of wgsim found in SAMtools, which was written by Heng Li, and forked from DNAA. It was modified to handle ABI SOLiD and Ion Torrent data, as well as various assumptions about aligners and positions of indels. Many new features have been subsequently added." + "github/rvaser/bioparser": { + "id": "github/rvaser/bioparser", + "title": "github/rvaser/bioparser", + "url": " https://rseng.github.io/software/repository/github/rvaser/bioparser", + "content": "C++ library for parsing several formats in bioinformatics" }, - "github/jstjohn/SeqPrep": { - "id": "github/jstjohn/SeqPrep", - "title": "github/jstjohn/SeqPrep", - "url": " https://rseng.github.io/software/repository/github/jstjohn/SeqPrep", - "content": "Tool for stripping adaptors and/or merging paired reads with overlap into single reads." + "github/rvaser/rampler": { + "id": "github/rvaser/rampler", + "title": "github/rvaser/rampler", + "url": " https://rseng.github.io/software/repository/github/rvaser/rampler", + "content": "module for sampling genomic sequences" }, - "github/musevlt/muse-psfr": { - "id": "github/musevlt/muse-psfr", - "title": "github/musevlt/muse-psfr", - "url": " https://rseng.github.io/software/repository/github/musevlt/muse-psfr", - "content": "MUSE-PSFR - PSF reconstruction for MUSE WFM-AO" + "github/rvaser/thread_pool": { + "id": "github/rvaser/thread_pool", + "title": "github/rvaser/thread_pool", + "url": " https://rseng.github.io/software/repository/github/rvaser/thread_pool", + "content": "C++ thread pool library" }, - "github/musevlt/origin": { - "id": "github/musevlt/origin", - "title": "github/musevlt/origin", - "url": " https://rseng.github.io/software/repository/github/musevlt/origin", - "content": "ORIGIN: detectiOn and extRactIon of Galaxy emIssion liNes" + "github/rvaser/spoa": { + "id": "github/rvaser/spoa", + "title": "github/rvaser/spoa", + "url": " https://rseng.github.io/software/repository/github/rvaser/spoa", + "content": "SIMD partial order alignment tool/library" }, - "github/ymocquar/HOODESolver.jl": { - "id": "github/ymocquar/HOODESolver.jl", - "title": "github/ymocquar/HOODESolver.jl", - "url": " https://rseng.github.io/software/repository/github/ymocquar/HOODESolver.jl", - "content": "High Oscillatory Ordinary Differential Equation Solver (write in Julia language)" + "github/astromb/PICsar2D": { + "id": "github/astromb/PICsar2D", + "title": "github/astromb/PICsar2D", + "url": " https://rseng.github.io/software/repository/github/astromb/PICsar2D", + "content": "Particle In Cell pulSAR code" }, - "github/Pas-Kapli/mptp": { - "id": "github/Pas-Kapli/mptp", - "title": "github/Pas-Kapli/mptp", - "url": " https://rseng.github.io/software/repository/github/Pas-Kapli/mptp", - "content": "mPTP - a tool for single-locus species delimitation" + "github/PEREGRINE-GW/peregrine": { + "id": "github/PEREGRINE-GW/peregrine", + "title": "github/PEREGRINE-GW/peregrine", + "url": " https://rseng.github.io/software/repository/github/PEREGRINE-GW/peregrine", + "content": "A simulation-based Inference (SBI) library designed to perform analysis on a wide class of gravitational wave signals" }, - "github/brettc/partitionfinder": { - "id": "github/brettc/partitionfinder", - "title": "github/brettc/partitionfinder", - "url": " https://rseng.github.io/software/repository/github/brettc/partitionfinder", - "content": "PartitionFinder discovers optimal partitioning schemes for DNA sequences." + "github/ToyotaCRDL/mahos": { + "id": "github/ToyotaCRDL/mahos", + "title": "github/ToyotaCRDL/mahos", + "url": " https://rseng.github.io/software/repository/github/ToyotaCRDL/mahos", + "content": "Measurement Automation Handling and Orchestration System" }, - 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"id": "github/mwalmsley/zoobot", - "title": "github/mwalmsley/zoobot", - "url": " https://rseng.github.io/software/repository/github/mwalmsley/zoobot", - "content": "Classifies galaxy morphology with Bayesian CNN" + "github/mraveri/tensiometer": { + "id": "github/mraveri/tensiometer", + "title": "github/mraveri/tensiometer", + "url": " https://rseng.github.io/software/repository/github/mraveri/tensiometer", + "content": "None" }, - "github/christopherlovell/sengi": { - "id": "github/christopherlovell/sengi", - "title": "github/christopherlovell/sengi", - "url": " https://rseng.github.io/software/repository/github/christopherlovell/sengi", - "content": "A small, fast, interactive viewer for SPS spectral outputs" + "github/chocoteam/choco-solver": { + "id": "github/chocoteam/choco-solver", + "title": "github/chocoteam/choco-solver", + "url": " https://rseng.github.io/software/repository/github/chocoteam/choco-solver", + "content": "An open-source Java library for Constraint Programming" }, - 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OpenSMOG uses OpenMM." + "github/schochastics/netrankr": { + "id": "github/schochastics/netrankr", + "title": "github/schochastics/netrankr", + "url": " https://rseng.github.io/software/repository/github/schochastics/netrankr", + "content": "An R package for network centrality" }, - "github/aksholokhov/pysr3": { - "id": "github/aksholokhov/pysr3", - "title": "github/aksholokhov/pysr3", - "url": " https://rseng.github.io/software/repository/github/aksholokhov/pysr3", - "content": "SciKit-Learn compatible library for training mixed-effects models." + "github/schochastics/graphlayouts": { + "id": "github/schochastics/graphlayouts", + "title": "github/schochastics/graphlayouts", + "url": " https://rseng.github.io/software/repository/github/schochastics/graphlayouts", + "content": "new layout algorithms for network visualizations in R" }, - "github/widdowquinn/pyani": { - "id": "github/widdowquinn/pyani", - "title": "github/widdowquinn/pyani", - "url": " https://rseng.github.io/software/repository/github/widdowquinn/pyani", - "content": "Application and Python module for average nucleotide identity analyses of microbes." + "github/D-Crake/HEADSS": { + "id": "github/D-Crake/HEADSS", + "title": "github/D-Crake/HEADSS", + "url": " https://rseng.github.io/software/repository/github/D-Crake/HEADSS", + "content": "HiErArchical Data Splitting and Stitching Software for Non-Distributed Clustering Algorithms" }, - "github/IndrajeetPatil/ggstatsplot": { - "id": "github/IndrajeetPatil/ggstatsplot", - "title": "github/IndrajeetPatil/ggstatsplot", - "url": " https://rseng.github.io/software/repository/github/IndrajeetPatil/ggstatsplot", - "content": "Enhancing `ggplot2` plots with statistical analysis 📊🎨📣" + "github/ryanvarley/exodata": { + "id": "github/ryanvarley/exodata", + "title": "github/ryanvarley/exodata", + "url": " https://rseng.github.io/software/repository/github/ryanvarley/exodata", + "content": "Exoplanet catalogue interface and exploratory analysis tool" }, - "github/IndrajeetPatil/statsExpressions": { - 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(2012) http://adsabs.harvard.edu/abs/2012ApJ...751..157F" + "github/N-Wouda/ALNS": { + "id": "github/N-Wouda/ALNS", + "title": "github/N-Wouda/ALNS", + "url": " https://rseng.github.io/software/repository/github/N-Wouda/ALNS", + "content": "Adaptive large neighbourhood search (and more!) in Python." }, - "github/BGI-Qingdao/TGS-GapCloser": { - "id": "github/BGI-Qingdao/TGS-GapCloser", - "title": "github/BGI-Qingdao/TGS-GapCloser", - "url": " https://rseng.github.io/software/repository/github/BGI-Qingdao/TGS-GapCloser", - "content": "A gap-closing software tool that uses long reads to enhance genome assembly." + "github/Alymantara/pydoppler": { + "id": "github/Alymantara/pydoppler", + "title": "github/Alymantara/pydoppler", + "url": " https://rseng.github.io/software/repository/github/Alymantara/pydoppler", + "content": "A python wrapper for Henk Spruit's doppler tomography software" }, - "github/y-256/libdivsufsort": { - "id": "github/y-256/libdivsufsort", - "title": "github/y-256/libdivsufsort", - "url": " https://rseng.github.io/software/repository/github/y-256/libdivsufsort", - "content": "A lightweight suffix-sorting library" + "github/nsoranzo/sspace_basic": { + "id": "github/nsoranzo/sspace_basic", + "title": "github/nsoranzo/sspace_basic", + "url": " https://rseng.github.io/software/repository/github/nsoranzo/sspace_basic", + "content": "SSPACE Basic, SSAKE-based Scaffolding of Pre-Assembled Contigs after Extension" }, - "github/warrickball/tomso": { - "id": "github/warrickball/tomso", - "title": "github/warrickball/tomso", - "url": " https://rseng.github.io/software/repository/github/warrickball/tomso", - "content": "TOMSO (Tools for Models of Stars and their Oscillations) is a set of Python modules for loading and saving input and output files for and from stellar evolution and oscillation codes." + "github/dzesmin/TEA": { + "id": "github/dzesmin/TEA", + "title": "github/dzesmin/TEA", + "url": " https://rseng.github.io/software/repository/github/dzesmin/TEA", + "content": "Thermochemical Equilibrium Abundances (TEA), a code to calculate gaseous molecular abundances under thermochemical equilibrium conditions" }, - "github/mgm8/pyngham": { - "id": "github/mgm8/pyngham", - "title": "github/mgm8/pyngham", - "url": " https://rseng.github.io/software/repository/github/mgm8/pyngham", - "content": "Python library of the NGHam protocol" + "github/halomod/halomod": { + "id": "github/halomod/halomod", + "title": "github/halomod/halomod", + "url": " https://rseng.github.io/software/repository/github/halomod/halomod", + "content": "Python package for dealing with the Halo Model" }, - "github/nservant/HiC-Pro": { - "id": "github/nservant/HiC-Pro", - "title": "github/nservant/HiC-Pro", - "url": " https://rseng.github.io/software/repository/github/nservant/HiC-Pro", - "content": "HiC-Pro: An optimized and flexible pipeline for Hi-C data processing" + "github/halomod/hmf": { + "id": "github/halomod/hmf", + "title": "github/halomod/hmf", + "url": " https://rseng.github.io/software/repository/github/halomod/hmf", + "content": "Python halo mass function calculator" }, - "github/miRTop/mirtop": { - "id": "github/miRTop/mirtop", - "title": "github/miRTop/mirtop", - "url": " https://rseng.github.io/software/repository/github/miRTop/mirtop", - "content": "command lines tool to annotate miRNAs with a standard mirna/isomir naming" + "github/miracum/ahd2fhir": { + "id": "github/miracum/ahd2fhir", + "title": "github/miracum/ahd2fhir", + "url": " https://rseng.github.io/software/repository/github/miracum/ahd2fhir", + "content": "A REST service for mapping text analysis results from Averbis Health Discovery to FHIR resources." }, - "github/khyox/recentrifuge": { - "id": "github/khyox/recentrifuge", - "title": "github/khyox/recentrifuge", - "url": " https://rseng.github.io/software/repository/github/khyox/recentrifuge", - "content": "Recentrifuge: robust comparative analysis and contamination removal for metagenomics" + "github/alexriss/SpmImageTycoon.jl": { + "id": "github/alexriss/SpmImageTycoon.jl", + "title": "github/alexriss/SpmImageTycoon.jl", + "url": " https://rseng.github.io/software/repository/github/alexriss/SpmImageTycoon.jl", + "content": "Organize Scanning Probe Microscopy (SPM, STM, AFM) Images and Spectra." }, "github/MikeHeiber/Excimontec": { "id": "github/MikeHeiber/Excimontec", @@ -8733,137 +8007,125 @@ "url": " https://rseng.github.io/software/repository/github/MikeHeiber/Excimontec", "content": "Excimontec is an open-source KMC simulation software package for modeling the optoelectronic processes in organic semiconductor materials and devices, such as OPVs, OLEDs, and more. 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"content": "paper for JOSS on pagmo and pygmo" + "github/mr-superonion/FPFS": { + "id": "github/mr-superonion/FPFS", + "title": "github/mr-superonion/FPFS", + "url": " https://rseng.github.io/software/repository/github/mr-superonion/FPFS", + "content": "A fast, accurate estimator for small shear distortion." }, - "github/esa/NIDN": { - "id": "github/esa/NIDN", - "title": "github/esa/NIDN", - "url": " https://rseng.github.io/software/repository/github/esa/NIDN", - "content": "Neural Inverse Design of Nanostructures" + "github/EoRImaging/FHD": { + "id": "github/EoRImaging/FHD", + "title": "github/EoRImaging/FHD", + "url": " https://rseng.github.io/software/repository/github/EoRImaging/FHD", + "content": "Fast Holographic Deconvolution" }, - "github/wangsiwei2010/FPMVS-CAG": { - "id": "github/wangsiwei2010/FPMVS-CAG", - "title": "github/wangsiwei2010/FPMVS-CAG", - "url": " https://rseng.github.io/software/repository/github/wangsiwei2010/FPMVS-CAG", - "content": "code of "Fast Parameter-free Multi-view Subspace Clustering with Consensus Anchor Guidance " published in IEEE TIP2022" + "github/labxscut/ksak": { + "id": "github/labxscut/ksak", + "title": "github/labxscut/ksak", + "url": " https://rseng.github.io/software/repository/github/labxscut/ksak", + "content": "None" }, - 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Includes also a binary version of the command line interface." + "github/rx-li/EasyCellType": { + "id": "github/rx-li/EasyCellType", + "title": "github/rx-li/EasyCellType", + "url": " https://rseng.github.io/software/repository/github/rx-li/EasyCellType", + "content": "None" }, - "github/JoeMcEwen/FAST-PT": { - "id": "github/JoeMcEwen/FAST-PT", - "title": "github/JoeMcEwen/FAST-PT", - "url": " https://rseng.github.io/software/repository/github/JoeMcEwen/FAST-PT", + "github/cns-iu/HRA-supporting-information": { + "id": "github/cns-iu/HRA-supporting-information", + "title": "github/cns-iu/HRA-supporting-information", + "url": " https://rseng.github.io/software/repository/github/cns-iu/HRA-supporting-information", "content": "None" }, - "github/FabianPlum/OmniTrax": { - "id": "github/FabianPlum/OmniTrax", - "title": "github/FabianPlum/OmniTrax", - "url": " https://rseng.github.io/software/repository/github/FabianPlum/OmniTrax", - "content": "Deep learning-driven multi animal tracking and pose estimation add-on for Blender" + "github/KolmogorovLab/Severus": { + "id": "github/KolmogorovLab/Severus", + "title": "github/KolmogorovLab/Severus", + "url": " https://rseng.github.io/software/repository/github/KolmogorovLab/Severus", + "content": "A tool for somatic structural variant calling using long reads" }, - "github/highamm/sptotal": { - "id": "github/highamm/sptotal", - "title": "github/highamm/sptotal", - "url": " https://rseng.github.io/software/repository/github/highamm/sptotal", - "content": "Package for Fitting Spatial Linear Models and Predicting Total Abundances for Finite Populations" + "github/chenwuperth/rgz_rcnn": { + "id": "github/chenwuperth/rgz_rcnn", + "title": "github/chenwuperth/rgz_rcnn", + "url": " https://rseng.github.io/software/repository/github/chenwuperth/rgz_rcnn", + "content": "ClaRAN: A deep learning classifier for radio morphologies" }, - "github/sensein/etelemetry-client": { - "id": "github/sensein/etelemetry-client", - "title": "github/sensein/etelemetry-client", - "url": " https://rseng.github.io/software/repository/github/sensein/etelemetry-client", - "content": "Etelemetry client" + "github/ablab/TandemTools": { + "id": "github/ablab/TandemTools", + "title": "github/ablab/TandemTools", + "url": " https://rseng.github.io/software/repository/github/ablab/TandemTools", + "content": "Tool for assessing/improving assembly quality in extra-long tandem repeats" }, - "github/deeptools/HiCExplorer": { - "id": "github/deeptools/HiCExplorer", - "title": "github/deeptools/HiCExplorer", - "url": " https://rseng.github.io/software/repository/github/deeptools/HiCExplorer", - "content": "HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data." + "github/ablab/spades": { + "id": "github/ablab/spades", + "title": "github/ablab/spades", + "url": " https://rseng.github.io/software/repository/github/ablab/spades", + "content": "SPAdes Genome Assembler" }, - "github/deeptools/deeptools_intervals": { - "id": "github/deeptools/deeptools_intervals", - "title": "github/deeptools/deeptools_intervals", - "url": " https://rseng.github.io/software/repository/github/deeptools/deeptools_intervals", - "content": "A python library for constructing interval trees with associated exon/annotation information" + "github/ablab/nerpa": { + "id": "github/ablab/nerpa", + "title": "github/ablab/nerpa", + "url": " https://rseng.github.io/software/repository/github/ablab/nerpa", + "content": "None" }, - "github/deeptools/deepTools": { - "id": "github/deeptools/deepTools", - "title": "github/deeptools/deepTools", - "url": " https://rseng.github.io/software/repository/github/deeptools/deepTools", - "content": "a suite of python tools particularly developed for the efficient analysis of high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq. deepTools contains useful modules to process the mapped reads data for multiple quality checks, creating normalized coverage files in standard bedGraph and bigWig file formats, that allow comparison between different files (for example, treatment and control). Finally, using such normalized and standardized files, …" + "github/GBLille/MassiveFold": { + "id": "github/GBLille/MassiveFold", + "title": "github/GBLille/MassiveFold", + "url": " https://rseng.github.io/software/repository/github/GBLille/MassiveFold", + "content": "None" }, - "github/deeptools/py2bit": { - "id": "github/deeptools/py2bit", - "title": "github/deeptools/py2bit", - "url": " https://rseng.github.io/software/repository/github/deeptools/py2bit", - "content": "A python library for accessing 2bit files" + "github/dixonlab/hic_breakfinder": { + "id": "github/dixonlab/hic_breakfinder", + "title": "github/dixonlab/hic_breakfinder", + "url": " https://rseng.github.io/software/repository/github/dixonlab/hic_breakfinder", + "content": "a framework that integrates optical mapping, high-throughput chromosome conformation capture (Hi-C), and whole genome sequencing to systematically detect SVs in a variety of normal or cancer samples and cell lines." }, - "github/tinglabs/scAIDE": { - "id": "github/tinglabs/scAIDE", - "title": "github/tinglabs/scAIDE", - "url": " https://rseng.github.io/software/repository/github/tinglabs/scAIDE", + "github/OPUS-MaLab/opus_fold3": { + "id": "github/OPUS-MaLab/opus_fold3", + "title": "github/OPUS-MaLab/opus_fold3", + "url": " https://rseng.github.io/software/repository/github/OPUS-MaLab/opus_fold3", "content": "None" }, - "github/wesleyburr/subMaldi": { - "id": "github/wesleyburr/subMaldi", - "title": "github/wesleyburr/subMaldi", - "url": " https://rseng.github.io/software/repository/github/wesleyburr/subMaldi", - "content": "subMaldi: a package for R" + "github/MIT-STARLab/deconfuser": { + "id": "github/MIT-STARLab/deconfuser", + "title": "github/MIT-STARLab/deconfuser", + "url": " https://rseng.github.io/software/repository/github/MIT-STARLab/deconfuser", + "content": "Fast orbit fitting to directly imaged multi-planetary systems" + }, + "github/ksahlin/strobealign": { + "id": "github/ksahlin/strobealign", + "title": "github/ksahlin/strobealign", + "url": " https://rseng.github.io/software/repository/github/ksahlin/strobealign", + "content": "Aligns short reads using dynamic seed size with strobemers" }, "github/leapigufpb/FuzzyClass": { "id": "github/leapigufpb/FuzzyClass", @@ -8871,971 +8133,977 @@ "url": " https://rseng.github.io/software/repository/github/leapigufpb/FuzzyClass", "content": "None" }, - "github/jdcphysics/validation": { - "id": "github/jdcphysics/validation", - "title": "github/jdcphysics/validation", - "url": " https://rseng.github.io/software/repository/github/jdcphysics/validation", - "content": "codes to compare simulation data to various observations" - }, - "github/tamarervin/SolAster": { - "id": "github/tamarervin/SolAster", - "title": "github/tamarervin/SolAster", - "url": " https://rseng.github.io/software/repository/github/tamarervin/SolAster", - "content": "Python package to independently derive 'Sun-as-a-star' radial velocity variations." - }, - "github/mattpitkin/psrqpy": { - "id": "github/mattpitkin/psrqpy", - "title": "github/mattpitkin/psrqpy", - "url": " https://rseng.github.io/software/repository/github/mattpitkin/psrqpy", - "content": "A python module to query the ATNF pulsar catalogue" - }, - "github/mattpitkin/lintegrate": { - "id": "github/mattpitkin/lintegrate", - "title": "github/mattpitkin/lintegrate", - "url": " https://rseng.github.io/software/repository/github/mattpitkin/lintegrate", - "content": "A numerical integration routine that works for the natural logarithm of functions " - }, - "github/Kingsford-Group/scallop": { - "id": "github/Kingsford-Group/scallop", - "title": "github/Kingsford-Group/scallop", - "url": " https://rseng.github.io/software/repository/github/Kingsford-Group/scallop", - "content": "Scallop is a reference-based transcriptome assembler for RNA-seq" + "github/lucaborsato/trades": { + "id": "github/lucaborsato/trades", + "title": "github/lucaborsato/trades", + "url": " https://rseng.github.io/software/repository/github/lucaborsato/trades", + "content": "Fortran90 code for the orbital simulation of exoplanetary system with simultaneous fit of Transit Times and Radial Velocities. " }, - "github/ejmackrell/tidyproteomics-interactive": { - "id": "github/ejmackrell/tidyproteomics-interactive", - "title": "github/ejmackrell/tidyproteomics-interactive", - "url": " https://rseng.github.io/software/repository/github/ejmackrell/tidyproteomics-interactive", - "content": "Interactive Shiny application for tidyproteomics" + "github/kjschmidlab/GGoutlieR": { + "id": "github/kjschmidlab/GGoutlieR", + "title": "github/kjschmidlab/GGoutlieR", + "url": " https://rseng.github.io/software/repository/github/kjschmidlab/GGoutlieR", + "content": "None" }, - "github/NeoGeographyToolkit/StereoPipeline": { - "id": "github/NeoGeographyToolkit/StereoPipeline", - "title": "github/NeoGeographyToolkit/StereoPipeline", - "url": " https://rseng.github.io/software/repository/github/NeoGeographyToolkit/StereoPipeline", - "content": "The NASA Ames Stereo Pipeline is a suite of automated geodesy & stereogrammetry tools designed for processing planetary imagery captured from orbiting and landed robotic explorers on other planets." + "github/jameschapman19/cca_zoo": { + "id": "github/jameschapman19/cca_zoo", + "title": "github/jameschapman19/cca_zoo", + "url": " https://rseng.github.io/software/repository/github/jameschapman19/cca_zoo", + "content": "Canonical Correlation Analysis Zoo: A collection of Regularized, Deep Learning based, Kernel, and Probabilistic methods in a scikit-learn style framework" }, - "github/tibordome/cosmic_profiles": { - "id": "github/tibordome/cosmic_profiles", - "title": "github/tibordome/cosmic_profiles", - "url": " https://rseng.github.io/software/repository/github/tibordome/cosmic_profiles", - "content": "Implements 3D point cloud algorithms for estimation and fitting of shape and density profiles" + "github/EdanRein/pyPplusS": { + "id": "github/EdanRein/pyPplusS", + "title": "github/EdanRein/pyPplusS", + "url": " https://rseng.github.io/software/repository/github/EdanRein/pyPplusS", + "content": "pyPplusS code package for modeling exoplanets with rings" }, - "github/arjunsavel/SImMER": { - "id": "github/arjunsavel/SImMER", - "title": "github/arjunsavel/SImMER", - "url": " https://rseng.github.io/software/repository/github/arjunsavel/SImMER", - "content": "An open-source & modular reduction pipeline for astronomical images of point sources." + "github/sdss/marvin": { + "id": "github/sdss/marvin", + "title": "github/sdss/marvin", + "url": " https://rseng.github.io/software/repository/github/sdss/marvin", + "content": "Data access and visualization for MaNGA. http://sdss-marvin.readthedocs.io/en/latest/" }, - "github/FastMLC/fMLC": { - "id": "github/FastMLC/fMLC", - "title": "github/FastMLC/fMLC", - "url": " https://rseng.github.io/software/repository/github/FastMLC/fMLC", - "content": "None" + "github/pni-lab/mlconfound": { + "id": "github/pni-lab/mlconfound", + "title": "github/pni-lab/mlconfound", + "url": " https://rseng.github.io/software/repository/github/pni-lab/mlconfound", + "content": "Tools for analyzing and quantifying effects of counfounder variables on machine learning model predictions." }, - "github/pyspeckit/pyspeckit": { - "id": "github/pyspeckit/pyspeckit", - "title": "github/pyspeckit/pyspeckit", - "url": " https://rseng.github.io/software/repository/github/pyspeckit/pyspeckit", - "content": "Python Spectroscopic Toolkit" + "github/cwru-pat/cosmograph": { + "id": "github/cwru-pat/cosmograph", + "title": "github/cwru-pat/cosmograph", + "url": " https://rseng.github.io/software/repository/github/cwru-pat/cosmograph", + "content": "COSMOlogical General Relativity And (Perfect fluid | Particle) Hydrodynamics" }, - 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tool" }, - "github/JuliaMatrices/BandedMatrices.jl": { - "id": "github/JuliaMatrices/BandedMatrices.jl", - "title": "github/JuliaMatrices/BandedMatrices.jl", - "url": " https://rseng.github.io/software/repository/github/JuliaMatrices/BandedMatrices.jl", - "content": "A Julia package for representing banded matrices" + "github/thegenemyers/DEXTRACTOR": { + "id": "github/thegenemyers/DEXTRACTOR", + "title": "github/thegenemyers/DEXTRACTOR", + "url": " https://rseng.github.io/software/repository/github/thegenemyers/DEXTRACTOR", + "content": "bax file decoder and data compressor." }, - "github/MonashSmartStructures/ospgrillage": { - "id": "github/MonashSmartStructures/ospgrillage", - "title": "github/MonashSmartStructures/ospgrillage", - "url": " https://rseng.github.io/software/repository/github/MonashSmartStructures/ospgrillage", - "content": "`ospgrillage` is a package that wraps `OpenSeesPy` with an interface dedicated to the development and analysis of regular bridge deck grillage models." + "github/thegenemyers/DALIGNER": { + "id": "github/thegenemyers/DALIGNER", + "title": "github/thegenemyers/DALIGNER", + "url": " https://rseng.github.io/software/repository/github/thegenemyers/DALIGNER", + "content": "finds all significant local alignments between reads." }, - "github/vallis/libstempo": { - "id": "github/vallis/libstempo", - "title": "github/vallis/libstempo", - "url": " https://rseng.github.io/software/repository/github/vallis/libstempo", - "content": "libstempo — a Python wrapper for tempo2" + "github/thegenemyers/DAMAPPER": { + "id": "github/thegenemyers/DAMAPPER", + "title": "github/thegenemyers/DAMAPPER", + "url": " https://rseng.github.io/software/repository/github/thegenemyers/DAMAPPER", + "content": "Long read to reference genome mapping tool" }, - "github/vallis/mc3pta": { - "id": "github/vallis/mc3pta", - "title": "github/vallis/mc3pta", - "url": " https://rseng.github.io/software/repository/github/vallis/mc3pta", - "content": "Bayesian-inference tools for pulsar-timing-array data" + "github/thegenemyers/DAZZ_DB": { + "id": "github/thegenemyers/DAZZ_DB", + "title": "github/thegenemyers/DAZZ_DB", + "url": " https://rseng.github.io/software/repository/github/thegenemyers/DAZZ_DB", + "content": "The Dazzler Data Base" }, - "github/Muhammad-Arif-NUST/BVP_Pred_Unb": { - "id": "github/Muhammad-Arif-NUST/BVP_Pred_Unb", - "title": "github/Muhammad-Arif-NUST/BVP_Pred_Unb", - "url": " https://rseng.github.io/software/repository/github/Muhammad-Arif-NUST/BVP_Pred_Unb", - "content": "None" + "github/aberer/RogueNaRok": { + "id": "github/aberer/RogueNaRok", + "title": "github/aberer/RogueNaRok", + "url": " https://rseng.github.io/software/repository/github/aberer/RogueNaRok", + "content": "A versatile and scalable algorithm for rogue taxon identification. Also includes implementations of the maximum agreement subtree, leaf stability index and taxonomic instability index" }, - "github/agnetelundgaard/BALDR": { - "id": "github/agnetelundgaard/BALDR", - "title": "github/agnetelundgaard/BALDR", - "url": " https://rseng.github.io/software/repository/github/agnetelundgaard/BALDR", - "content": "None" + "github/egonw/bacting": { + "id": "github/egonw/bacting", + "title": "github/egonw/bacting", + "url": " https://rseng.github.io/software/repository/github/egonw/bacting", + "content": "Bacting := acting as the Bioclipse TNG" }, - "github/ukoethe/vigra": { - "id": "github/ukoethe/vigra", - "title": "github/ukoethe/vigra", - "url": " https://rseng.github.io/software/repository/github/ukoethe/vigra", - "content": "a generic C++ library for image analysis" + "github/bio-phys/BioEn": { + "id": "github/bio-phys/BioEn", + "title": "github/bio-phys/BioEn", + "url": " https://rseng.github.io/software/repository/github/bio-phys/BioEn", + "content": "BioEn - Bayesian Inference Of ENsembles" }, - "github/jonas-fuchs/varVAMP": { - "id": "github/jonas-fuchs/varVAMP", - "title": "github/jonas-fuchs/varVAMP", - "url": " https://rseng.github.io/software/repository/github/jonas-fuchs/varVAMP", - "content": "Design degenerated primers on highly variable alignments for full genome sequencing or qPCR. Specifically developed for viruses." + "github/brian-team/brian2": { + "id": "github/brian-team/brian2", + "title": "github/brian-team/brian2", + "url": " https://rseng.github.io/software/repository/github/brian-team/brian2", + "content": "Brian is a free, open source simulator for spiking neural networks. " }, - "github/sonny-harman/snowball": { - "id": "github/sonny-harman/snowball", - "title": "github/sonny-harman/snowball", - "url": " https://rseng.github.io/software/repository/github/sonny-harman/snowball", - "content": "Generalizable atmospheric mass loss calculator" + "github/samhforbes/PupillometryR": { + "id": "github/samhforbes/PupillometryR", + "title": "github/samhforbes/PupillometryR", + "url": " https://rseng.github.io/software/repository/github/samhforbes/PupillometryR", + "content": "An R package for preparing and analysing pupillometry data" }, - "github/chanzuckerberg/idseq-dag": { - "id": "github/chanzuckerberg/idseq-dag", - "title": "github/chanzuckerberg/idseq-dag", - "url": " https://rseng.github.io/software/repository/github/chanzuckerberg/idseq-dag", - "content": "Please see https://github.com/chanzuckerberg/czid-workflows for the latest version of CZ ID workflows." + "github/dsavransky/EXOSIMS": { + "id": "github/dsavransky/EXOSIMS", + "title": "github/dsavransky/EXOSIMS", + "url": " https://rseng.github.io/software/repository/github/dsavransky/EXOSIMS", + "content": "Simulator for exoplanet direct imaging space missions" }, - "github/chanzuckerberg/shasta": { - "id": "github/chanzuckerberg/shasta", - "title": "github/chanzuckerberg/shasta", - "url": " https://rseng.github.io/software/repository/github/chanzuckerberg/shasta", - "content": "De novo assembly from Oxford Nanopore reads." + "github/mlegr/EqualISER": { + "id": "github/mlegr/EqualISER", + "title": "github/mlegr/EqualISER", + "url": " https://rseng.github.io/software/repository/github/mlegr/EqualISER", + "content": "None" }, - "github/chanzuckerberg/cellxgene": { - "id": "github/chanzuckerberg/cellxgene", - "title": "github/chanzuckerberg/cellxgene", - "url": " https://rseng.github.io/software/repository/github/chanzuckerberg/cellxgene", - "content": "an interactive explorer for single-cell transcriptomics data" + "github/dgobbi/vtk-dicom": { + "id": "github/dgobbi/vtk-dicom", + "title": "github/dgobbi/vtk-dicom", + "url": " https://rseng.github.io/software/repository/github/dgobbi/vtk-dicom", + "content": "A set of classes for using DICOM in VTK." }, - "github/QibangLiu/PDLSM-FEM_mpi": { - "id": "github/QibangLiu/PDLSM-FEM_mpi", - "title": "github/QibangLiu/PDLSM-FEM_mpi", - "url": " https://rseng.github.io/software/repository/github/QibangLiu/PDLSM-FEM_mpi", - "content": "PDLSM-FEM solver is a parallel implementation of (adaptively) coupled peridynamics least squares minimization and finite element method (PDLSM-FEM) in 2D and 3D using MPI parallelism. This cross-platform solver is written in a C++ language and includes implicit static, explicit dynamic, and implicit dynamic solvers for structure analysis under displacement or traction loading." + "github/alicia-ziying-yang/conTEXT-explorer": { + "id": "github/alicia-ziying-yang/conTEXT-explorer", + "title": "github/alicia-ziying-yang/conTEXT-explorer", + "url": " https://rseng.github.io/software/repository/github/alicia-ziying-yang/conTEXT-explorer", + "content": "ConTEXT Explorer is an open Web-based system for exploring and visualizing concepts (combinations of occurring words and phrases) over time in the text documents." }, - "github/dalya/WeirdestGalaxies": { - "id": "github/dalya/WeirdestGalaxies", - "title": "github/dalya/WeirdestGalaxies", - "url": " https://rseng.github.io/software/repository/github/dalya/WeirdestGalaxies", - "content": "This repository contains the basic outlier detection algorithm that we use to find the weirdest SDSS galaxies." + "github/taranu/AllStarFit": { + "id": "github/taranu/AllStarFit", + "title": "github/taranu/AllStarFit", + "url": " https://rseng.github.io/software/repository/github/taranu/AllStarFit", + "content": "Experimental R package for source detection, PSF and multi-component galaxy fitting" }, - "github/tronsgaard/barycorr": { - "id": "github/tronsgaard/barycorr", - "title": "github/tronsgaard/barycorr", - "url": " https://rseng.github.io/software/repository/github/tronsgaard/barycorr", - "content": "Python interface for barycentric correction web applets" + "github/SchmollerLab/Cell_ACDC": { + "id": "github/SchmollerLab/Cell_ACDC", + "title": "github/SchmollerLab/Cell_ACDC", + "url": " https://rseng.github.io/software/repository/github/SchmollerLab/Cell_ACDC", + "content": "A Python GUI-based framework for segmentation, tracking and cell cycle annotations of micrscopy data" }, - "github/GregoryFaust/samblaster": { - "id": "github/GregoryFaust/samblaster", - "title": "github/GregoryFaust/samblaster", - "url": " https://rseng.github.io/software/repository/github/GregoryFaust/samblaster", - "content": "samblaster: a tool to mark duplicates and extract discordant and split reads from sam files." + "github/casacore/casacore": { + "id": "github/casacore/casacore", + "title": "github/casacore/casacore", + "url": " https://rseng.github.io/software/repository/github/casacore/casacore", + "content": "Suite of C++ libraries for radio astronomy data processing" }, - "github/GregoryFaust/yaha": { - "id": "github/GregoryFaust/yaha", - "title": "github/GregoryFaust/yaha", - "url": " https://rseng.github.io/software/repository/github/GregoryFaust/yaha", - "content": "yaha: a flexible, sensitive and accurate DNA alignment tool designed to find optimal split-read mappings on single-end queries from 100bp to 32kb." + "github/Ramialison-Lab-ARMI/3DCardiomics": { + "id": "github/Ramialison-Lab-ARMI/3DCardiomics", + "title": "github/Ramialison-Lab-ARMI/3DCardiomics", + "url": " https://rseng.github.io/software/repository/github/Ramialison-Lab-ARMI/3DCardiomics", + "content": "A visual system for the exploration of cardiac transcriptome data" }, - "github/QingyuLiaib/PLA-MoRe": { - "id": "github/QingyuLiaib/PLA-MoRe", - "title": "github/QingyuLiaib/PLA-MoRe", - "url": " https://rseng.github.io/software/repository/github/QingyuLiaib/PLA-MoRe", - "content": "None" + "github/jstuecker/adiabatic-tides": { + "id": "github/jstuecker/adiabatic-tides", + "title": "github/jstuecker/adiabatic-tides", + "url": " https://rseng.github.io/software/repository/github/jstuecker/adiabatic-tides", + "content": "Code for evaluating the tidal stripping of dark matter (sub)haloes in the adiabatic limit" }, - "github/mindearth/mobilkit": { - "id": "github/mindearth/mobilkit", - "title": "github/mindearth/mobilkit", - "url": " https://rseng.github.io/software/repository/github/mindearth/mobilkit", - "content": "A Python Toolkit for Urban Resilience and Disaster Risk Management Analytics using High Frequency Human Mobility Data" + "github/wesleyburr/subMaldi": { + "id": "github/wesleyburr/subMaldi", + "title": "github/wesleyburr/subMaldi", + "url": " https://rseng.github.io/software/repository/github/wesleyburr/subMaldi", + "content": "subMaldi: a package for R" }, - "github/daiqile96/OTTERS_paper": { - "id": "github/daiqile96/OTTERS_paper", - "title": "github/daiqile96/OTTERS_paper", - "url": " https://rseng.github.io/software/repository/github/daiqile96/OTTERS_paper", - "content": "None" + "github/mary77/scQcut": { + "id": "github/mary77/scQcut", + "title": "github/mary77/scQcut", + "url": " https://rseng.github.io/software/repository/github/mary77/scQcut", + "content": "A completely parameter-free method for graph-based single cell RNA-seq clustering" }, - "github/PopMedNet-Team/popmednet": { - "id": "github/PopMedNet-Team/popmednet", - "title": "github/PopMedNet-Team/popmednet", - "url": " https://rseng.github.io/software/repository/github/PopMedNet-Team/popmednet", - "content": "This is the repository for the open source code of the distributed data network platform PopMedNet" + "github/arhstevens/DarkSage": { + "id": "github/arhstevens/DarkSage", + "title": "github/arhstevens/DarkSage", + "url": " https://rseng.github.io/software/repository/github/arhstevens/DarkSage", + "content": "The Dark Sage semi-analytic model" }, - "github/sbird/fake_spectra": { - "id": "github/sbird/fake_spectra", - "title": "github/sbird/fake_spectra", - "url": " https://rseng.github.io/software/repository/github/sbird/fake_spectra", - "content": "A code for generating fake spectra from a cosmological simulation" + "github/ocxtal/minialign": { + "id": "github/ocxtal/minialign", + "title": "github/ocxtal/minialign", + "url": " https://rseng.github.io/software/repository/github/ocxtal/minialign", + "content": "[IMPORTANT: not for real data analysis, only for algorithm evaluation] fast and accurate alignment tool for PacBio and Nanopore long reads" }, - "github/sbird/GenPK": { - "id": "github/sbird/GenPK", - "title": "github/sbird/GenPK", - "url": " https://rseng.github.io/software/repository/github/sbird/GenPK", - "content": "Program for finding the matter power spectrum from Gadget format files. Uses FFTW3 and GadgetReader." + "github/pierrepo/autoclassweb": { + "id": "github/pierrepo/autoclassweb", + "title": "github/pierrepo/autoclassweb", + "url": " https://rseng.github.io/software/repository/github/pierrepo/autoclassweb", + "content": "AutoClassWeb: a web app to run AutoClass C Bayesian clustering :package: :rocket:" }, - "github/DavidT3/XGA": { - "id": "github/DavidT3/XGA", - "title": "github/DavidT3/XGA", - "url": " https://rseng.github.io/software/repository/github/DavidT3/XGA", - "content": "X-ray: Generate and Analyse is a module designed to make the analysis of XMM observations simple and efficient. It provides an interface with SAS for the creation of XMM data products, as well as a way to easily perform fits (scalable for multiple observations) and retrieve information about an object, all within a Python package. " + "github/rvalieris/parallel-fastq-dump": { + "id": "github/rvalieris/parallel-fastq-dump", + "title": "github/rvalieris/parallel-fastq-dump", + "url": " https://rseng.github.io/software/repository/github/rvalieris/parallel-fastq-dump", + "content": "parallel fastq-dump wrapper" }, - "github/FireflySpectra/firefly_release": { - "id": "github/FireflySpectra/firefly_release", - "title": "github/FireflySpectra/firefly_release", - "url": " https://rseng.github.io/software/repository/github/FireflySpectra/firefly_release", - "content": "Firefly, a full spectral fitting code. This repository contains the main code and examples on how to use it." + "github/maho3/ltu-ili": { + "id": "github/maho3/ltu-ili", + "title": "github/maho3/ltu-ili", + "url": " https://rseng.github.io/software/repository/github/maho3/ltu-ili", + "content": "Robust ML in Astro" }, - "github/amiralih/MembraneAnalysis.jl": { - "id": "github/amiralih/MembraneAnalysis.jl", - "title": "github/amiralih/MembraneAnalysis.jl", - "url": " https://rseng.github.io/software/repository/github/amiralih/MembraneAnalysis.jl", - "content": "A package for analyzing molecular dynamics simulations of lipid membranes" + "github/hanyue36/nanoplexer": { + "id": "github/hanyue36/nanoplexer", + "title": "github/hanyue36/nanoplexer", + "url": " https://rseng.github.io/software/repository/github/hanyue36/nanoplexer", + "content": "Tool for demultiplexing Nanopore barcode sequence data" }, - "github/COMBINE-lab/salmon": { - "id": "github/COMBINE-lab/salmon", - "title": "github/COMBINE-lab/salmon", - "url": " https://rseng.github.io/software/repository/github/COMBINE-lab/salmon", - "content": "🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment" + "github/asntech/intervene": { + "id": "github/asntech/intervene", + "title": "github/asntech/intervene", + "url": " https://rseng.github.io/software/repository/github/asntech/intervene", + "content": "Intervene: a tool for intersection and visualization of multiple genomic region and gene sets" }, - "github/COMBINE-lab/alevin-fry": { - "id": "github/COMBINE-lab/alevin-fry", - "title": "github/COMBINE-lab/alevin-fry", - "url": " https://rseng.github.io/software/repository/github/COMBINE-lab/alevin-fry", - "content": "🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding." + "github/markheckmann/OpenRepGrid.ic": { + "id": "github/markheckmann/OpenRepGrid.ic", + "title": "github/markheckmann/OpenRepGrid.ic", + "url": " https://rseng.github.io/software/repository/github/markheckmann/OpenRepGrid.ic", + "content": "shiny app for interpretive clustering of repgrids:" }, - "github/COMBINE-lab/pufferfish": { - "id": "github/COMBINE-lab/pufferfish", - "title": "github/COMBINE-lab/pufferfish", - "url": " https://rseng.github.io/software/repository/github/COMBINE-lab/pufferfish", - "content": "An efficient index for the colored, compacted, de Bruijn graph" + "github/sjforeman/StringFast": { + "id": "github/sjforeman/StringFast", + "title": "github/sjforeman/StringFast", + "url": " https://rseng.github.io/software/repository/github/sjforeman/StringFast", + "content": "A fast code to compute CMB power spectra induced by a network of cosmic strings" }, - "github/COMBINE-lab/simpleaf": { - "id": "github/COMBINE-lab/simpleaf", - "title": "github/COMBINE-lab/simpleaf", - "url": " https://rseng.github.io/software/repository/github/COMBINE-lab/simpleaf", - "content": "A rust framework to make using alevin-fry even simpler" + "github/sjforeman/bskit": { + "id": "github/sjforeman/bskit", + "title": "github/sjforeman/bskit", + "url": " https://rseng.github.io/software/repository/github/sjforeman/bskit", + "content": "Code for measuring bispectra from cosmological simulation snapshots" }, - "github/COMBINE-lab/RapMap": { - "id": "github/COMBINE-lab/RapMap", - "title": "github/COMBINE-lab/RapMap", - "url": " https://rseng.github.io/software/repository/github/COMBINE-lab/RapMap", - "content": "Rapid sensitive and accurate read mapping via quasi-mapping" + "github/maxmahlke/ssos": { + "id": "github/maxmahlke/ssos", + "title": "github/maxmahlke/ssos", + "url": " https://rseng.github.io/software/repository/github/maxmahlke/ssos", + "content": "Pipeline to recover astrometry and photometry of Solar System Objects in imaging surveys" }, - "github/COMBINE-lab/terminus": { - "id": "github/COMBINE-lab/terminus", - "title": "github/COMBINE-lab/terminus", - "url": " https://rseng.github.io/software/repository/github/COMBINE-lab/terminus", - "content": "enables the discovery of data-driven, robust transcript groups from RNA-seq data." + "github/agshumate/LiftoffTools": { + "id": "github/agshumate/LiftoffTools", + "title": "github/agshumate/LiftoffTools", + "url": " https://rseng.github.io/software/repository/github/agshumate/LiftoffTools", + "content": "is a toolkit to compare genes lifted between genome assemblies." }, - "github/COMBINE-lab/libgff": { - "id": "github/COMBINE-lab/libgff", - "title": "github/COMBINE-lab/libgff", - "url": " https://rseng.github.io/software/repository/github/COMBINE-lab/libgff", - "content": "GFF/GTF parsing from cufflinks as a library" + "github/panoptes-organization/panoptes": { + "id": "github/panoptes-organization/panoptes", + "title": "github/panoptes-organization/panoptes", + "url": " https://rseng.github.io/software/repository/github/panoptes-organization/panoptes", + "content": "Monitor computational workflows in real time" }, - "github/COMBINE-lab/cuttlefish": { - "id": "github/COMBINE-lab/cuttlefish", - "title": "github/COMBINE-lab/cuttlefish", - "url": " https://rseng.github.io/software/repository/github/COMBINE-lab/cuttlefish", - "content": "a fast, parallel, and very lightweight memory tool to construct the compacted de Bruijn graph from genome reference(s)." + "github/pylops/pyproximal": { + "id": "github/pylops/pyproximal", + "title": "github/pylops/pyproximal", + "url": " https://rseng.github.io/software/repository/github/pylops/pyproximal", + "content": "PyProximal – Proximal Operators and Algorithms in Python" + }, + "github/a-renzini/pygwb": { + "id": "github/a-renzini/pygwb", + "title": "github/a-renzini/pygwb", + "url": " https://rseng.github.io/software/repository/github/a-renzini/pygwb", + "content": "None" }, - "github/bezuidenhoutmc/SeeKAT": { - "id": "github/bezuidenhoutmc/SeeKAT", - "title": "github/bezuidenhoutmc/SeeKAT", - "url": " https://rseng.github.io/software/repository/github/bezuidenhoutmc/SeeKAT", - "content": "A code for localising a single pulse detected in multiple interferometer beams." + "github/paulbrodersen/netgraph": { + "id": "github/paulbrodersen/netgraph", + "title": "github/paulbrodersen/netgraph", + "url": " https://rseng.github.io/software/repository/github/paulbrodersen/netgraph", + "content": "Publication-quality network visualisations in python" }, - "github/vavrines/Kinetic.jl": { - "id": "github/vavrines/Kinetic.jl", - "title": "github/vavrines/Kinetic.jl", - "url": " https://rseng.github.io/software/repository/github/vavrines/Kinetic.jl", - "content": "Universal modeling and simulation of fluid dynamics upon machine learning" + "github/jcibanezm/DustCharge": { + "id": "github/jcibanezm/DustCharge", + "title": "github/jcibanezm/DustCharge", + "url": " https://rseng.github.io/software/repository/github/jcibanezm/DustCharge", + "content": "Calculate the equilibrium charge distribution for a dust grain of a given size and composition, depending on the local interstellar medium conditions, such as: density, temperature, ionization fraction, local radiation field strength and cosmic ray ionization fraction." }, - 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"github/andreaminio/haplosync": { - "id": "github/andreaminio/haplosync", - "title": "github/andreaminio/haplosync", - "url": " https://rseng.github.io/software/repository/github/andreaminio/haplosync", - "content": "Tools for haplotype-wise reconstruction of pseudomolecules" + "github/mlipatov/paint_atmospheres": { + "id": "github/mlipatov/paint_atmospheres", + "title": "github/mlipatov/paint_atmospheres", + "url": " https://rseng.github.io/software/repository/github/mlipatov/paint_atmospheres", + "content": "Synthetic spectra of rotating stars" }, - "github/baiwenjia/ukbb_cardiac": { - "id": "github/baiwenjia/ukbb_cardiac", - "title": "github/baiwenjia/ukbb_cardiac", - "url": " https://rseng.github.io/software/repository/github/baiwenjia/ukbb_cardiac", - "content": "Some code for processing and analysing UK Biobank cardiac MR images." + "github/evanoconnor/GR1D": { + "id": "github/evanoconnor/GR1D", + "title": "github/evanoconnor/GR1D", + "url": " https://rseng.github.io/software/repository/github/evanoconnor/GR1D", + "content": "General Relativistic, Spherically Symmetry, Neutrino Transport Code for Stellar Collapse" }, - "github/mifumagalli/cluster-cloc": { - "id": "github/mifumagalli/cluster-cloc", - "title": "github/mifumagalli/cluster-cloc", - "url": " https://rseng.github.io/software/repository/github/mifumagalli/cluster-cloc", - "content": "Automatically exported from code.google.com/p/cluster-cloc" + "github/reneshbedre/bioinfokit": { + "id": "github/reneshbedre/bioinfokit", + "title": "github/reneshbedre/bioinfokit", + "url": " https://rseng.github.io/software/repository/github/reneshbedre/bioinfokit", + "content": "The bioinfokit toolkit aims to provide various easy-to-use functionalities to analyze, visualize, and interpret the biological data generated from genome-scale omics experiments." + }, + "github/HLasse/TextDescriptives": { + "id": "github/HLasse/TextDescriptives", + "title": "github/HLasse/TextDescriptives", + "url": " https://rseng.github.io/software/repository/github/HLasse/TextDescriptives", + "content": "A Python library for calculating a large variety of metrics from text" + }, + "github/abonaldi/TRECS": { + "id": "github/abonaldi/TRECS", + "title": "github/abonaldi/TRECS", + "url": " https://rseng.github.io/software/repository/github/abonaldi/TRECS", + "content": "This repository contains the code used to produce the Tiered Radio Extragalactic Continuum Simulation (T-RECS, Bonaldi et al. 2018)" }, - "github/paulhjkelly/taskgraph-metaprogramming": { - "id": "github/paulhjkelly/taskgraph-metaprogramming", - "title": "github/paulhjkelly/taskgraph-metaprogramming", - "url": " https://rseng.github.io/software/repository/github/paulhjkelly/taskgraph-metaprogramming", - "content": "The TaskGraph Meta-programming Library is a C++ package that supports run-time code generation - programs that generate code on the fly, then execute it. And having built a piece of code, you can apply various transformations to it (such as loop interchange and tiling)." + "github/neuroanatomy/reorient": { + "id": "github/neuroanatomy/reorient", + "title": "github/neuroanatomy/reorient", + "url": " https://rseng.github.io/software/repository/github/neuroanatomy/reorient", + "content": "A tool for reorienting and cropping MRI data" }, - "github/lucabaldini/ixpeobssim": { - "id": "github/lucabaldini/ixpeobssim", - "title": "github/lucabaldini/ixpeobssim", - "url": " https://rseng.github.io/software/repository/github/lucabaldini/ixpeobssim", - "content": "Simulation and analysis framework for the Imaging X-ray Polarimetry Explorer" + "github/pavolgaj/ObsPlanner": { + "id": "github/pavolgaj/ObsPlanner", + "title": "github/pavolgaj/ObsPlanner", + "url": " https://rseng.github.io/software/repository/github/pavolgaj/ObsPlanner", + "content": "Simple program for planning and managing astronomical observations" }, - "github/ethankruse/koi3278": { - "id": "github/ethankruse/koi3278", - "title": "github/ethankruse/koi3278", - "url": " https://rseng.github.io/software/repository/github/ethankruse/koi3278", - "content": "Analysis files for the KOI-3278 system" + "github/pavolgaj/OCFit": { + "id": "github/pavolgaj/OCFit", + "title": "github/pavolgaj/OCFit", + "url": " https://rseng.github.io/software/repository/github/pavolgaj/OCFit", + "content": "Python package for fitting of O-C diagrams." }, - "github/mpound/pdrtpy": { - "id": "github/mpound/pdrtpy", - "title": "github/mpound/pdrtpy", - "url": " https://rseng.github.io/software/repository/github/mpound/pdrtpy", - "content": "PhotoDissociation Region Toolbox Python module" + "github/PopMedNet-Team/popmednet": { + "id": "github/PopMedNet-Team/popmednet", + "title": "github/PopMedNet-Team/popmednet", + "url": " https://rseng.github.io/software/repository/github/PopMedNet-Team/popmednet", + "content": "This is the repository for the open source code of the distributed data network platform PopMedNet" }, - "github/mpound/comb": { - "id": "github/mpound/comb", - "title": "github/mpound/comb", - "url": " https://rseng.github.io/software/repository/github/mpound/comb", - "content": "The AT&T Bell labs singledish radio astronomy data reduction package" + "github/moustakas/iSEDfit": { + "id": "github/moustakas/iSEDfit", + "title": "github/moustakas/iSEDfit", + "url": " https://rseng.github.io/software/repository/github/moustakas/iSEDfit", + "content": "iSEDfit is a Bayesian spectral energy distribution fitting code designed to extract the physical properties of galaxies from broadband photometry." }, - "github/21cmfast/21cmEMU": { - "id": "github/21cmfast/21cmEMU", - "title": "github/21cmfast/21cmEMU", - "url": " https://rseng.github.io/software/repository/github/21cmfast/21cmEMU", - "content": "An emulator of 21cmFAST summaries." + "github/enveda/RPath": { + "id": "github/enveda/RPath", + "title": "github/enveda/RPath", + "url": " https://rseng.github.io/software/repository/github/enveda/RPath", + "content": "Source code and data for "Causal reasoning over knowledge graphs leveraging drug-perturbed and disease-specific transcriptomic signatures for drug discovery"" }, - "github/deepskies/deeplenstronomy": { - "id": "github/deepskies/deeplenstronomy", - "title": "github/deepskies/deeplenstronomy", - "url": " https://rseng.github.io/software/repository/github/deepskies/deeplenstronomy", - "content": "A pipeline for versatile strong lens sample simulations" + "github/UBC-Astrophysics/kd-match": { + "id": "github/UBC-Astrophysics/kd-match", + "title": "github/UBC-Astrophysics/kd-match", + "url": " https://rseng.github.io/software/repository/github/UBC-Astrophysics/kd-match", + "content": "Rapidly matches stellar catalogues" }, - "github/cameronliang/BayesVP": { - "id": "github/cameronliang/BayesVP", - "title": "github/cameronliang/BayesVP", - "url": " https://rseng.github.io/software/repository/github/cameronliang/BayesVP", - "content": "None" + "github/bayzidlab/SAINT-Angle": { + "id": "github/bayzidlab/SAINT-Angle", + "title": "github/bayzidlab/SAINT-Angle", + "url": " https://rseng.github.io/software/repository/github/bayzidlab/SAINT-Angle", + "content": "This repository contains the official implementation of our paper titled SAINT-Angle: self-attention augmented inception-inside-inception network and transfer learning improve protein backbone torsion angles prediction." }, - "github/dstndstn/tractor": { - "id": "github/dstndstn/tractor", - "title": "github/dstndstn/tractor", - "url": " https://rseng.github.io/software/repository/github/dstndstn/tractor", - "content": "The Tractor: measuring astronomical sources via probabilistic inference" + "github/DidierMurilloF/FielDHub": { + "id": "github/DidierMurilloF/FielDHub", + "title": "github/DidierMurilloF/FielDHub", + "url": " https://rseng.github.io/software/repository/github/DidierMurilloF/FielDHub", + "content": "FielDHub is an R Shiny design of experiments (DOE) app that aids in the creation of traditional, unreplicated, augmented and partially-replicated designs applied to agriculture, plant breeding, forestry, animal and biological sciences." }, - "github/dstndstn/astrometry.net": { - "id": "github/dstndstn/astrometry.net", - "title": "github/dstndstn/astrometry.net", - "url": " https://rseng.github.io/software/repository/github/dstndstn/astrometry.net", - "content": "Astrometry.net -- automatic recognition of astronomical images" + "github/MichaelSel/edoJS": { + "id": "github/MichaelSel/edoJS", + "title": "github/MichaelSel/edoJS", + "url": " https://rseng.github.io/software/repository/github/MichaelSel/edoJS", + "content": "A set of functions for manipulating musical pitches within a given EDO" }, - "github/hveerten/boxfit": { - "id": "github/hveerten/boxfit", - "title": "github/hveerten/boxfit", - "url": " https://rseng.github.io/software/repository/github/hveerten/boxfit", - "content": "boxfit, a gamma-ray burst afterglow light curve generator based on two-dimensional hydrodynamics simulations" + "github/veg/tn93": { + "id": "github/veg/tn93", + "title": "github/veg/tn93", + "url": " https://rseng.github.io/software/repository/github/veg/tn93", + "content": "TN93 fast distance calculator" }, - "github/hveerten/katu": { - "id": "github/hveerten/katu", - "title": "github/hveerten/katu", - "url": " https://rseng.github.io/software/repository/github/hveerten/katu", - "content": "None" + "github/wwood/kingfisher-download": { + "id": "github/wwood/kingfisher-download", + "title": "github/wwood/kingfisher-download", + "url": " https://rseng.github.io/software/repository/github/wwood/kingfisher-download", + "content": "Easier download/extract of FASTA/Q read data and metadata from the ENA, NCBI, AWS or GCP." }, - "github/blackrim/phyutility": { - "id": "github/blackrim/phyutility", - "title": "github/blackrim/phyutility", - "url": " https://rseng.github.io/software/repository/github/blackrim/phyutility", - "content": "simple analyses or modifications on both phylogenetic trees and data matrices" + "github/bbuchfink/diamond": { + "id": "github/bbuchfink/diamond", + "title": "github/bbuchfink/diamond", + "url": " https://rseng.github.io/software/repository/github/bbuchfink/diamond", + "content": "Accelerated BLAST compatible local sequence aligner." }, - "github/SofieVG/FlowSOM": { - "id": "github/SofieVG/FlowSOM", - "title": "github/SofieVG/FlowSOM", - "url": " https://rseng.github.io/software/repository/github/SofieVG/FlowSOM", - "content": "Using self-organizing maps for visualization and interpretation of cytometry data" + "github/laristra/flecsph": { + "id": "github/laristra/flecsph", + "title": "github/laristra/flecsph", + "url": " https://rseng.github.io/software/repository/github/laristra/flecsph", + "content": "A Parallel and Distributed SPH Implementation Based on the FleCSI" }, - "github/mingzehuang/latentcor": { - "id": "github/mingzehuang/latentcor", - "title": "github/mingzehuang/latentcor", - "url": " https://rseng.github.io/software/repository/github/mingzehuang/latentcor", - "content": "latentcor is an R package provides estimation for latent correlation with mixed data types (continuous, binary, truncated and ternary)." + "github/feature-engine/feature_engine": { + "id": "github/feature-engine/feature_engine", + "title": "github/feature-engine/feature_engine", + "url": " https://rseng.github.io/software/repository/github/feature-engine/feature_engine", + "content": "Feature engineering package with sklearn like functionality" }, - "github/dusanmarceta/Synthetic-Population-of-Interstellar-Objects": { - "id": "github/dusanmarceta/Synthetic-Population-of-Interstellar-Objects", - "title": "github/dusanmarceta/Synthetic-Population-of-Interstellar-Objects", - "url": " https://rseng.github.io/software/repository/github/dusanmarceta/Synthetic-Population-of-Interstellar-Objects", - "content": "None" + "github/FRED-2/OptiType": { + "id": "github/FRED-2/OptiType", + "title": "github/FRED-2/OptiType", + "url": " https://rseng.github.io/software/repository/github/FRED-2/OptiType", + "content": "Precision HLA typing from next-generation sequencing data" }, - "github/dusanmarceta/Synthetic-Population-of-Interstellar-Obejcts": { - "id": "github/dusanmarceta/Synthetic-Population-of-Interstellar-Obejcts", - "title": "github/dusanmarceta/Synthetic-Population-of-Interstellar-Obejcts", - "url": " https://rseng.github.io/software/repository/github/dusanmarceta/Synthetic-Population-of-Interstellar-Obejcts", + "github/yungkipreos/Min-CaLM": { + "id": "github/yungkipreos/Min-CaLM", + "title": "github/yungkipreos/Min-CaLM", + "url": " https://rseng.github.io/software/repository/github/yungkipreos/Min-CaLM", + "content": "This python package can perform automated mineral compositional analysis on debris disk spectra. It will determine which minerals are present and what their relative abundances are within the debris disk. This code is used in a paper that has been submitted to the American Journal of Undergraduate Research (AJUR), titled "An Unbiased Mineral Compositional Analysis Technique for Debris Disks" by Yung Kipreos and Dr. Inseok Song.." + }, + "github/KTH-Nek5000/UQit": { + "id": "github/KTH-Nek5000/UQit", + "title": "github/KTH-Nek5000/UQit", + "url": " https://rseng.github.io/software/repository/github/KTH-Nek5000/UQit", "content": "None" }, - "github/jacobblum/simDRIFT": { - "id": "github/jacobblum/simDRIFT", - "title": "github/jacobblum/simDRIFT", - "url": " https://rseng.github.io/software/repository/github/jacobblum/simDRIFT", - "content": "simDRIFT - A software package for massively parallel forward simulation of Pulsed Gradient Spin Echo diffusion weighted MRI experiments on biophysically accurate tissue systems. " + "github/imr-framework/OCTOPUS": { + "id": "github/imr-framework/OCTOPUS", + "title": "github/imr-framework/OCTOPUS", + "url": " https://rseng.github.io/software/repository/github/imr-framework/OCTOPUS", + "content": "Off-resonance Correction OPen soUrce Software" }, - "github/pyomeca/biosiglive": { - "id": "github/pyomeca/biosiglive", - "title": "github/pyomeca/biosiglive", - "url": " https://rseng.github.io/software/repository/github/pyomeca/biosiglive", + "github/NielsenBerkeleyLab/sconce": { + "id": "github/NielsenBerkeleyLab/sconce", + "title": "github/NielsenBerkeleyLab/sconce", + "url": " https://rseng.github.io/software/repository/github/NielsenBerkeleyLab/sconce", "content": "None" }, - "github/pyomeca/ezc3d": { - "id": "github/pyomeca/ezc3d", - "title": "github/pyomeca/ezc3d", - "url": " https://rseng.github.io/software/repository/github/pyomeca/ezc3d", - "content": "Easy to use C3D reader/writer for C++, Python and Matlab" - }, - "github/pyomeca/biorbd": { - "id": "github/pyomeca/biorbd", - "title": "github/pyomeca/biorbd", - "url": " https://rseng.github.io/software/repository/github/pyomeca/biorbd", - "content": "Biomechanical add-ons to the RigidBody Dynamics Library" + "github/tanhevg/GpABC.jl": { + "id": "github/tanhevg/GpABC.jl", + "title": "github/tanhevg/GpABC.jl", + "url": " https://rseng.github.io/software/repository/github/tanhevg/GpABC.jl", + "content": "None" }, - "github/xmuyulab/DreamDIA-XMBD": { - "id": "github/xmuyulab/DreamDIA-XMBD", - "title": "github/xmuyulab/DreamDIA-XMBD", - "url": " https://rseng.github.io/software/repository/github/xmuyulab/DreamDIA-XMBD", - "content": "Software for data-independent acquisition (DIA) proteomic data processing with deep representation features." + "github/JorenSix/Panako": { + "id": "github/JorenSix/Panako", + "title": "github/JorenSix/Panako", + "url": " https://rseng.github.io/software/repository/github/JorenSix/Panako", + "content": "The Panako acoustic fingerprinting system." }, - "github/ggciag/mandyoc": { - "id": "github/ggciag/mandyoc", - "title": "github/ggciag/mandyoc", - "url": " https://rseng.github.io/software/repository/github/ggciag/mandyoc", - "content": "MANDYOC is a finite element code written on top of the PETSc library to simulate thermo-chemical convection of the Earth's mantle" + "github/JorenSix/Olaf": { + "id": "github/JorenSix/Olaf", + "title": "github/JorenSix/Olaf", + "url": " https://rseng.github.io/software/repository/github/JorenSix/Olaf", + "content": "Olaf: Overly Lightweight Acoustic Fingerprinting is a portable acoustic fingerprinting system." }, - "github/Hi-COLACode/Hi-COLA": { - "id": "github/Hi-COLACode/Hi-COLA", - "title": "github/Hi-COLACode/Hi-COLA", - "url": " https://rseng.github.io/software/repository/github/Hi-COLACode/Hi-COLA", - "content": "Hi-COLA simulates cosmological large-scale structure for a wide class of Horndeski theories. Built using a COLA solver forked from FML by HAWinther." + "github/sheinasim/HiFiAdapterFilt": { + "id": "github/sheinasim/HiFiAdapterFilt", + "title": "github/sheinasim/HiFiAdapterFilt", + "url": " https://rseng.github.io/software/repository/github/sheinasim/HiFiAdapterFilt", + "content": "Remove CCS reads with remnant PacBio adapter sequences and convert outputs to a compressed .fastq (.fastq.gz)." }, - "github/wmalab/EnHiC": { - "id": "github/wmalab/EnHiC", - "title": "github/wmalab/EnHiC", - "url": " https://rseng.github.io/software/repository/github/wmalab/EnHiC", - "content": "Enhancing Hi-C matrix resolution" + "github/csabiu/kstat": { + "id": "github/csabiu/kstat", + "title": "github/csabiu/kstat", + "url": " https://rseng.github.io/software/repository/github/csabiu/kstat", + "content": "Fast KD-tree MPI correlation statistics package - Author: Cristiano Sabiu" }, - "github/szpiech/selscan": { - "id": "github/szpiech/selscan", - "title": "github/szpiech/selscan", - "url": " https://rseng.github.io/software/repository/github/szpiech/selscan", - "content": "Haplotype based scans for selection" + "github/m2aia/m2aia": { + "id": "github/m2aia/m2aia", + "title": "github/m2aia/m2aia", + "url": " https://rseng.github.io/software/repository/github/m2aia/m2aia", + "content": "Mass spectrometry imaging applications for interactive analysis in MITK (M²aia)" }, - "github/toros-astro/corral": { - "id": "github/toros-astro/corral", - "title": "github/toros-astro/corral", - "url": " https://rseng.github.io/software/repository/github/toros-astro/corral", - "content": "The Powerful Pipeline Framework" + "github/iopenshell/ezSpectrum": { + "id": "github/iopenshell/ezSpectrum", + "title": "github/iopenshell/ezSpectrum", + "url": " https://rseng.github.io/software/repository/github/iopenshell/ezSpectrum", + "content": "None" }, - "github/toros-astro/astroalign-legacy": { - "id": "github/toros-astro/astroalign-legacy", - "title": "github/toros-astro/astroalign-legacy", - "url": " https://rseng.github.io/software/repository/github/toros-astro/astroalign-legacy", - "content": "A tool to align astronomical images based on asterism matching" + "github/FourierFlows/GeophysicalFlows.jl": { + "id": "github/FourierFlows/GeophysicalFlows.jl", + "title": "github/FourierFlows/GeophysicalFlows.jl", + "url": " https://rseng.github.io/software/repository/github/FourierFlows/GeophysicalFlows.jl", + "content": "Geophysical fluid dynamics pseudospectral solvers with Julia and FourierFlows.jl." }, - "github/scikit-learn-contrib/hdbscan": { - "id": "github/scikit-learn-contrib/hdbscan", - "title": "github/scikit-learn-contrib/hdbscan", - "url": " https://rseng.github.io/software/repository/github/scikit-learn-contrib/hdbscan", - "content": "A high performance implementation of HDBSCAN clustering." + "github/hongwanliu/DarkHistory": { + "id": "github/hongwanliu/DarkHistory", + "title": "github/hongwanliu/DarkHistory", + "url": " https://rseng.github.io/software/repository/github/hongwanliu/DarkHistory", + "content": "A code package for calculating modified cosmic ionization and thermal histories with dark matter and other exotic energy injections" }, - "github/ChenfuShi/HiChIP_peaks": { - "id": "github/ChenfuShi/HiChIP_peaks", - "title": "github/ChenfuShi/HiChIP_peaks", - "url": " https://rseng.github.io/software/repository/github/ChenfuShi/HiChIP_peaks", - "content": "A tool to analyse HiChIP data" + "github/surhh/nfitsview": { + "id": "github/surhh/nfitsview", + "title": "github/surhh/nfitsview", + "url": " https://rseng.github.io/software/repository/github/surhh/nfitsview", + "content": "nFITSview - A simple and user-friendly FITS image viewer" }, - "github/cosmicrays/hermes": { - "id": "github/cosmicrays/hermes", - "title": "github/cosmicrays/hermes", - "url": " https://rseng.github.io/software/repository/github/cosmicrays/hermes", - "content": "HERMES is a publicly available computational framework for the line of sight integration over galactic radiative processes which creates sky maps in the HEALPix-compatibile format." + "github/neeravkaushal/RIDs-in-WCDs": { + "id": "github/neeravkaushal/RIDs-in-WCDs", + "title": "github/neeravkaushal/RIDs-in-WCDs", + "url": " https://rseng.github.io/software/repository/github/neeravkaushal/RIDs-in-WCDs", + "content": "None" }, - "github/cosmicrays/DRAGON": { - "id": "github/cosmicrays/DRAGON", - "title": "github/cosmicrays/DRAGON", - "url": " https://rseng.github.io/software/repository/github/cosmicrays/DRAGON", - "content": "First version of the code - last update Dec 2015" + "github/InsightSoftwareConsortium/ITK": { + "id": "github/InsightSoftwareConsortium/ITK", + "title": "github/InsightSoftwareConsortium/ITK", + "url": " https://rseng.github.io/software/repository/github/InsightSoftwareConsortium/ITK", + "content": "Insight Toolkit (ITK) -- Official Repository" }, - "github/oruhnau/when2heat": { - "id": "github/oruhnau/when2heat", - "title": "github/oruhnau/when2heat", - "url": " https://rseng.github.io/software/repository/github/oruhnau/when2heat", - "content": "Heating Profiles" + "github/RemoteSensingTools/vSmartMOM.jl": { + "id": "github/RemoteSensingTools/vSmartMOM.jl", + "title": "github/RemoteSensingTools/vSmartMOM.jl", + "url": " https://rseng.github.io/software/repository/github/RemoteSensingTools/vSmartMOM.jl", + "content": "A full end-to-end modular software suite for radiative transfer and related atmospheric analysis" }, - "github/dankelley/oce": { - "id": "github/dankelley/oce", - "title": "github/dankelley/oce", - "url": " https://rseng.github.io/software/repository/github/dankelley/oce", - "content": "R package for oceanographic processing" + "github/wilsonrljr/sysidentpy": { + "id": "github/wilsonrljr/sysidentpy", + "title": "github/wilsonrljr/sysidentpy", + "url": " https://rseng.github.io/software/repository/github/wilsonrljr/sysidentpy", + "content": "A Python package for System Identification using NARMAX models" }, - "github/BU-ISCIII/plasmidID": { - "id": "github/BU-ISCIII/plasmidID", - "title": "github/BU-ISCIII/plasmidID", - "url": " https://rseng.github.io/software/repository/github/BU-ISCIII/plasmidID", - "content": "PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identification." + "github/BoevaLab/FREEC": { + "id": "github/BoevaLab/FREEC", + "title": "github/BoevaLab/FREEC", + "url": " https://rseng.github.io/software/repository/github/BoevaLab/FREEC", + "content": "Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data" }, - "github/BU-ISCIII/iSkyLIMS": { - "id": "github/BU-ISCIII/iSkyLIMS", - "title": "github/BU-ISCIII/iSkyLIMS", - "url": " https://rseng.github.io/software/repository/github/BU-ISCIII/iSkyLIMS", - "content": "is an open-source LIMS (laboratory Information Management System) for Next Generation Sequencing sample management, statistics and reports, and bioinformatics analysis service management." + "github/Music-and-Culture-Technology-Lab/omnizart": { + "id": "github/Music-and-Culture-Technology-Lab/omnizart", + "title": "github/Music-and-Culture-Technology-Lab/omnizart", + "url": " https://rseng.github.io/software/repository/github/Music-and-Culture-Technology-Lab/omnizart", + "content": "Omniscient Mozart, being able to transcribe everything in the music, including vocal, drum, chord, beat, instruments, and more." }, - "github/BU-ISCIII/taranis": { - "id": "github/BU-ISCIII/taranis", - "title": "github/BU-ISCIII/taranis", - "url": " https://rseng.github.io/software/repository/github/BU-ISCIII/taranis", - "content": "cg/wgMLST allele calling software, schema evaluation and allele distance estimation for outbreak reserch." + "github/elliohow/fMRI_ROI_Analysis_Tool": { + "id": "github/elliohow/fMRI_ROI_Analysis_Tool", + "title": "github/elliohow/fMRI_ROI_Analysis_Tool", + "url": " https://rseng.github.io/software/repository/github/elliohow/fMRI_ROI_Analysis_Tool", + "content": "An analysis tool that uses per-voxel statistical maps in conjunction with FSL atlases to create per-region statistical maps. Current usage includes the creation of regional maps of temporal signal to noise ratio." }, - "github/numba/numba": { - "id": "github/numba/numba", - "title": "github/numba/numba", - "url": " https://rseng.github.io/software/repository/github/numba/numba", - "content": "NumPy aware dynamic Python compiler using LLVM" + "github/traja-team/traja": { + "id": "github/traja-team/traja", + "title": "github/traja-team/traja", + "url": " https://rseng.github.io/software/repository/github/traja-team/traja", + "content": "Python tools for spatial trajectory and time-series data analysis" }, - "github/bregaldo/pywst": { - "id": "github/bregaldo/pywst", - "title": "github/bregaldo/pywst", - "url": " https://rseng.github.io/software/repository/github/bregaldo/pywst", - "content": "Python package for WST and RWST analyses of astrophysical data." + "github/EvolBioInf/phylonium": { + "id": "github/EvolBioInf/phylonium", + "title": "github/EvolBioInf/phylonium", + "url": " https://rseng.github.io/software/repository/github/EvolBioInf/phylonium", + "content": "♥ Fast and Accurate Estimation of Evolutionary Distances" }, - "github/dgbowl/yadg": { - "id": "github/dgbowl/yadg", - "title": "github/dgbowl/yadg", - "url": " https://rseng.github.io/software/repository/github/dgbowl/yadg", - "content": "yadg: yet another datagram" + "github/EvolBioInf/andi": { + "id": "github/EvolBioInf/andi", + "title": "github/EvolBioInf/andi", + "url": " https://rseng.github.io/software/repository/github/EvolBioInf/andi", + "content": "♥ Efficient Estimation of Evolutionary Distances" }, - "github/gilestrolab/pySolo": { - "id": "github/gilestrolab/pySolo", - "title": "github/gilestrolab/pySolo", - "url": " https://rseng.github.io/software/repository/github/gilestrolab/pySolo", - "content": "A software for sleep analysis in Drosophila" + "github/pedro-acunha/SHEEP": { + "id": "github/pedro-acunha/SHEEP", + "title": "github/pedro-acunha/SHEEP", + "url": " https://rseng.github.io/software/repository/github/pedro-acunha/SHEEP", + "content": "Machine Learning pipeline to classify astronomical sources into galaxies, quasars and stars using photometric data." }, - "github/gilestrolab/ethoscope": { - "id": "github/gilestrolab/ethoscope", - "title": "github/gilestrolab/ethoscope", - "url": " https://rseng.github.io/software/repository/github/gilestrolab/ethoscope", - "content": "a platform from monitoring animal behaviour in real time from a raspberry pi" + "github/csuhjhjhj/GCNCMI": { + "id": "github/csuhjhjhj/GCNCMI", + "title": "github/csuhjhjhj/GCNCMI", + "url": " https://rseng.github.io/software/repository/github/csuhjhjhj/GCNCMI", + "content": "CircRNA-miRNA interaction Prediction Based on Graph Neural Network" }, - "github/linuxscout/pyarabic": { - "id": "github/linuxscout/pyarabic", - "title": "github/linuxscout/pyarabic", - "url": " https://rseng.github.io/software/repository/github/linuxscout/pyarabic", - "content": "pyarabic" + "github/tariks/peakachu": { + "id": "github/tariks/peakachu", + "title": "github/tariks/peakachu", + "url": " https://rseng.github.io/software/repository/github/tariks/peakachu", + "content": "Genome-wide contact analysis using sklearn" }, - "github/rychallener/ThERESA": { - "id": "github/rychallener/ThERESA", - "title": "github/rychallener/ThERESA", - "url": " https://rseng.github.io/software/repository/github/rychallener/ThERESA", - "content": "3D Exoplanet Cartography" + "github/cmelab/flowerMD": { + "id": "github/cmelab/flowerMD", + "title": "github/cmelab/flowerMD", + "url": " https://rseng.github.io/software/repository/github/cmelab/flowerMD", + "content": "Flexible Library of Organic Workflows and Extensible Recipes for Molecular Dynamics." }, - "github/carronj/lenspyx": { - "id": "github/carronj/lenspyx", - "title": "github/carronj/lenspyx", - "url": " https://rseng.github.io/software/repository/github/carronj/lenspyx", - "content": "Curved-sky python lensed CMB maps simulation package" + "github/henrycousins/gspa": { + "id": "github/henrycousins/gspa", + "title": "github/henrycousins/gspa", + "url": " https://rseng.github.io/software/repository/github/henrycousins/gspa", + "content": "Python implementation of gene set proximity analysis" }, - "github/carronj/plancklens": { - "id": "github/carronj/plancklens", - "title": "github/carronj/plancklens", - "url": " https://rseng.github.io/software/repository/github/carronj/plancklens", - "content": "Planck 2018 lensing pipeline" + "github/ladsantos/p-winds": { + "id": "github/ladsantos/p-winds", + "title": "github/ladsantos/p-winds", + "url": " https://rseng.github.io/software/repository/github/ladsantos/p-winds", + "content": "Python implementation of Parker wind models for exoplanet atmospheres" }, - "github/ageorgakakis/StructureFunction": { - "id": "github/ageorgakakis/StructureFunction", - "title": "github/ageorgakakis/StructureFunction", - "url": " https://rseng.github.io/software/repository/github/ageorgakakis/StructureFunction", + "github/ladsantos/flatstar": { + "id": "github/ladsantos/flatstar", + "title": "github/ladsantos/flatstar", + "url": " https://rseng.github.io/software/repository/github/ladsantos/flatstar", + "content": "Make 2d intensity maps of limb-darkened stars." + }, + "github/girder/viime": { + "id": "github/girder/viime", + "title": "github/girder/viime", + "url": " https://rseng.github.io/software/repository/github/girder/viime", "content": "None" }, - "github/reproducible-biomedical-modeling/Biosimulations": { - "id": "github/reproducible-biomedical-modeling/Biosimulations", - "title": "github/reproducible-biomedical-modeling/Biosimulations", - "url": " https://rseng.github.io/software/repository/github/reproducible-biomedical-modeling/Biosimulations", - "content": "Platform for sharing and reusing biomodeling studies including models, simulations, and visualizations of their results" + "github/cochran4/GEMB": { + "id": "github/cochran4/GEMB", + "title": "github/cochran4/GEMB", + "url": " https://rseng.github.io/software/repository/github/cochran4/GEMB", + "content": "Gene-set enrichment with math biology" }, - "github/ModellingWebLab/chaste-codegen": { - "id": "github/ModellingWebLab/chaste-codegen", - "title": "github/ModellingWebLab/chaste-codegen", - "url": " https://rseng.github.io/software/repository/github/ModellingWebLab/chaste-codegen", - "content": "Code generation for Chaste based on cellmlmanip" + "github/KVSlab/VaMPy": { + "id": "github/KVSlab/VaMPy", + "title": "github/KVSlab/VaMPy", + "url": " https://rseng.github.io/software/repository/github/KVSlab/VaMPy", + "content": "A collection of tools for pre-processing, simulating, and post-processing vascular morphologies." }, - "github/ahudde/greeks": { - "id": "github/ahudde/greeks", - "title": "github/ahudde/greeks", - "url": " https://rseng.github.io/software/repository/github/ahudde/greeks", - "content": "Sensitivities of Prices of Financial Options and Implied Volatilites" + "github/KVSlab/turtleFSI": { + "id": "github/KVSlab/turtleFSI", + "title": "github/KVSlab/turtleFSI", + "url": " https://rseng.github.io/software/repository/github/KVSlab/turtleFSI", + "content": "Monolithic Fluid-Structure Interaction (FSI) solver" }, - "github/smithlabcode/abismal": { - "id": "github/smithlabcode/abismal", - "title": "github/smithlabcode/abismal", - "url": " https://rseng.github.io/software/repository/github/smithlabcode/abismal", - "content": "Abismal is a mapper of FASTQ bisulfite-converted short reads (between 50 and 1000 bases) to a FASTA reference genome." + "github/prajwel/curvit": { + "id": "github/prajwel/curvit", + "title": "github/prajwel/curvit", + "url": " https://rseng.github.io/software/repository/github/prajwel/curvit", + "content": "Create light curves from UVIT data." }, - "github/smithlabcode/dnmtools": { - "id": "github/smithlabcode/dnmtools", - "title": "github/smithlabcode/dnmtools", - "url": " https://rseng.github.io/software/repository/github/smithlabcode/dnmtools", - "content": "Tools for analyzing DNA methylation data" + "github/delphes/delphes": { + "id": "github/delphes/delphes", + "title": "github/delphes/delphes", + "url": " https://rseng.github.io/software/repository/github/delphes/delphes", + "content": "A framework for fast simulation of a generic collider experiment" }, - "github/smithlabcode/preseq": { - "id": "github/smithlabcode/preseq", - "title": "github/smithlabcode/preseq", - "url": " https://rseng.github.io/software/repository/github/smithlabcode/preseq", - "content": "Software for predicting library complexity and genome coverage in high-throughput sequencing." + "github/martinsparre/XSHPipelineManager": { + "id": "github/martinsparre/XSHPipelineManager", + "title": "github/martinsparre/XSHPipelineManager", + "url": " https://rseng.github.io/software/repository/github/martinsparre/XSHPipelineManager", + "content": "A script to run the X-shooter pipeline" }, - "github/smithlabcode/falco": { - "id": "github/smithlabcode/falco", - "title": "github/smithlabcode/falco", - "url": " https://rseng.github.io/software/repository/github/smithlabcode/falco", - "content": "A C++ drop-in replacement of FastQC to assess the quality of sequence read data" + "github/moranegg/AffectationRO": { + "id": "github/moranegg/AffectationRO", + "title": "github/moranegg/AffectationRO", + "url": " https://rseng.github.io/software/repository/github/moranegg/AffectationRO", + "content": "Projet en recherche opérationelle " }, - "github/Tomcxf/FASTdRNA": { - "id": "github/Tomcxf/FASTdRNA", - "title": "github/Tomcxf/FASTdRNA", - "url": " https://rseng.github.io/software/repository/github/Tomcxf/FASTdRNA", - "content": "FASTdRNA is a workflow for analysis of ONT direct RNA seq dataset" + "github/moranegg/deposit-template": { + "id": "github/moranegg/deposit-template", + "title": "github/moranegg/deposit-template", + "url": " https://rseng.github.io/software/repository/github/moranegg/deposit-template", + "content": "This is a deposit template repository to help researchers in starting their project in a online VCS" }, - "github/pmelsted/pizzly": { - "id": "github/pmelsted/pizzly", - "title": "github/pmelsted/pizzly", - "url": " https://rseng.github.io/software/repository/github/pmelsted/pizzly", - "content": "Fast fusion detection using kallisto" + "github/alex-b-davis/gubas": { + "id": "github/alex-b-davis/gubas", + "title": "github/alex-b-davis/gubas", + "url": " https://rseng.github.io/software/repository/github/alex-b-davis/gubas", + "content": "General Use Binary Asteroid Simulator" }, - "github/snfactory/binaryoffset": { - "id": "github/snfactory/binaryoffset", - "title": "github/snfactory/binaryoffset", - "url": " https://rseng.github.io/software/repository/github/snfactory/binaryoffset", - "content": "Detecting and Correcting the Binary Offset Effect in CCDs" + "github/samsledje/ConPLex_dev": { + "id": "github/samsledje/ConPLex_dev", + "title": "github/samsledje/ConPLex_dev", + "url": " https://rseng.github.io/software/repository/github/samsledje/ConPLex_dev", + "content": "None" }, - "github/thomas0809/MolScribe": { - "id": "github/thomas0809/MolScribe", - "title": "github/thomas0809/MolScribe", - "url": " https://rseng.github.io/software/repository/github/thomas0809/MolScribe", - "content": "Robust Molecular Structure Recognition with Image-to-Graph Generation" + "github/wajidarshad/ESIDE": { + "id": "github/wajidarshad/ESIDE", + "title": "github/wajidarshad/ESIDE", + "url": " https://rseng.github.io/software/repository/github/wajidarshad/ESIDE", + "content": "Earthworm Species IDEntification" }, - "github/CRPropa/CRPropa3": { - "id": "github/CRPropa/CRPropa3", - "title": "github/CRPropa/CRPropa3", - "url": " https://rseng.github.io/software/repository/github/CRPropa/CRPropa3", - "content": " CRPropa is a public astrophysical simulation framework for propagating extraterrestrial ultra-high energy particles. https://crpropa.github.io/CRPropa3/" + "github/cbrnr/sigviewer": { + "id": "github/cbrnr/sigviewer", + "title": "github/cbrnr/sigviewer", + "url": " https://rseng.github.io/software/repository/github/cbrnr/sigviewer", + "content": "SigViewer is a viewing application for biosignals." }, - "github/CRPropa/CRPropa2": { - "id": "github/CRPropa/CRPropa2", - "title": "github/CRPropa/CRPropa2", - "url": " https://rseng.github.io/software/repository/github/CRPropa/CRPropa2", - "content": "Previous version of CRPropa" + "github/mlinderm/npsv": { + "id": "github/mlinderm/npsv", + "title": "github/mlinderm/npsv", + "url": " https://rseng.github.io/software/repository/github/mlinderm/npsv", + "content": "Non-parametric structural variant genotyper" }, - "github/mp3guy/ElasticFusion": { - "id": "github/mp3guy/ElasticFusion", - "title": "github/mp3guy/ElasticFusion", - "url": " https://rseng.github.io/software/repository/github/mp3guy/ElasticFusion", - "content": "Real-time dense visual SLAM system" + "github/relipmoc/skewer": { + "id": "github/relipmoc/skewer", + "title": "github/relipmoc/skewer", + "url": " https://rseng.github.io/software/repository/github/relipmoc/skewer", + "content": "implements the bit-masked k-difference matching algorithm dedicated to the task of adapter trimming. It is specially designed for processing next-generation sequencing (NGS) paired-end sequences." }, - "github/EdoardoCarlesi/cmbeasy": { - "id": "github/EdoardoCarlesi/cmbeasy", - "title": "github/EdoardoCarlesi/cmbeasy", - "url": " https://rseng.github.io/software/repository/github/EdoardoCarlesi/cmbeasy", - "content": "My CMBEASY implementation" + "github/NCAR/NCAR-Classic-Libraries-for-Geophysics": { + "id": "github/NCAR/NCAR-Classic-Libraries-for-Geophysics", + "title": "github/NCAR/NCAR-Classic-Libraries-for-Geophysics", + "url": " https://rseng.github.io/software/repository/github/NCAR/NCAR-Classic-Libraries-for-Geophysics", + "content": "None" }, - "github/plumed/plumed2": { - "id": "github/plumed/plumed2", - "title": "github/plumed/plumed2", - "url": " https://rseng.github.io/software/repository/github/plumed/plumed2", - "content": "Development version of plumed 2" + "github/deepmedic/deepmedic": { + "id": "github/deepmedic/deepmedic", + "title": "github/deepmedic/deepmedic", + "url": " https://rseng.github.io/software/repository/github/deepmedic/deepmedic", + "content": "Efficient Multi-Scale 3D Convolutional Neural Network for Segmentation of 3D Medical Scans" }, - "github/PCMSolver/pcmsolver": { - "id": "github/PCMSolver/pcmsolver", - "title": "github/PCMSolver/pcmsolver", - "url": " https://rseng.github.io/software/repository/github/PCMSolver/pcmsolver", - "content": "An API for the Polarizable Continuum Model" + "github/deepsphere/deepsphere-cosmo-tf1": { + "id": "github/deepsphere/deepsphere-cosmo-tf1", + "title": "github/deepsphere/deepsphere-cosmo-tf1", + "url": " https://rseng.github.io/software/repository/github/deepsphere/deepsphere-cosmo-tf1", + "content": "A spherical convolutional neural network for cosmology (TFv1)." }, "github/ERA-URBAN/fm128_radar": { "id": "github/ERA-URBAN/fm128_radar", @@ -9849,3707 +9117,3971 @@ "url": " https://rseng.github.io/software/repository/github/ERA-URBAN/netcdf2littler", "content": "An application to convert NetCDF files to the Little-R format. The Little-R format is the accepted input format for the WRF data assimilation system (WRFDA) preprocessor (obsproc). Currently only the conversion of synoptical weather stations are supported by this application." }, - "github/MD-Studio/cerise": { - "id": "github/MD-Studio/cerise", - "title": "github/MD-Studio/cerise", - "url": " https://rseng.github.io/software/repository/github/MD-Studio/cerise", - "content": "A REST service for running CWL workflows on remote clusters" + "github/lutteropp/NetRAX": { + "id": "github/lutteropp/NetRAX", + "title": "github/lutteropp/NetRAX", + "url": " https://rseng.github.io/software/repository/github/lutteropp/NetRAX", + "content": "Phylogenetic Network Inference without ILS" }, - "github/MD-Studio/cerulean": { - "id": "github/MD-Studio/cerulean", - "title": "github/MD-Studio/cerulean", - "url": " https://rseng.github.io/software/repository/github/MD-Studio/cerulean", - "content": "A Python 3 library for talking to HPC clusters and supercomputers" + "github/silx-kit/pyFAI": { + "id": "github/silx-kit/pyFAI", + "title": "github/silx-kit/pyFAI", + "url": " https://rseng.github.io/software/repository/github/silx-kit/pyFAI", + "content": "Fast Azimuthal Integration in Python" }, - "github/MD-Studio/MDStudio": { - "id": "github/MD-Studio/MDStudio", - "title": "github/MD-Studio/MDStudio", - "url": " https://rseng.github.io/software/repository/github/MD-Studio/MDStudio", - "content": "A general framework for microservice based distributed applications" + "github/QingyuLiaib/PLA-MoRe": { + "id": "github/QingyuLiaib/PLA-MoRe", + "title": "github/QingyuLiaib/PLA-MoRe", + "url": " https://rseng.github.io/software/repository/github/QingyuLiaib/PLA-MoRe", + "content": "None" + }, + "github/OttoStruve/muler": { + "id": "github/OttoStruve/muler", + "title": "github/OttoStruve/muler", + "url": " https://rseng.github.io/software/repository/github/OttoStruve/muler", + "content": "A Python package for working with pipeline-produced spectra from IGRINS, HPF, and Keck NIRSPEC" + }, + "github/nlppln/nlppln": { + "id": "github/nlppln/nlppln", + "title": "github/nlppln/nlppln", + "url": " https://rseng.github.io/software/repository/github/nlppln/nlppln", + "content": "NLP pipeline software using common workflow language" + }, + "github/ELELAB/RosettaDDGPrediction": { + "id": "github/ELELAB/RosettaDDGPrediction", + "title": "github/ELELAB/RosettaDDGPrediction", + "url": " https://rseng.github.io/software/repository/github/ELELAB/RosettaDDGPrediction", + "content": "None" + }, + "github/ELELAB/cancermuts": { + "id": "github/ELELAB/cancermuts", + "title": "github/ELELAB/cancermuts", + "url": " https://rseng.github.io/software/repository/github/ELELAB/cancermuts", + "content": "Software for the automatic annotation of cancer mutations" + }, + "github/ELELAB/CAncer-bioMarker-Prediction-Pipeline-CAMPP": { + "id": "github/ELELAB/CAncer-bioMarker-Prediction-Pipeline-CAMPP", + "title": "github/ELELAB/CAncer-bioMarker-Prediction-Pipeline-CAMPP", + "url": " https://rseng.github.io/software/repository/github/ELELAB/CAncer-bioMarker-Prediction-Pipeline-CAMPP", + "content": "The Cancer bioMarker Prediction Pipeline (CAMPP) " + }, + "github/ELELAB/LipidDyn": { + "id": "github/ELELAB/LipidDyn", + "title": "github/ELELAB/LipidDyn", + "url": " https://rseng.github.io/software/repository/github/ELELAB/LipidDyn", + "content": "repository associated to our pipeline for lipid dynamics" + }, + "github/astro-friedel/CADRE": { + "id": "github/astro-friedel/CADRE", + "title": "github/astro-friedel/CADRE", + "url": " https://rseng.github.io/software/repository/github/astro-friedel/CADRE", + "content": "CARMA Data Reduction Pipeline" + }, + "github/exoplanet-dev/exoplanet": { + "id": "github/exoplanet-dev/exoplanet", + "title": "github/exoplanet-dev/exoplanet", + "url": " https://rseng.github.io/software/repository/github/exoplanet-dev/exoplanet", + "content": "Fast & scalable MCMC for all your exoplanet needs! " + }, + "github/exoplanet-dev/celerite2": { + "id": "github/exoplanet-dev/celerite2", + "title": "github/exoplanet-dev/celerite2", + "url": " https://rseng.github.io/software/repository/github/exoplanet-dev/celerite2", + "content": "Fast & scalable Gaussian Processes in one dimension" + }, + "github/nmslib/hnswlib": { + "id": "github/nmslib/hnswlib", + "title": "github/nmslib/hnswlib", + "url": " https://rseng.github.io/software/repository/github/nmslib/hnswlib", + "content": "Header-only C++/python library for fast approximate nearest neighbors" + }, + "github/bpp/bpp": { + "id": "github/bpp/bpp", + "title": "github/bpp/bpp", + "url": " https://rseng.github.io/software/repository/github/bpp/bpp", + "content": "implements a versatile high-performance version of the BPP software" + }, + "github/sxs-collaboration/gwsurrogate": { + "id": "github/sxs-collaboration/gwsurrogate", + "title": "github/sxs-collaboration/gwsurrogate", + "url": " https://rseng.github.io/software/repository/github/sxs-collaboration/gwsurrogate", + "content": "An easy to use interface to gravitational wave surrogate models" + }, + "github/sxs-collaboration/spectre": { + "id": "github/sxs-collaboration/spectre", + "title": "github/sxs-collaboration/spectre", + "url": " https://rseng.github.io/software/repository/github/sxs-collaboration/spectre", + "content": "SpECTRE is a code for multi-scale, multi-physics problems in astrophysics and gravitational physics." + }, + "github/debian-tex/biber": { + "id": "github/debian-tex/biber", + "title": "github/debian-tex/biber", + "url": " https://rseng.github.io/software/repository/github/debian-tex/biber", + "content": "Much-augmented BibTeX replacement for BibLaTeX users" + }, + "github/debian-tex/texlive-nonbin": { + "id": "github/debian-tex/texlive-nonbin", + "title": "github/debian-tex/texlive-nonbin", + "url": " https://rseng.github.io/software/repository/github/debian-tex/texlive-nonbin", + "content": "debian non-bin texlive pkgs" + }, + "github/pnnl/interflow": { + "id": "github/pnnl/interflow", + "title": "github/pnnl/interflow", + "url": " https://rseng.github.io/software/repository/github/pnnl/interflow", + "content": "A Python package for organizing and calculating cross-sectoral interdependency flow values" }, - "github/xiaofengsong/pHisPred": { - "id": "github/xiaofengsong/pHisPred", - "title": "github/xiaofengsong/pHisPred", - "url": " https://rseng.github.io/software/repository/github/xiaofengsong/pHisPred", - "content": "A bioinformatic tool for identifying protein histidine phosphorylation sites" + "github/pnnl/HyperNetX": { + "id": "github/pnnl/HyperNetX", + "title": "github/pnnl/HyperNetX", + "url": " https://rseng.github.io/software/repository/github/pnnl/HyperNetX", + "content": "Python package for hypergraph analysis and visualization." }, - "github/smaret/thindisk": { - "id": "github/smaret/thindisk", - "title": "github/smaret/thindisk", - "url": " https://rseng.github.io/software/repository/github/smaret/thindisk", - "content": "Compute the line emission from a geometrically thin protoplanetary disk" + "github/lanzen/ampliconnoise": { + "id": "github/lanzen/ampliconnoise", + "title": "github/lanzen/ampliconnoise", + "url": " https://rseng.github.io/software/repository/github/lanzen/ampliconnoise", + "content": "Automatically exported from code.google.com/p/ampliconnoise" }, - "github/smaret/astrochem": { - "id": "github/smaret/astrochem", - "title": "github/smaret/astrochem", - "url": " https://rseng.github.io/software/repository/github/smaret/astrochem", - "content": "A code to compute the abundances of chemical species in the interstellar medium" + "github/jiujiezz/tsnad": { + "id": "github/jiujiezz/tsnad", + "title": "github/jiujiezz/tsnad", + "url": " https://rseng.github.io/software/repository/github/jiujiezz/tsnad", + "content": "Detecting somatic mutations and predicting tumor-specific neo-antigens" }, - "github/atzberg/mlmod": { - "id": "github/atzberg/mlmod", - "title": "github/atzberg/mlmod", - "url": " https://rseng.github.io/software/repository/github/atzberg/mlmod", - "content": "Machine learning package for data-driven modeling and simulation in LAMMPs." + "github/fchuffar/epimedtools": { + "id": "github/fchuffar/epimedtools", + "title": "github/fchuffar/epimedtools", + "url": " https://rseng.github.io/software/repository/github/fchuffar/epimedtools", + "content": "A package allowing multi-omics analysis using R" }, - "github/bradkav/EarthShadow": { - "id": "github/bradkav/EarthShadow", - "title": "github/bradkav/EarthShadow", - "url": " https://rseng.github.io/software/repository/github/bradkav/EarthShadow", - "content": "A tool for calculating the impact of Earth-scattering on the distribution of Dark Matter (DM) particles. Includes (Mathematica) code, numerical results, plots and animations." + "github/fchuffar/dmethr": { + "id": "github/fchuffar/dmethr", + "title": "github/fchuffar/dmethr", + "url": " https://rseng.github.io/software/repository/github/fchuffar/dmethr", + "content": "DNA Methylation repression of transcriptional activity" }, - "github/bradkav/EarthScatterLikelihood": { - "id": "github/bradkav/EarthScatterLikelihood", - "title": "github/bradkav/EarthScatterLikelihood", - "url": " https://rseng.github.io/software/repository/github/bradkav/EarthScatterLikelihood", - "content": "Code for calculating event rates and likelihoods for Dark Matter direct detection experiments in the presence of Earth-Scattering" + "github/fchuffar/protopackage": { + "id": "github/fchuffar/protopackage", + "title": "github/fchuffar/protopackage", + "url": " https://rseng.github.io/software/repository/github/fchuffar/protopackage", + "content": "None" }, - "github/bradkav/verne": { - "id": "github/bradkav/verne", - "title": "github/bradkav/verne", - "url": " https://rseng.github.io/software/repository/github/bradkav/verne", - "content": "Python code for calculating the Earth-stopping effect for super-heavy Dark Matter (DM)." + "github/kbarbary/sep": { + "id": "github/kbarbary/sep", + "title": "github/kbarbary/sep", + "url": " https://rseng.github.io/software/repository/github/kbarbary/sep", + "content": "Python and C library for source extraction and photometry" }, - "github/bradkav/WIMpy_NREFT": { - "id": "github/bradkav/WIMpy_NREFT", - "title": "github/bradkav/WIMpy_NREFT", - "url": " https://rseng.github.io/software/repository/github/bradkav/WIMpy_NREFT", - "content": "WIMpy_NREFT is a code for calculating Dark Matter direct detection rates in the framework of non-relativistic effective field theory (NREFT)." + "github/kbarbary/extinction": { + "id": "github/kbarbary/extinction", + "title": "github/kbarbary/extinction", + "url": " https://rseng.github.io/software/repository/github/kbarbary/extinction", + "content": "Fast interstellar dust extinction laws in Python" }, - "github/bradkav/AntiparticleDM": { - "id": "github/bradkav/AntiparticleDM", - "title": "github/bradkav/AntiparticleDM", - "url": " https://rseng.github.io/software/repository/github/bradkav/AntiparticleDM", - "content": "Prospects for discriminating between Majorana and Dirac Dark Matter using future direct detection data. " + "github/kbarbary/nestle": { + "id": "github/kbarbary/nestle", + "title": "github/kbarbary/nestle", + "url": " https://rseng.github.io/software/repository/github/kbarbary/nestle", + "content": "Pure Python, MIT-licensed implementation of nested sampling algorithms for evaluating Bayesian evidence." }, - "github/bradkav/runDM": { - "id": "github/bradkav/runDM", - "title": "github/bradkav/runDM", - "url": " https://rseng.github.io/software/repository/github/bradkav/runDM", - "content": "A tool (in Mathematica and Python) for calculating the running of the couplings of Dark Matter (DM) to the Standard Model (SM) in simplified models with vector mediators." + "github/ericagol/TTVFaster": { + "id": "github/ericagol/TTVFaster", + "title": "github/ericagol/TTVFaster", + "url": " https://rseng.github.io/software/repository/github/ericagol/TTVFaster", + "content": "First order eccentricity transit timing variations computed in Agol & Deck (2015)" }, - "github/bradkav/DMRadon": { - "id": "github/bradkav/DMRadon", - "title": "github/bradkav/DMRadon", - "url": " https://rseng.github.io/software/repository/github/bradkav/DMRadon", - "content": "Tools for calculating the Radon Transform, for use in the analysis of Directional Dark Matter Direct Detection" + "github/ProjectPyRhO/PyRhO": { + "id": "github/ProjectPyRhO/PyRhO", + "title": "github/ProjectPyRhO/PyRhO", + "url": " https://rseng.github.io/software/repository/github/ProjectPyRhO/PyRhO", + "content": "A virtual optogenetics laboratory" }, - "github/bradkav/BlackHolesDarkDress": { - "id": "github/bradkav/BlackHolesDarkDress", - "title": "github/bradkav/BlackHolesDarkDress", - "url": " https://rseng.github.io/software/repository/github/bradkav/BlackHolesDarkDress", - "content": "Code for studying primordial black hole (PBH) binaries, clothed in dark matter (DM) halos, associated with the paper "Black Holes' Dark Dress: On the merger rate of a subdominant population of primordial black holes"." + "github/jeffcsauer/arcos_arcospy_information": { + "id": "github/jeffcsauer/arcos_arcospy_information", + "title": "github/jeffcsauer/arcos_arcospy_information", + "url": " https://rseng.github.io/software/repository/github/jeffcsauer/arcos_arcospy_information", + "content": "This is an informational landing page for the R arcos and Python arcospy software" }, - "github/bradkav/CEvNS": { - "id": "github/bradkav/CEvNS", - "title": "github/bradkav/CEvNS", - "url": " https://rseng.github.io/software/repository/github/bradkav/CEvNS", - "content": "Code for calculating Coherent Elastic Neutrino-Nucleus Scattering (CEvNS) cross sections and recoil spectra. Also includes code for obtaining New Physics constraints from the COHERENT-2017 results." + "github/tkchafin/autostreamtree": { + "id": "github/tkchafin/autostreamtree", + "title": "github/tkchafin/autostreamtree", + "url": " https://rseng.github.io/software/repository/github/tkchafin/autostreamtree", + "content": "Stream trees for SNP datasets" }, - "github/latrop/DECA": { - "id": "github/latrop/DECA", - "title": "github/latrop/DECA", - "url": " https://rseng.github.io/software/repository/github/latrop/DECA", - "content": "A tool for decomposition of images of galaxies" + "github/jgrembi/riskCommunicator": { + "id": "github/jgrembi/riskCommunicator", + "title": "github/jgrembi/riskCommunicator", + "url": " https://rseng.github.io/software/repository/github/jgrembi/riskCommunicator", + "content": "An R package for estimating risk differences and relative risk measures" }, - "github/gui11aume/starcode": { - "id": "github/gui11aume/starcode", - "title": "github/gui11aume/starcode", - "url": " https://rseng.github.io/software/repository/github/gui11aume/starcode", - "content": "All pairs search and sequence clustering" + "github/mlares/hearsay": { + "id": "github/mlares/hearsay", + "title": "github/mlares/hearsay", + "url": " https://rseng.github.io/software/repository/github/mlares/hearsay", + "content": "Simulations for the probability of alien contact" }, - "github/locasto/libdisorder": { - "id": "github/locasto/libdisorder", - "title": "github/locasto/libdisorder", - "url": " https://rseng.github.io/software/repository/github/locasto/libdisorder", - "content": "A simple C library for entropy measurement of byte streams and other data." + "github/javicarron/pynkowski": { + "id": "github/javicarron/pynkowski", + "title": "github/javicarron/pynkowski", + "url": " https://rseng.github.io/software/repository/github/javicarron/pynkowski", + "content": "Pynkowski is a Python package to compute Minkowski Functionals, as well as their expected values for different fields." }, - "github/bids-standard/bids-validator": { - "id": "github/bids-standard/bids-validator", - "title": "github/bids-standard/bids-validator", - "url": " https://rseng.github.io/software/repository/github/bids-standard/bids-validator", - "content": "Validator for the Brain Imaging Data Structure" + "github/javicarron/mtneedlet": { + "id": "github/javicarron/mtneedlet", + "title": "github/javicarron/mtneedlet", + "url": " https://rseng.github.io/software/repository/github/javicarron/mtneedlet", + "content": "This is a Python Package aimed at the use of needlets to filter spherical maps, detecting the maxima within the maps and analysing them using a multiple testing approach." }, - "github/CatarinaMMarques/FisherCosmology": { - "id": "github/CatarinaMMarques/FisherCosmology", - "title": "github/CatarinaMMarques/FisherCosmology", - "url": " https://rseng.github.io/software/repository/github/CatarinaMMarques/FisherCosmology", - "content": "Forecasting Code for Redshift Drift and Alpha Measurements" + "github/singularityhub/sregistry": { + "id": "github/singularityhub/sregistry", + "title": "github/singularityhub/sregistry", + "url": " https://rseng.github.io/software/repository/github/singularityhub/sregistry", + "content": "server for storage and management of singularity images" }, - "github/c3s-magic/c3s-magic-wps": { - "id": "github/c3s-magic/c3s-magic-wps", - "title": "github/c3s-magic/c3s-magic-wps", - "url": " https://rseng.github.io/software/repository/github/c3s-magic/c3s-magic-wps", - "content": "None" + "github/singularityhub/singularity-compose": { + "id": "github/singularityhub/singularity-compose", + "title": "github/singularityhub/singularity-compose", + "url": " https://rseng.github.io/software/repository/github/singularityhub/singularity-compose", + "content": "orchestration for singularity containers (under development)" }, - "github/inpefess/gym-saturation": { - "id": "github/inpefess/gym-saturation", - "title": "github/inpefess/gym-saturation", - "url": " https://rseng.github.io/software/repository/github/inpefess/gym-saturation", - "content": "an OpenAI Gym environment for saturation provers" + "github/singularityhub/singularity-hpc": { + "id": "github/singularityhub/singularity-hpc", + "title": "github/singularityhub/singularity-hpc", + "url": " https://rseng.github.io/software/repository/github/singularityhub/singularity-hpc", + "content": "Local filesystem registry for containers (intended for HPC) using Lmod or Environement Modules. Works for users and admins." }, - "github/jobovy/streamgap-pepper": { - "id": "github/jobovy/streamgap-pepper", - "title": "github/jobovy/streamgap-pepper", - "url": " https://rseng.github.io/software/repository/github/jobovy/streamgap-pepper", - "content": "Code exploring the effect of peppering of streams with many small impacts" + "github/indrops/indrops": { + "id": "github/indrops/indrops", + "title": "github/indrops/indrops", + "url": " https://rseng.github.io/software/repository/github/indrops/indrops", + "content": "Pipeline for processing inDrops sequencing data" }, - "github/jobovy/simple-m2m": { - "id": "github/jobovy/simple-m2m", - "title": "github/jobovy/simple-m2m", - "url": " https://rseng.github.io/software/repository/github/jobovy/simple-m2m", - "content": "Simple M2M setup to explore some new ideas" + "github/cameronliang/BayesVP": { + "id": "github/cameronliang/BayesVP", + "title": "github/cameronliang/BayesVP", + "url": " https://rseng.github.io/software/repository/github/cameronliang/BayesVP", + "content": "None" }, - 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"github/geodynamics/burnman": { - "id": "github/geodynamics/burnman", - "title": "github/geodynamics/burnman", - "url": " https://rseng.github.io/software/repository/github/geodynamics/burnman", - "content": "BurnMan is a library for modeling mantle thermodynamics and thermoelasticity constrained by mineral physics experiments." + "github/rgerum/pylustrator": { + "id": "github/rgerum/pylustrator", + "title": "github/rgerum/pylustrator", + "url": " https://rseng.github.io/software/repository/github/rgerum/pylustrator", + "content": "Visualisations of data are at the core of every publication of scientific research results. They have to be as clear as possible to facilitate the communication of research. As data can have different formats and shapes, the visualisations often have to be adapted to reflect the data as well as possible. We developed Pylustrator, an interface to directly edit python generated matplotlib graphs to finalize them for publication. Therefore, subplots can be resized and dragged around by the mouse, text and annotations can be added. The changes can be saved to the initial plot file as python code." }, - "github/geodynamics/Rayleigh": { - "id": "github/geodynamics/Rayleigh", - "title": "github/geodynamics/Rayleigh", - "url": " https://rseng.github.io/software/repository/github/geodynamics/Rayleigh", - "content": "Rayleigh: Pseudo-spectral MHD" + "github/trevisanj/PFANT": { + "id": "github/trevisanj/PFANT", + "title": "github/trevisanj/PFANT", + "url": " https://rseng.github.io/software/repository/github/trevisanj/PFANT", + "content": "Stellar Spectral Synthesis code for Astronomy" }, - "github/portsmouth/cmbview": { - "id": "github/portsmouth/cmbview", - "title": "github/portsmouth/cmbview", - "url": " https://rseng.github.io/software/repository/github/portsmouth/cmbview", - "content": "Automatically exported from code.google.com/p/cmbview" + "github/timothydmorton/isochrones": { + "id": "github/timothydmorton/isochrones", + "title": "github/timothydmorton/isochrones", + "url": " https://rseng.github.io/software/repository/github/timothydmorton/isochrones", + "content": "Pythonic stellar model grid access; easy MCMC fitting of stellar properties" }, - "github/kadyb/rgugik": { - "id": "github/kadyb/rgugik", - "title": "github/kadyb/rgugik", - "url": " https://rseng.github.io/software/repository/github/kadyb/rgugik", - "content": "Download datasets from Polish Head Office of Geodesy and Cartography" + "github/timothydmorton/vespa": { + "id": "github/timothydmorton/vespa", + "title": "github/timothydmorton/vespa", + "url": " https://rseng.github.io/software/repository/github/timothydmorton/vespa", + "content": "Validation of Exoplanet Signals using a Probabilistic Algorithm--- calculating false positive probabilities for transit signals" }, - "github/oneilsh/tidytensor": { - "id": "github/oneilsh/tidytensor", - "title": "github/oneilsh/tidytensor", - "url": " https://rseng.github.io/software/repository/github/oneilsh/tidytensor", - "content": "Utilities for multidimensional arrays as named hierarchical structures" + "github/annacrnn/rebound_fragmentation": { + "id": "github/annacrnn/rebound_fragmentation", + "title": "github/annacrnn/rebound_fragmentation", + "url": " https://rseng.github.io/software/repository/github/annacrnn/rebound_fragmentation", + "content": "Fragmentation and bulk composition tracking code for the C version of REBOUND. Based on Childs & Steffen 2021." }, - "github/mms-fcul/PypKa": { - "id": "github/mms-fcul/PypKa", - "title": "github/mms-fcul/PypKa", - "url": " https://rseng.github.io/software/repository/github/mms-fcul/PypKa", - "content": "A python module for flexible Poisson-Boltzmann based pKa calculations with proton tautomerism" + "github/cmbant/getdist": { + "id": "github/cmbant/getdist", + "title": "github/cmbant/getdist", + "url": " https://rseng.github.io/software/repository/github/cmbant/getdist", + "content": "MCMC sample analysis, kernel densities, plotting, and GUI" }, - "github/clawpack/pyclaw": { - "id": "github/clawpack/pyclaw", - "title": "github/clawpack/pyclaw", - "url": " https://rseng.github.io/software/repository/github/clawpack/pyclaw", - "content": "PyClaw is a Python-based interface to the algorithms of Clawpack and SharpClaw. It also contains the PetClaw package, which adds parallelism through PETSc." + "github/NoahSailer/FishLSS": { + "id": "github/NoahSailer/FishLSS", + "title": "github/NoahSailer/FishLSS", + "url": " https://rseng.github.io/software/repository/github/NoahSailer/FishLSS", + "content": "Fisher forecasting code for Large Scale Structure surveys using Lagrangian Perturbation Theory." }, - "github/clawpack/clawpack": { - "id": "github/clawpack/clawpack", - "title": "github/clawpack/clawpack", - "url": " https://rseng.github.io/software/repository/github/clawpack/clawpack", - "content": "Package for solving hyperbolic systems of partial differential equations" + "github/yatiml/yatiml": { + "id": "github/yatiml/yatiml", + "title": "github/yatiml/yatiml", + "url": " https://rseng.github.io/software/repository/github/yatiml/yatiml", + "content": "Python library for YAML type inference, schema checking and syntactic sugar" }, - "github/dirac-institute/asterogap": { - "id": "github/dirac-institute/asterogap", - "title": "github/dirac-institute/asterogap", - "url": " https://rseng.github.io/software/repository/github/dirac-institute/asterogap", - "content": "A Bayesian-based Gaussian Process model set to fit sparsely-sampled asteroid light curves." + "github/alan-turing-institute/monitoring-ecosystem-resilience": { + "id": "github/alan-turing-institute/monitoring-ecosystem-resilience", + "title": "github/alan-turing-institute/monitoring-ecosystem-resilience", + "url": " https://rseng.github.io/software/repository/github/alan-turing-institute/monitoring-ecosystem-resilience", + "content": "Repository for mini-projects in the Data science for Sustainable development project " }, - "github/ageller/firefly": { - "id": "github/ageller/firefly", - "title": "github/ageller/firefly", - "url": " https://rseng.github.io/software/repository/github/ageller/firefly", - "content": "A WebGL interactive particle viewer" + "github/alan-turing-institute/MLJ.jl": { + "id": "github/alan-turing-institute/MLJ.jl", + "title": "github/alan-turing-institute/MLJ.jl", + "url": " https://rseng.github.io/software/repository/github/alan-turing-institute/MLJ.jl", + "content": "A Julia machine learning framework" }, - "github/OrchardLANL/DPFEHM.jl": { - "id": "github/OrchardLANL/DPFEHM.jl", - "title": "github/OrchardLANL/DPFEHM.jl", - "url": " https://rseng.github.io/software/repository/github/OrchardLANL/DPFEHM.jl", - "content": "DPFEHM: A Differentiable Subsurface Flow Simulator" + "github/alan-turing-institute/Palaeoanalytics": { + "id": "github/alan-turing-institute/Palaeoanalytics", + "title": "github/alan-turing-institute/Palaeoanalytics", + "url": " https://rseng.github.io/software/repository/github/alan-turing-institute/Palaeoanalytics", + "content": "Repository for the Paleoanalytics project." }, - "github/epic-astronomy/EPIC": { - "id": "github/epic-astronomy/EPIC", - "title": "github/epic-astronomy/EPIC", - "url": " https://rseng.github.io/software/repository/github/epic-astronomy/EPIC", - "content": "None" + "github/alan-turing-institute/DetectorChecker": { + "id": "github/alan-turing-institute/DetectorChecker", + "title": "github/alan-turing-institute/DetectorChecker", + "url": " https://rseng.github.io/software/repository/github/alan-turing-institute/DetectorChecker", + "content": " Project to develop software to assess developing detector screen damage (Web App based on the original DetectorChecker package)" + }, + "github/21cmFAST/21cmFAST": { + "id": "github/21cmFAST/21cmFAST", + "title": "github/21cmFAST/21cmFAST", + "url": " https://rseng.github.io/software/repository/github/21cmFAST/21cmFAST", + "content": "Official repository for 21cmFAST: a code for generating fast simulations of the cosmological 21cm signal" }, - "github/SwissClinicalTrialOrganisation/secuTrialR": { - "id": "github/SwissClinicalTrialOrganisation/secuTrialR", - "title": "github/SwissClinicalTrialOrganisation/secuTrialR", - "url": " https://rseng.github.io/software/repository/github/SwissClinicalTrialOrganisation/secuTrialR", - "content": "Handling of data from the clinical data management system secuTrial" + "github/konfound-project/konfound": { + "id": "github/konfound-project/konfound", + "title": "github/konfound-project/konfound", + "url": " https://rseng.github.io/software/repository/github/konfound-project/konfound", + "content": "R package for carrying out sensitivity analysis" }, - "github/olivecha/guitarsounds": { - "id": "github/olivecha/guitarsounds", - "title": "github/olivecha/guitarsounds", - "url": " https://rseng.github.io/software/repository/github/olivecha/guitarsounds", - "content": "python library to analyse guitar sounds" + "github/pandas-dev/pandas": { + "id": "github/pandas-dev/pandas", + "title": "github/pandas-dev/pandas", + "url": " https://rseng.github.io/software/repository/github/pandas-dev/pandas", + "content": "Flexible and powerful data analysis / manipulation library for Python, providing labeled data structures similar to R data.frame objects, statistical functions, and much more" }, - "github/EISy-as-Py/hardy": { - "id": "github/EISy-as-Py/hardy", - "title": "github/EISy-as-Py/hardy", - "url": " https://rseng.github.io/software/repository/github/EISy-as-Py/hardy", - "content": "Handling Arbitrary Recognition of Data! y not?" + "github/QuaCaTeam/quaca": { + "id": "github/QuaCaTeam/quaca", + "title": "github/QuaCaTeam/quaca", + "url": " https://rseng.github.io/software/repository/github/QuaCaTeam/quaca", + "content": "QuaCa is an open-source library which provides fast calculations of nonequilibrium atom-surface interactions." }, - "github/gridap/Gridap.jl": { - "id": "github/gridap/Gridap.jl", - "title": "github/gridap/Gridap.jl", - "url": " https://rseng.github.io/software/repository/github/gridap/Gridap.jl", - "content": "Grid-based approximation of partial differential equations in Julia" + "github/DJArmstrong/TransitSOM": { + "id": "github/DJArmstrong/TransitSOM", + "title": "github/DJArmstrong/TransitSOM", + "url": " https://rseng.github.io/software/repository/github/DJArmstrong/TransitSOM", + "content": "A Self-Organising Map for Kepler and K2 Transits" }, - "github/yymao/abundancematching": { - "id": "github/yymao/abundancematching", - "title": "github/yymao/abundancematching", - "url": " https://rseng.github.io/software/repository/github/yymao/abundancematching", - "content": "A Python package for subhalo abundance matching (SHAM) with scatter." + "github/rhyspoulton/OrbWeaver": { + "id": "github/rhyspoulton/OrbWeaver", + "title": "github/rhyspoulton/OrbWeaver", + "url": " https://rseng.github.io/software/repository/github/rhyspoulton/OrbWeaver", + "content": "Galaxy/(sub)halo orbital processing tool" }, - "github/ChileanVirtualObservatory/indexing_utfsm": { - "id": "github/ChileanVirtualObservatory/indexing_utfsm", - "title": "github/ChileanVirtualObservatory/indexing_utfsm", - "url": " https://rseng.github.io/software/repository/github/ChileanVirtualObservatory/indexing_utfsm", - "content": "R implementation of RoiSE algorithm" + "github/rhyspoulton/WhereWolf": { + "id": "github/rhyspoulton/WhereWolf", + "title": "github/rhyspoulton/WhereWolf", + "url": " https://rseng.github.io/software/repository/github/rhyspoulton/WhereWolf", + "content": "Galaxy/(sub)Halo ghosting tool for N-body simulations" }, - "github/astroCV/astroCV": { - "id": "github/astroCV/astroCV", - "title": "github/astroCV/astroCV", - "url": " https://rseng.github.io/software/repository/github/astroCV/astroCV", - "content": "Computer Vision library for Astronomy" + "github/cog-imperial/GPdoemd": { + "id": "github/cog-imperial/GPdoemd", + "title": "github/cog-imperial/GPdoemd", + "url": " https://rseng.github.io/software/repository/github/cog-imperial/GPdoemd", + "content": "Design of experiments for model discrimination using Gaussian process surrogate models" }, - "github/matthias-mayr/Cartesian-Impedance-Controller": { - "id": "github/matthias-mayr/Cartesian-Impedance-Controller", - "title": "github/matthias-mayr/Cartesian-Impedance-Controller", - "url": " https://rseng.github.io/software/repository/github/matthias-mayr/Cartesian-Impedance-Controller", - "content": "A C++ implementation of Cartesian impedance control for torque-controlled manipulators with ROS bindings." + "github/cog-imperial/suspect": { + "id": "github/cog-imperial/suspect", + "title": "github/cog-imperial/suspect", + "url": " https://rseng.github.io/software/repository/github/cog-imperial/suspect", + "content": "Special Structure Detection for Pyomo" }, - "github/ofionnad/radiowinds": { - "id": "github/ofionnad/radiowinds", - "title": "github/ofionnad/radiowinds", - "url": " https://rseng.github.io/software/repository/github/ofionnad/radiowinds", - "content": "Calculate the thermal bremsstrahlung emission from stellar winds" + "github/cog-imperial/galini": { + "id": "github/cog-imperial/galini", + "title": "github/cog-imperial/galini", + "url": " https://rseng.github.io/software/repository/github/cog-imperial/galini", + "content": "An extensible MINLP solver" }, - "github/lu-yizhou/ClusterSeg": { - "id": "github/lu-yizhou/ClusterSeg", - "title": "github/lu-yizhou/ClusterSeg", - "url": " https://rseng.github.io/software/repository/github/lu-yizhou/ClusterSeg", + "github/cog-imperial/entmoot": { + "id": "github/cog-imperial/entmoot", + "title": "github/cog-imperial/entmoot", + "url": " https://rseng.github.io/software/repository/github/cog-imperial/entmoot", "content": "None" }, - "github/facebookresearch/segment-anything": { - "id": "github/facebookresearch/segment-anything", - "title": "github/facebookresearch/segment-anything", - "url": " https://rseng.github.io/software/repository/github/facebookresearch/segment-anything", - "content": "The repository provides code for running inference with the SegmentAnything Model (SAM), links for downloading the trained model checkpoints, and example notebooks that show how to use the model." + "github/1054/Crab.Toolkit.michi2": { + "id": "github/1054/Crab.Toolkit.michi2", + "title": "github/1054/Crab.Toolkit.michi2", + "url": " https://rseng.github.io/software/repository/github/1054/Crab.Toolkit.michi2", + "content": "crab minimum chi2 toolkit" }, - "github/facebookresearch/faiss": { - "id": "github/facebookresearch/faiss", - "title": "github/facebookresearch/faiss", - "url": " https://rseng.github.io/software/repository/github/facebookresearch/faiss", - "content": "A library for efficient similarity search and clustering of dense vectors." + "github/SPARTA-dev/SPARTA": { + "id": "github/SPARTA-dev/SPARTA", + "title": "github/SPARTA-dev/SPARTA", + "url": " https://rseng.github.io/software/repository/github/SPARTA-dev/SPARTA", + "content": "None" }, - 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It can be used to model a variety of axisymmetric astronomical dust systems." }, - "github/tp2vis/distribute": { - "id": "github/tp2vis/distribute", - "title": "github/tp2vis/distribute", - "url": " https://rseng.github.io/software/repository/github/tp2vis/distribute", + "github/portsmouth/cmbview": { + "id": "github/portsmouth/cmbview", + "title": "github/portsmouth/cmbview", + "url": " https://rseng.github.io/software/repository/github/portsmouth/cmbview", + "content": "Automatically exported from code.google.com/p/cmbview" + }, + "github/cgarraffo/StelNet": { + "id": "github/cgarraffo/StelNet", + "title": "github/cgarraffo/StelNet", + "url": " https://rseng.github.io/software/repository/github/cgarraffo/StelNet", "content": "None" }, - "github/nevrome/bleiglas": { - "id": "github/nevrome/bleiglas", - "title": "github/nevrome/bleiglas", - "url": " https://rseng.github.io/software/repository/github/nevrome/bleiglas", - "content": "R Package - Spatiotemporal Data Interpolation and Visualisation based on 3D Tessellation" + "github/ocean-eddy-cpt/gcm-filters": { + "id": "github/ocean-eddy-cpt/gcm-filters", + "title": "github/ocean-eddy-cpt/gcm-filters", + "url": " https://rseng.github.io/software/repository/github/ocean-eddy-cpt/gcm-filters", + "content": "Diffusion-based Spatial Filtering of Gridded Data" }, - "github/GalSim-developers/GalSim": { - "id": "github/GalSim-developers/GalSim", - "title": "github/GalSim-developers/GalSim", - "url": " https://rseng.github.io/software/repository/github/GalSim-developers/GalSim", - "content": "The modular galaxy image simulation toolkit. Documentation:" + "github/sfschen/velocileptors": { + "id": "github/sfschen/velocileptors", + "title": "github/sfschen/velocileptors", + "url": " https://rseng.github.io/software/repository/github/sfschen/velocileptors", + "content": "A code for velocity-based Lagrangian and Eulerian PT expansions of redshift-space distortions." }, - "github/tuoyl/tat-pulsar": { - "id": "github/tuoyl/tat-pulsar", - "title": "github/tuoyl/tat-pulsar", - "url": " https://rseng.github.io/software/repository/github/tuoyl/tat-pulsar", - "content": "A Python based pulsar timing analysis tools (TAT)." + "github/hsso/crete": { + "id": "github/hsso/crete", + "title": "github/hsso/crete", + "url": " https://rseng.github.io/software/repository/github/hsso/crete", + "content": "Comet RadiativE Transfer and Excitation" }, - "github/dvallesp/vortex": { - "id": "github/dvallesp/vortex", - "title": "github/dvallesp/vortex", - "url": " https://rseng.github.io/software/repository/github/dvallesp/vortex", - "content": "Implements Helmholtz-Hodge decomposition for an AMR velocity field" + "github/deweylab/RSEM": { + "id": "github/deweylab/RSEM", + "title": "github/deweylab/RSEM", + "url": " https://rseng.github.io/software/repository/github/deweylab/RSEM", + "content": "RSEM: accurate quantification of gene and isoform expression from RNA-Seq data" }, - "github/dvallesp/asohf": { - "id": "github/dvallesp/asohf", - "title": "github/dvallesp/asohf", - "url": " https://rseng.github.io/software/repository/github/dvallesp/asohf", - "content": "Adaptive Spherical Overdensity Halo Finder (Planelles & Quilis, 2010. A&A, 519:A94; Vallés-Pérez, Planelles & Quilis, 2022. 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Functionality is also present for standard point-charge based force fields, pure MM, and pure QM calculations." + "github/parafields/parafields": { + "id": "github/parafields/parafields", + "title": "github/parafields/parafields", + "url": " https://rseng.github.io/software/repository/github/parafields/parafields", + "content": "Parallel Parameter Field Generator for Python" }, - "github/bwkeller/PASTA": { - "id": "github/bwkeller/PASTA", - "title": "github/bwkeller/PASTA", - "url": " https://rseng.github.io/software/repository/github/bwkeller/PASTA", - "content": "Python Astronomical Stacking Tool Array" + "github/dputhier/pygtftk": { + "id": "github/dputhier/pygtftk", + "title": "github/dputhier/pygtftk", + "url": " https://rseng.github.io/software/repository/github/dputhier/pygtftk", + "content": "A python package and a set of shell commands to handle GTF files" }, - "github/fcs-analysis/PyScanFCS": { - "id": "github/fcs-analysis/PyScanFCS", - "title": "github/fcs-analysis/PyScanFCS", - 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Based on Childs & Steffen 2021." + "github/ulelab/ultraplex": { + "id": "github/ulelab/ultraplex", + "title": "github/ulelab/ultraplex", + "url": " https://rseng.github.io/software/repository/github/ulelab/ultraplex", + "content": "Ultra-fast 5' and 3' demultiplexer" }, - "github/ialopezt/GalLenspy": { - "id": "github/ialopezt/GalLenspy", - "title": "github/ialopezt/GalLenspy", - "url": " https://rseng.github.io/software/repository/github/ialopezt/GalLenspy", - "content": "This is a open code whose purpose is the reconstruction of mass profile in disc-like galaxies from the gravitational lensing effect." + "github/Pithikos/C-Thread-Pool": { + "id": "github/Pithikos/C-Thread-Pool", + "title": "github/Pithikos/C-Thread-Pool", + "url": " https://rseng.github.io/software/repository/github/Pithikos/C-Thread-Pool", + "content": "A minimal but powerful thread pool in ANSI C" }, - "github/annayqho/TheCannon": { - "id": "github/annayqho/TheCannon", - "title": "github/annayqho/TheCannon", - "url": " https://rseng.github.io/software/repository/github/annayqho/TheCannon", - "content": "a data-driven method for determining stellar parameters and abundances from stellar spectra" + "github/cjneely10/EukMetaSanity": { + "id": "github/cjneely10/EukMetaSanity", + "title": "github/cjneely10/EukMetaSanity", + "url": " https://rseng.github.io/software/repository/github/cjneely10/EukMetaSanity", + "content": "Structural and functional annotation of eukaryotic metagenome-assembled genomes" }, - "github/andr1976/HydDown": { - "id": "github/andr1976/HydDown", - "title": "github/andr1976/HydDown", - "url": " https://rseng.github.io/software/repository/github/andr1976/HydDown", - "content": "Hydrogen (or other pure gas phase species) depressurization calculations" + "github/mrtommyb/ktransit": { + "id": "github/mrtommyb/ktransit", + "title": "github/mrtommyb/ktransit", + "url": " https://rseng.github.io/software/repository/github/mrtommyb/ktransit", + "content": "A simple exoplanet transit modeling tool in python" }, - "github/MIT-STARLab/deconfuser": { - "id": "github/MIT-STARLab/deconfuser", - "title": "github/MIT-STARLab/deconfuser", - "url": " https://rseng.github.io/software/repository/github/MIT-STARLab/deconfuser", - "content": "Fast orbit fitting to directly imaged multi-planetary systems" + "github/CAMI-challenge/CAMITAX": { + "id": "github/CAMI-challenge/CAMITAX", + "title": "github/CAMI-challenge/CAMITAX", + "url": " https://rseng.github.io/software/repository/github/CAMI-challenge/CAMITAX", + "content": "CAMITAX: Taxon labels for microbial genomes" }, - "github/jharno/cubep3m": { - "id": "github/jharno/cubep3m", - "title": "github/jharno/cubep3m", - "url": " https://rseng.github.io/software/repository/github/jharno/cubep3m", - "content": "cosmological n-body code" + "github/cistib/origami": { + "id": "github/cistib/origami", + "title": "github/cistib/origami", + "url": " https://rseng.github.io/software/repository/github/cistib/origami", + "content": "MATLAB-based image analysis pipeline for extracting single-cell direction-variant shape features from fluorescence images of folding epithelial sheets." }, - 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"id": "github/exosports/MARGE", - "title": "github/exosports/MARGE", - "url": " https://rseng.github.io/software/repository/github/exosports/MARGE", - "content": "Machine learning Algorithm for Radiative transfer of Generated Exoplanets" + "github/dh4gan/grapus": { + "id": "github/dh4gan/grapus", + "title": "github/dh4gan/grapus", + "url": " https://rseng.github.io/software/repository/github/dh4gan/grapus", + "content": "Population synthesis of self-gravitating disc fragmentation and tidal downsizing in protostellar discs" }, - "github/exosports/BART": { - "id": "github/exosports/BART", - "title": "github/exosports/BART", - "url": " https://rseng.github.io/software/repository/github/exosports/BART", - "content": "Bayesian Atmospheric Radiative Transfer fitting code" + "github/dh4gan/oberon": { + "id": "github/dh4gan/oberon", + "title": "github/dh4gan/oberon", + "url": " https://rseng.github.io/software/repository/github/dh4gan/oberon", + "content": "This C++ code models the climate of Earthlike planets under the effects of an arbitrary number and arrangement of other bodies, such as stars, planets and moons." }, - 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It is highly flexible, with a built-in scripting language, and has a cross-platform graphical modeling environment called SLiMgui." }, - "github/freemed/freeshim": { - "id": "github/freemed/freeshim", - "title": "github/freemed/freeshim", - "url": " https://rseng.github.io/software/repository/github/freemed/freeshim", - "content": "opensource multiplatform medical device interface" + "github/xiaofengsong/pHisPred": { + "id": "github/xiaofengsong/pHisPred", + "title": "github/xiaofengsong/pHisPred", + "url": " https://rseng.github.io/software/repository/github/xiaofengsong/pHisPred", + "content": "A bioinformatic tool for identifying protein histidine phosphorylation sites" }, - "github/brian-team/brian2": { - "id": "github/brian-team/brian2", - "title": "github/brian-team/brian2", - "url": " https://rseng.github.io/software/repository/github/brian-team/brian2", - "content": "Brian is a free, open source simulator for spiking neural networks. " + "github/cdanielmachado/carveme": { + "id": "github/cdanielmachado/carveme", + "title": "github/cdanielmachado/carveme", + "url": " https://rseng.github.io/software/repository/github/cdanielmachado/carveme", + "content": "CarveMe: genome-scale metabolic model reconstruction" }, - "github/OpenMDAO/dymos": { - "id": "github/OpenMDAO/dymos", - "title": "github/OpenMDAO/dymos", - "url": " https://rseng.github.io/software/repository/github/OpenMDAO/dymos", - "content": "Open Source Optimization of Dynamic Multidisciplinary Systems" + "github/cdanielmachado/reframed": { + "id": "github/cdanielmachado/reframed", + "title": "github/cdanielmachado/reframed", + "url": " https://rseng.github.io/software/repository/github/cdanielmachado/reframed", + "content": "ReFramed: metabolic modeling package" + }, + "github/AgrDataSci/climatrends": { + "id": "github/AgrDataSci/climatrends", + "title": "github/AgrDataSci/climatrends", + "url": " https://rseng.github.io/software/repository/github/AgrDataSci/climatrends", + "content": "Climate Variability Indices for Ecological Modelling" }, - "github/fwhigh/stellar-locus-regression": { - "id": "github/fwhigh/stellar-locus-regression", - "title": "github/fwhigh/stellar-locus-regression", - "url": " https://rseng.github.io/software/repository/github/fwhigh/stellar-locus-regression", - "content": "Automatically exported from code.google.com/p/stellar-locus-regression" + "github/vincentlab/PyFR": { + "id": "github/vincentlab/PyFR", + "title": "github/vincentlab/PyFR", + "url": " https://rseng.github.io/software/repository/github/vincentlab/PyFR", + "content": "PyFR" }, - "github/jbytecode/JMcDM": { - "id": "github/jbytecode/JMcDM", - "title": "github/jbytecode/JMcDM", - "url": " https://rseng.github.io/software/repository/github/jbytecode/JMcDM", - "content": "A package for Multiple criteria decision-making techniques in Julia" + "github/FelixKrueger/TrimGalore": { + "id": "github/FelixKrueger/TrimGalore", + "title": "github/FelixKrueger/TrimGalore", + "url": " https://rseng.github.io/software/repository/github/FelixKrueger/TrimGalore", + "content": "A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data" }, - "github/jbytecode/LinRegOutliers": { - "id": "github/jbytecode/LinRegOutliers", - "title": "github/jbytecode/LinRegOutliers", - "url": " https://rseng.github.io/software/repository/github/jbytecode/LinRegOutliers", - "content": "Direct and robust methods for outlier detection in linear regression" + "github/adrn/pyia": { + "id": "github/adrn/pyia", + "title": "github/adrn/pyia", + "url": " https://rseng.github.io/software/repository/github/adrn/pyia", + "content": "a Python package for working with data from the Gaia mission" }, - "github/McMahonCosmologyGroup/holosim-ml": { - "id": "github/McMahonCosmologyGroup/holosim-ml", - "title": "github/McMahonCosmologyGroup/holosim-ml", - "url": " https://rseng.github.io/software/repository/github/McMahonCosmologyGroup/holosim-ml", - "content": "machine learning applied to the efficient analysis of radio holography measurements of complex optical systems" + "github/adrn/schwimmbad": { + "id": "github/adrn/schwimmbad", + "title": "github/adrn/schwimmbad", + "url": " https://rseng.github.io/software/repository/github/adrn/schwimmbad", + "content": "A common interface to processing pools." }, - "github/quatrope/ProperImage": { - "id": "github/quatrope/ProperImage", - "title": "github/quatrope/ProperImage", - "url": " https://rseng.github.io/software/repository/github/quatrope/ProperImage", - "content": "Proper Image utils for astronomy. " + "github/adrn/SuperFreq": { + "id": "github/adrn/SuperFreq", + "title": "github/adrn/SuperFreq", + "url": " https://rseng.github.io/software/repository/github/adrn/SuperFreq", + "content": "Numerically determine the fundamental frequencies of an orbit" }, - "github/quatrope/feets": { - "id": "github/quatrope/feets", - "title": "github/quatrope/feets", - "url": " https://rseng.github.io/software/repository/github/quatrope/feets", - "content": "feATURE eXTRACTOR FOR tIME sERIES" + "github/reproducible-biomedical-modeling/Biosimulations": { + "id": "github/reproducible-biomedical-modeling/Biosimulations", + "title": "github/reproducible-biomedical-modeling/Biosimulations", + "url": " https://rseng.github.io/software/repository/github/reproducible-biomedical-modeling/Biosimulations", + "content": "Platform for sharing and reusing biomodeling studies including models, simulations, and visualizations of their results" }, - "github/pymatting/pymatting": { - "id": "github/pymatting/pymatting", - "title": "github/pymatting/pymatting", - "url": " https://rseng.github.io/software/repository/github/pymatting/pymatting", - "content": "A Python library for alpha matting" + "github/DistrictDataLabs/yellowbrick": { + "id": "github/DistrictDataLabs/yellowbrick", + "title": "github/DistrictDataLabs/yellowbrick", + "url": " https://rseng.github.io/software/repository/github/DistrictDataLabs/yellowbrick", + "content": "Visual analysis and diagnostic tools to facilitate machine learning model selection." }, - "github/jorittmo/singcar": { - "id": "github/jorittmo/singcar", - "title": "github/jorittmo/singcar", - "url": " https://rseng.github.io/software/repository/github/jorittmo/singcar", - "content": "singcar: A package for analysing case comparisons to normative controls" + "github/rajeshrinet/pystokes": { + "id": "github/rajeshrinet/pystokes", + "title": "github/rajeshrinet/pystokes", + "url": " https://rseng.github.io/software/repository/github/rajeshrinet/pystokes", + "content": "PyStokes: phoresis and Stokesian hydrodynamics in Python: https://github.com/rajeshrinet/pystokes" }, - "github/kimberg/voxbo": { - "id": "github/kimberg/voxbo", - "title": "github/kimberg/voxbo", - "url": " https://rseng.github.io/software/repository/github/kimberg/voxbo", - "content": "free software for brain image analysis" + "github/seclark/RHT": { + "id": "github/seclark/RHT", + "title": "github/seclark/RHT", + "url": " https://rseng.github.io/software/repository/github/seclark/RHT", + "content": "The Rolling Hough Transform" }, - "github/DeepRegNet/DeepReg": { - "id": "github/DeepRegNet/DeepReg", - "title": "github/DeepRegNet/DeepReg", - "url": " https://rseng.github.io/software/repository/github/DeepRegNet/DeepReg", - "content": "Medical image registration using deep learning" + "github/dfujim/bfit": { + "id": "github/dfujim/bfit", + "title": "github/dfujim/bfit", + "url": " https://rseng.github.io/software/repository/github/dfujim/bfit", + "content": "A Python application for the analysis of β-NMR and β-NQR data taken at TRIUMF." }, - "github/PyPO-dev/PyPO": { - "id": "github/PyPO-dev/PyPO", - "title": "github/PyPO-dev/PyPO", - "url": " https://rseng.github.io/software/repository/github/PyPO-dev/PyPO", - "content": "📡 Open-source physical optics simulation package." + "github/pynbody/pynbody": { + "id": "github/pynbody/pynbody", + "title": "github/pynbody/pynbody", + "url": " https://rseng.github.io/software/repository/github/pynbody/pynbody", + "content": "N-body and hydro analysis tools for Python 3. (Older versions support Python 2.)" }, - "github/guilledufort/EnanoFASTQ": { - "id": "github/guilledufort/EnanoFASTQ", - "title": "github/guilledufort/EnanoFASTQ", - "url": " https://rseng.github.io/software/repository/github/guilledufort/EnanoFASTQ", - "content": "A FASTQ lossless compression algorithm especially designed for nanopore sequencing FASTQ files." + "github/pynbody/tangos": { + "id": "github/pynbody/tangos", + "title": "github/pynbody/tangos", + "url": " https://rseng.github.io/software/repository/github/pynbody/tangos", + "content": "The Agile Numerical Galaxy Organisation System" }, - "github/cytham/nanovar": { - "id": "github/cytham/nanovar", - "title": "github/cytham/nanovar", - "url": " https://rseng.github.io/software/repository/github/cytham/nanovar", - "content": "Structural variant caller for low-depth long-read sequencing data" + "github/pynbody/genetIC": { + "id": "github/pynbody/genetIC", + "title": "github/pynbody/genetIC", + "url": " https://rseng.github.io/software/repository/github/pynbody/genetIC", + "content": "The GM initial conditions generator" }, - "github/JSB-UCLA/scPNMF": { - "id": "github/JSB-UCLA/scPNMF", - "title": "github/JSB-UCLA/scPNMF", - "url": " https://rseng.github.io/software/repository/github/JSB-UCLA/scPNMF", - "content": "None" + "github/institut-de-genomique/HAPO-G": { + "id": "github/institut-de-genomique/HAPO-G", + "title": "github/institut-de-genomique/HAPO-G", + "url": " https://rseng.github.io/software/repository/github/institut-de-genomique/HAPO-G", + "content": "Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads." }, - "github/taoliu/MACS": { - "id": "github/taoliu/MACS", - "title": "github/taoliu/MACS", - "url": " https://rseng.github.io/software/repository/github/taoliu/MACS", - "content": "MACS -- Model-based Analysis of ChIP-Seq" + "github/GilbertLabUCSF/CanDI": { + "id": "github/GilbertLabUCSF/CanDI", + "title": "github/GilbertLabUCSF/CanDI", + "url": " https://rseng.github.io/software/repository/github/GilbertLabUCSF/CanDI", + "content": "CanDI - A global cancer data integrator" }, - "github/xcompact3d/Incompact3d": { - "id": "github/xcompact3d/Incompact3d", - "title": "github/xcompact3d/Incompact3d", - "url": " https://rseng.github.io/software/repository/github/xcompact3d/Incompact3d", - "content": "New version of our solver for the incompressible Navier-Stokes equations" + "github/UCD4IDS/WaveletsExt.jl": { + "id": "github/UCD4IDS/WaveletsExt.jl", + "title": "github/UCD4IDS/WaveletsExt.jl", + "url": " https://rseng.github.io/software/repository/github/UCD4IDS/WaveletsExt.jl", + "content": "A Julia extension package to Wavelets.jl" }, - "github/creaneroDIAS/beamModelTester": { - "id": "github/creaneroDIAS/beamModelTester", - "title": "github/creaneroDIAS/beamModelTester", - "url": " https://rseng.github.io/software/repository/github/creaneroDIAS/beamModelTester", - "content": "a general-purpose tool for evaluation of models of radio telescope beams." + "github/bencebeky/spotrod": { + "id": "github/bencebeky/spotrod", + "title": "github/bencebeky/spotrod", + "url": " https://rseng.github.io/software/repository/github/bencebeky/spotrod", + "content": "A semi-analytic model for transits of spotted stars -- C implementation and Python API" }, - "github/PyFstat/PyFstat": { - "id": "github/PyFstat/PyFstat", - "title": "github/PyFstat/PyFstat", - "url": " https://rseng.github.io/software/repository/github/PyFstat/PyFstat", - "content": "a python package for gravitational wave analysis with the F-statistic" + "github/PACurran/MCSpearman": { + "id": "github/PACurran/MCSpearman", + "title": "github/PACurran/MCSpearman", + "url": " https://rseng.github.io/software/repository/github/PACurran/MCSpearman", + "content": "Monte Carlo error analyses of Spearman’s rank test" }, - "github/rgerum/pylustrator": { - "id": "github/rgerum/pylustrator", - "title": "github/rgerum/pylustrator", - "url": " https://rseng.github.io/software/repository/github/rgerum/pylustrator", - "content": "Visualisations of data are at the core of every publication of scientific research results. They have to be as clear as possible to facilitate the communication of research. As data can have different formats and shapes, the visualisations often have to be adapted to reflect the data as well as possible. We developed Pylustrator, an interface to directly edit python generated matplotlib graphs to finalize them for publication. Therefore, subplots can be resized and dragged around by the mouse, text and annotations can be added. The changes can be saved to the initial plot file as python code." + "github/maayane/catsHTM": { + "id": "github/maayane/catsHTM", + "title": "github/maayane/catsHTM", + "url": " https://rseng.github.io/software/repository/github/maayane/catsHTM", + "content": "A tool for fast accessing and cross-matching large astronomical catalogs" }, - "github/jfalconbarroso/BAYES-LOSVD": { - "id": "github/jfalconbarroso/BAYES-LOSVD", - "title": "github/jfalconbarroso/BAYES-LOSVD", - "url": " https://rseng.github.io/software/repository/github/jfalconbarroso/BAYES-LOSVD", - "content": "Non-parametric recovery of the LOSVD of galaxies" + "github/ni1o1/transbigdata": { + "id": "github/ni1o1/transbigdata", + "title": "github/ni1o1/transbigdata", + "url": " https://rseng.github.io/software/repository/github/ni1o1/transbigdata", + "content": "A Python package develop for transportation spatio-temporal big data processing, analysis and visualization." }, - "github/mneeleman/qubefit": { - "id": "github/mneeleman/qubefit", - "title": "github/mneeleman/qubefit", - "url": " https://rseng.github.io/software/repository/github/mneeleman/qubefit", - "content": "None" + "github/solislemuslab/minaa": { + "id": "github/solislemuslab/minaa", + "title": "github/solislemuslab/minaa", + "url": " https://rseng.github.io/software/repository/github/solislemuslab/minaa", + "content": "MiNAA aligns a pair of networks based their topologies and biologies." }, - "github/obreschkow/dftools": { - "id": "github/obreschkow/dftools", - "title": "github/obreschkow/dftools", - "url": " https://rseng.github.io/software/repository/github/obreschkow/dftools", - "content": "None" + "github/AlphonsG/Rainbow-Optical-Flow-For-ALI": { + "id": "github/AlphonsG/Rainbow-Optical-Flow-For-ALI", + "title": "github/AlphonsG/Rainbow-Optical-Flow-For-ALI", + "url": " https://rseng.github.io/software/repository/github/AlphonsG/Rainbow-Optical-Flow-For-ALI", + "content": "Repository for software detailed in 'Rainbow: Automated Air-Liquid Interface Cell Culture Analysis Using Deep Optical Flow' software paper. See Readme for more details." }, - "github/jarvist/Julia-Phonons": { - "id": "github/jarvist/Julia-Phonons", - "title": "github/jarvist/Julia-Phonons", - "url": " https://rseng.github.io/software/repository/github/jarvist/Julia-Phonons", - "content": "Julia codes to play with Phonons" + "github/kavir1698/EvoDynamics.jl": { + "id": "github/kavir1698/EvoDynamics.jl", + "title": "github/kavir1698/EvoDynamics.jl", + "url": " https://rseng.github.io/software/repository/github/kavir1698/EvoDynamics.jl", + "content": "Simulation of eco-evolutionary dynamics on multi-trait networks" }, - "github/mentatpsi/OSGenome": { - "id": "github/mentatpsi/OSGenome", - "title": "github/mentatpsi/OSGenome", - "url": " https://rseng.github.io/software/repository/github/mentatpsi/OSGenome", - "content": "An Open Source Web Application for Genetic Data (SNPs) using 23AndMe and Data Crawling Technologies" + "github/nemesiscode/radtrancode": { + "id": "github/nemesiscode/radtrancode", + "title": "github/nemesiscode/radtrancode", + "url": " https://rseng.github.io/software/repository/github/nemesiscode/radtrancode", + "content": "This is the repository of the NEMESIS/RADTRANS project. 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It also has a function to query the GDR2 RVS sample selection function." + }, + "github/jan-rybizki/Galaxia_wrap": { + "id": "github/jan-rybizki/Galaxia_wrap", + "title": "github/jan-rybizki/Galaxia_wrap", + "url": " https://rseng.github.io/software/repository/github/jan-rybizki/Galaxia_wrap", + "content": "A few python scripts and a tutorial notebook to create and manipulate Galaxia mock catalogues" }, - "github/grburgess/popsynth": { - "id": "github/grburgess/popsynth", - "title": "github/grburgess/popsynth", - "url": " https://rseng.github.io/software/repository/github/grburgess/popsynth", - "content": "A generic flux/parameter population synthesis code" + "github/jan-rybizki/Chempy": { + "id": "github/jan-rybizki/Chempy", + "title": "github/jan-rybizki/Chempy", + "url": " https://rseng.github.io/software/repository/github/jan-rybizki/Chempy", + "content": "Start with the Chempy tutorial" }, - "github/grburgess/ronswanson": { - "id": "github/grburgess/ronswanson", - "title": "github/grburgess/ronswanson", - "url": " https://rseng.github.io/software/repository/github/grburgess/ronswanson", - "content": "Ron Swanson builds tables for 3ML" + "github/yogi-tud/space_gpu": { + "id": "github/yogi-tud/space_gpu", + "title": "github/yogi-tud/space_gpu", + "url": " https://rseng.github.io/software/repository/github/yogi-tud/space_gpu", + "content": "None" }, - "github/Kamuish/archi": { - "id": "github/Kamuish/archi", - "title": "github/Kamuish/archi", - "url": " https://rseng.github.io/software/repository/github/Kamuish/archi", - "content": "Pipeline to study CHEOPS background stars" + "github/mortonne/psifr": { + "id": "github/mortonne/psifr", + "title": "github/mortonne/psifr", + "url": " https://rseng.github.io/software/repository/github/mortonne/psifr", + "content": "Psifr: Analysis and visualization of free recall data" }, - "github/fredstro/hilbertmodgroup": { - "id": "github/fredstro/hilbertmodgroup", - "title": "github/fredstro/hilbertmodgroup", - "url": " https://rseng.github.io/software/repository/github/fredstro/hilbertmodgroup", - "content": "Implementation of Hilbert modular groups using SageMath" + "github/JuliaSmoothOptimizers/PDENLPModels.jl": { + "id": "github/JuliaSmoothOptimizers/PDENLPModels.jl", + "title": "github/JuliaSmoothOptimizers/PDENLPModels.jl", + "url": " https://rseng.github.io/software/repository/github/JuliaSmoothOptimizers/PDENLPModels.jl", + "content": "A NLPModel API for optimization problems with PDE-constraints" }, - "github/kushaltirumala/WaldoInSky": { - "id": "github/kushaltirumala/WaldoInSky", - "title": "github/kushaltirumala/WaldoInSky", - "url": " https://rseng.github.io/software/repository/github/kushaltirumala/WaldoInSky", - "content": "Code Repository for `Where is Waldo (and his friends)? A comparison of anomaly detection algorithms for time-domain astronomy`" + "github/JuliaSmoothOptimizers/DCISolver.jl": { + "id": "github/JuliaSmoothOptimizers/DCISolver.jl", + "title": "github/JuliaSmoothOptimizers/DCISolver.jl", + "url": " https://rseng.github.io/software/repository/github/JuliaSmoothOptimizers/DCISolver.jl", + "content": "None" }, - "github/csb-toolbox/CSB": { - "id": "github/csb-toolbox/CSB", - "title": "github/csb-toolbox/CSB", - "url": " https://rseng.github.io/software/repository/github/csb-toolbox/CSB", - "content": "A Python framework for structural bioinformatics." + "github/venkateshgopinath/FAlCon-DNS": { + "id": "github/venkateshgopinath/FAlCon-DNS", + "title": "github/venkateshgopinath/FAlCon-DNS", + "url": " https://rseng.github.io/software/repository/github/venkateshgopinath/FAlCon-DNS", + "content": "FAlCon-DNS (Framework of time schemes for Direct Numerical Simulation of Annular Convection) is a code to solve 2D thermal convection in an annulus. 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A program for operating on MCMC chains and related lists of samples from a function or distribution." + "github/statgen/popscle": { + "id": "github/statgen/popscle", + "title": "github/statgen/popscle", + "url": " https://rseng.github.io/software/repository/github/statgen/popscle", + "content": "A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxilary tools" }, - "github/CTU-Bern/presize": { - "id": "github/CTU-Bern/presize", - "title": "github/CTU-Bern/presize", - "url": " https://rseng.github.io/software/repository/github/CTU-Bern/presize", - "content": "Precision Based Sample Size Calculation" + "github/SWIFTSIM/emulator": { + "id": "github/SWIFTSIM/emulator", + "title": "github/SWIFTSIM/emulator", + "url": " https://rseng.github.io/software/repository/github/SWIFTSIM/emulator", + "content": "The SWIFT simulation cosmological emulator (swift-emulator)" }, - "github/ptriska/WavesDash": { - "id": "github/ptriska/WavesDash", - 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"content": "The Julia Language: A fresh approach to technical computing." + "github/timchurches/NetEpi-Collection": { + "id": "github/timchurches/NetEpi-Collection", + "title": "github/timchurches/NetEpi-Collection", + "url": " https://rseng.github.io/software/repository/github/timchurches/NetEpi-Collection", + "content": "Communicable disease and epidemiological data collection and management system" }, - "github/bommert/stabm": { - "id": "github/bommert/stabm", - "title": "github/bommert/stabm", - "url": " https://rseng.github.io/software/repository/github/bommert/stabm", - "content": "Stability measures" + "github/timchurches/NetEpi-Analysis": { + "id": "github/timchurches/NetEpi-Analysis", + "title": "github/timchurches/NetEpi-Analysis", + "url": " https://rseng.github.io/software/repository/github/timchurches/NetEpi-Analysis", + "content": "Web-based object-oriented data exploration and analysis system" }, - "github/HenrykHaniewicz/PSRVoid": { - "id": "github/HenrykHaniewicz/PSRVoid", - "title": "github/HenrykHaniewicz/PSRVoid", - "url": " https://rseng.github.io/software/repository/github/HenrykHaniewicz/PSRVoid", - "content": "The statistical suite to determine which integrated pulse profiles should go into your times-of-arrival! Also able to mine data from the ATNF catalog." + "github/hz1010/FIPRESCI_data_analysis": { + "id": "github/hz1010/FIPRESCI_data_analysis", + "title": "github/hz1010/FIPRESCI_data_analysis", + "url": " https://rseng.github.io/software/repository/github/hz1010/FIPRESCI_data_analysis", + "content": "Code for FIPERSCI data" }, - "github/fraserw/TRIPPy": { - "id": "github/fraserw/TRIPPy", - "title": "github/fraserw/TRIPPy", - "url": " https://rseng.github.io/software/repository/github/fraserw/TRIPPy", - "content": "Python based Trailed Source Photometry" + "github/rferdman/afr": { + "id": "github/rferdman/afr", + "title": "github/rferdman/afr", + "url": " https://rseng.github.io/software/repository/github/rferdman/afr", + "content": "Software package that includes various routines and tools allowing the user to reduce, process, and manipulate pulsar data, and create times-of-arrival compatible with tempo and tempo2 timing software. " }, - "github/AdmiralenOla/Scoary": { - "id": "github/AdmiralenOla/Scoary", - "title": "github/AdmiralenOla/Scoary", - "url": " https://rseng.github.io/software/repository/github/AdmiralenOla/Scoary", - "content": "Pan-genome wide association studies" + "github/mirapy-org/mirapy": { + "id": "github/mirapy-org/mirapy", + "title": "github/mirapy-org/mirapy", + "url": " https://rseng.github.io/software/repository/github/mirapy-org/mirapy", + "content": "MiraPy: A Python package for Deep Learning in Astronomy" }, - "github/SciML/GlobalSensitivity.jl": { - "id": "github/SciML/GlobalSensitivity.jl", - "title": "github/SciML/GlobalSensitivity.jl", - "url": " https://rseng.github.io/software/repository/github/SciML/GlobalSensitivity.jl", - "content": "None" + "github/stevengj/nlopt": { + "id": "github/stevengj/nlopt", + "title": "github/stevengj/nlopt", + "url": " https://rseng.github.io/software/repository/github/stevengj/nlopt", + "content": "library for nonlinear optimization, wrapping many algorithms for global and local, constrained or unconstrained, optimization" }, - "github/mrc-ide/dde": { - "id": "github/mrc-ide/dde", - "title": "github/mrc-ide/dde", - "url": " https://rseng.github.io/software/repository/github/mrc-ide/dde", - "content": ":clock1130::soon::clock9: Delay differential equation solver" + "github/yangao07/abPOA": { + "id": "github/yangao07/abPOA", + "title": "github/yangao07/abPOA", + "url": " https://rseng.github.io/software/repository/github/yangao07/abPOA", + "content": "abPOA: an SIMD-based C library for fast partial order alignment using adaptive band" + }, + "github/yangao07/TideHunter": { + "id": "github/yangao07/TideHunter", + "title": "github/yangao07/TideHunter", + "url": " https://rseng.github.io/software/repository/github/yangao07/TideHunter", + "content": "TideHunter: efficient and sensitive tandem repeat detection from noisy long reads using seed-and-chain" }, - "github/mrc-ide/global-lmic-reports-orderly": { - "id": "github/mrc-ide/global-lmic-reports-orderly", - "title": "github/mrc-ide/global-lmic-reports-orderly", - "url": " https://rseng.github.io/software/repository/github/mrc-ide/global-lmic-reports-orderly", - "content": "COVID-19 forecast reports for LMICs" + "github/STEllAR-GROUP/hpx": { + "id": "github/STEllAR-GROUP/hpx", + "title": "github/STEllAR-GROUP/hpx", + "url": " https://rseng.github.io/software/repository/github/STEllAR-GROUP/hpx", + "content": "The C++ Standard Library for Parallelism and Concurrency" }, - "github/mrc-ide/rrq": { - "id": "github/mrc-ide/rrq", - "title": "github/mrc-ide/rrq", - "url": " https://rseng.github.io/software/repository/github/mrc-ide/rrq", - "content": ":runner::runner::runner: Lightweight Redis queues" + "github/STEllAR-GROUP/octotiger": { + "id": "github/STEllAR-GROUP/octotiger", + "title": "github/STEllAR-GROUP/octotiger", + "url": " https://rseng.github.io/software/repository/github/STEllAR-GROUP/octotiger", + "content": "Astrophysics program simulating the evolution of star systems based on the fast multipole method on adaptive Octrees" }, - "github/mrc-ide/odin": { - "id": "github/mrc-ide/odin", - "title": "github/mrc-ide/odin", - "url": " https://rseng.github.io/software/repository/github/mrc-ide/odin", - "content": "ᚩ A DSL for describing and solving differential equations in R" + "github/SterlingYM/astroPIPS": { + "id": "github/SterlingYM/astroPIPS", + "title": "github/SterlingYM/astroPIPS", + "url": " https://rseng.github.io/software/repository/github/SterlingYM/astroPIPS", + "content": "A set of tools for photometric analysis. 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Documentation at:" + "github/aamedinburgh/igmtransmission": { + "id": "github/aamedinburgh/igmtransmission", + "title": "github/aamedinburgh/igmtransmission", + "url": " https://rseng.github.io/software/repository/github/aamedinburgh/igmtransmission", + "content": "Automatically exported from code.google.com/p/igmtransmission" }, - "github/mrc-ide/covid19-forecasts-orderly": { - "id": "github/mrc-ide/covid19-forecasts-orderly", - "title": "github/mrc-ide/covid19-forecasts-orderly", - "url": " https://rseng.github.io/software/repository/github/mrc-ide/covid19-forecasts-orderly", + "github/UM-Bridge/umbridge": { + "id": "github/UM-Bridge/umbridge", + "title": "github/UM-Bridge/umbridge", + "url": " https://rseng.github.io/software/repository/github/UM-Bridge/umbridge", "content": "None" }, - "github/mrc-ide/sircovid": { - "id": "github/mrc-ide/sircovid", - "title": "github/mrc-ide/sircovid", - "url": " https://rseng.github.io/software/repository/github/mrc-ide/sircovid", - "content": "None" + "github/jhayer/baargin": { + "id": "github/jhayer/baargin", + "title": "github/jhayer/baargin", + "url": " https://rseng.github.io/software/repository/github/jhayer/baargin", + "content": "Bacterial Assembly and Antimicrobial Resistance Genes In NextFlow" }, - "github/mrc-ide/cinterpolate": { - "id": "github/mrc-ide/cinterpolate", - "title": "github/mrc-ide/cinterpolate", - "url": " https://rseng.github.io/software/repository/github/mrc-ide/cinterpolate", - "content": ":bar_chart::arrow_right::wavy_dash: Interpolating functions from C, in R" + "github/PacificBiosciences/FALCON": { + "id": "github/PacificBiosciences/FALCON", + "title": "github/PacificBiosciences/FALCON", + "url": " https://rseng.github.io/software/repository/github/PacificBiosciences/FALCON", + "content": "FALCON: experimental PacBio diploid assembler -- Out-of-date -- Please use a binary release: https://github.com/PacificBiosciences/FALCON_unzip/wiki/Binaries" }, - "github/mrc-ide/covid-sim": { - "id": "github/mrc-ide/covid-sim", - "title": "github/mrc-ide/covid-sim", - "url": " https://rseng.github.io/software/repository/github/mrc-ide/covid-sim", - "content": "This is the COVID-19 CovidSim microsimulation model developed by the MRC Centre for Global Infectious Disease Analysis hosted at Imperial College, London." + "github/PacificBiosciences/blasr": { + "id": "github/PacificBiosciences/blasr", + "title": "github/PacificBiosciences/blasr", + "url": " https://rseng.github.io/software/repository/github/PacificBiosciences/blasr", + "content": "BLASR (Basic Local Alignment with Successive Refinement) maps Single Molecule Sequencing (SMS) reads that are thousands of bases long, with divergence between the read and genome dominated by insertion and deletion error." }, - "github/mrc-ide/EpiEstim": { - "id": "github/mrc-ide/EpiEstim", - "title": "github/mrc-ide/EpiEstim", - "url": " https://rseng.github.io/software/repository/github/mrc-ide/EpiEstim", - "content": "A tool to estimate time varying instantaneous reproduction number during epidemics" + "github/PacificBiosciences/IsoSeq": { + "id": "github/PacificBiosciences/IsoSeq", + "title": "github/PacificBiosciences/IsoSeq", + "url": " https://rseng.github.io/software/repository/github/PacificBiosciences/IsoSeq", + "content": "IsoSeq3 - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads" }, - "github/mrc-ide/PlasmoMAPI": { - "id": "github/mrc-ide/PlasmoMAPI", - "title": "github/mrc-ide/PlasmoMAPI", - "url": " https://rseng.github.io/software/repository/github/mrc-ide/PlasmoMAPI", - "content": "Mapping Plasmodium Spatial Connectivity from Genetic Data" + "github/PacificBiosciences/pbalign": { + "id": "github/PacificBiosciences/pbalign", + "title": "github/PacificBiosciences/pbalign", + "url": " https://rseng.github.io/software/repository/github/PacificBiosciences/pbalign", + "content": "pbalign aligns PacBio reads to reference sequences, filters aligned reads according to user-specific filtering criteria, and converts the output to either the SAM format or PacBio Compare HDF5 (e.g., .cmp.h5) format. The output Compare HDF5 file will be compatible with Quiver if --forQuiver option is specified." }, - "github/mrc-ide/PhyDyn": { - "id": "github/mrc-ide/PhyDyn", - "title": "github/mrc-ide/PhyDyn", - "url": " https://rseng.github.io/software/repository/github/mrc-ide/PhyDyn", - "content": "PhyDyn: Epidemiological modelling in BEAST" + "github/PacificBiosciences/pbmm2": { + "id": "github/PacificBiosciences/pbmm2", + "title": "github/PacificBiosciences/pbmm2", + "url": " https://rseng.github.io/software/repository/github/PacificBiosciences/pbmm2", + "content": "A minimap2 frontend for PacBio native data formats" }, - "github/mrc-ide/dust": { - "id": "github/mrc-ide/dust", - "title": "github/mrc-ide/dust", - "url": " https://rseng.github.io/software/repository/github/mrc-ide/dust", - "content": ":sparkles::sparkles::sparkles: Iterate multiple realisations of stochastic models" + "github/PacificBiosciences/pbcore": { + "id": "github/PacificBiosciences/pbcore", + "title": "github/PacificBiosciences/pbcore", + "url": " https://rseng.github.io/software/repository/github/PacificBiosciences/pbcore", + "content": "A Python library for reading and writing PacBio® data files" }, - 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Flexible Atomic Code by Ming Feng Gu" }, - "github/reedacartwright/ngila": { - "id": "github/reedacartwright/ngila", - "title": "github/reedacartwright/ngila", - "url": " https://rseng.github.io/software/repository/github/reedacartwright/ngila", - "content": "Ngila is a global alignment program that can align pairs of sequences using logarithmic and affine gap penalties." + "github/NarlikarLab/exoDIVERSITY": { + "id": "github/NarlikarLab/exoDIVERSITY", + "title": "github/NarlikarLab/exoDIVERSITY", + "url": " https://rseng.github.io/software/repository/github/NarlikarLab/exoDIVERSITY", + "content": "None" }, - "github/reedacartwright/dawg": { - "id": "github/reedacartwright/dawg", - "title": "github/reedacartwright/dawg", - "url": " https://rseng.github.io/software/repository/github/reedacartwright/dawg", - "content": "Simulating Sequence Evolution" + "github/ropensci-archive/reviewer": { + "id": "github/ropensci-archive/reviewer", + "title": "github/ropensci-archive/reviewer", + "url": " https://rseng.github.io/software/repository/github/ropensci-archive/reviewer", + "content": ":no_entry: ARCHIVED :no_entry: Improving the track changes and reviewing experience in R markdown" }, - 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"url": " https://rseng.github.io/software/repository/github/Bishop-Laboratory/RLoop-QC-Meta-Analysis-Miller-2022", - "content": "Generates figures for "Quality-controlled R-loop meta-analysis reveals the characteristics of R-loop consensus regions"" + "github/ropensci-archive/monkeylearn": { + "id": "github/ropensci-archive/monkeylearn", + "title": "github/ropensci-archive/monkeylearn", + "url": " https://rseng.github.io/software/repository/github/ropensci-archive/monkeylearn", + "content": ":no_entry: ARCHIVED :no_entry: :monkey: R package for text analysis with Monkeylearn :monkey:" }, - "github/cicirello/rho-mu": { - "id": "github/cicirello/rho-mu", - "title": "github/cicirello/rho-mu", - "url": " https://rseng.github.io/software/repository/github/cicirello/rho-mu", - "content": "ρμ - a Java library of Randomization enHancements and Other Math Utilities" + "github/NSAPH-Software/GPCERF": { + "id": "github/NSAPH-Software/GPCERF", + "title": "github/NSAPH-Software/GPCERF", + "url": " https://rseng.github.io/software/repository/github/NSAPH-Software/GPCERF", + "content": "None" }, - "github/cicirello/Chips-n-Salsa": { - "id": "github/cicirello/Chips-n-Salsa", - "title": "github/cicirello/Chips-n-Salsa", - "url": " https://rseng.github.io/software/repository/github/cicirello/Chips-n-Salsa", - "content": "Chips-n-Salsa - A Java library of customizable, hybridizable, iterative, parallel, stochastic, and self-adaptive local search algorithms" + "github/NSAPH-Software/CRE": { + "id": "github/NSAPH-Software/CRE", + "title": "github/NSAPH-Software/CRE", + "url": " https://rseng.github.io/software/repository/github/NSAPH-Software/CRE", + "content": "The Causal Rule Ensemble Method" }, - "github/RadioAstronomySoftwareGroup/pyuvdata": { - "id": "github/RadioAstronomySoftwareGroup/pyuvdata", - "title": "github/RadioAstronomySoftwareGroup/pyuvdata", - "url": " https://rseng.github.io/software/repository/github/RadioAstronomySoftwareGroup/pyuvdata", - "content": "A pythonic interface for radio astronomy interferometry data (uvfits, miriad, others)" + "github/SMI/SmiServices": { + "id": "github/SMI/SmiServices", + "title": "github/SMI/SmiServices", + "url": " https://rseng.github.io/software/repository/github/SMI/SmiServices", + "content": "Scale-able loading, linking and anonymisation of DICOM images for healthcare research environments (e.g. Safe Havens)" }, - "github/prioritizr/wdpar": { - "id": "github/prioritizr/wdpar", - "title": "github/prioritizr/wdpar", - "url": " https://rseng.github.io/software/repository/github/prioritizr/wdpar", - "content": "Interface to the World Database on Protected Areas" + "github/synchrofit/synchrofit": { + "id": "github/synchrofit/synchrofit", + "title": "github/synchrofit/synchrofit", + "url": " https://rseng.github.io/software/repository/github/synchrofit/synchrofit", + "content": "Code for modelling a radio spectrum using the JP, KP or CI models. " }, - "github/CNIC-Proteomics/TurboPutative-web": { - "id": "github/CNIC-Proteomics/TurboPutative-web", - "title": "github/CNIC-Proteomics/TurboPutative-web", - "url": " https://rseng.github.io/software/repository/github/CNIC-Proteomics/TurboPutative-web", - "content": "None" + "github/ejhigson/nestcheck": { + "id": "github/ejhigson/nestcheck", + "title": "github/ejhigson/nestcheck", + "url": " https://rseng.github.io/software/repository/github/ejhigson/nestcheck", + "content": "Error analysis, diagnostic tests and plots for nested sampling calculations." }, - "github/erikbern/ann-benchmarks": { - "id": "github/erikbern/ann-benchmarks", - "title": "github/erikbern/ann-benchmarks", - "url": " https://rseng.github.io/software/repository/github/erikbern/ann-benchmarks", - "content": "Benchmarks of approximate nearest neighbor libraries in Python" + "github/ejhigson/perfectns": { + "id": "github/ejhigson/perfectns", + "title": "github/ejhigson/perfectns", + "url": " https://rseng.github.io/software/repository/github/ejhigson/perfectns", + "content": ""Perfect" dynamic and standard nested sampling for spherically symmetric likelihoods and priors." }, - "github/AstroAccelerateOrg/astro-accelerate": { - "id": "github/AstroAccelerateOrg/astro-accelerate", - "title": "github/AstroAccelerateOrg/astro-accelerate", - "url": " https://rseng.github.io/software/repository/github/AstroAccelerateOrg/astro-accelerate", - "content": "AstroAccelerate is a many-core accelerated software package for processing time-domain radio-astronomy data." + "github/ejhigson/dyPolyChord": { + "id": "github/ejhigson/dyPolyChord", + "title": "github/ejhigson/dyPolyChord", + "url": " https://rseng.github.io/software/repository/github/ejhigson/dyPolyChord", + "content": "Super fast dynamic nested sampling with PolyChord (Python, C++ and Fortran likelihoods)." }, - "github/fjankowsk/scatfit": { - "id": "github/fjankowsk/scatfit", - "title": "github/fjankowsk/scatfit", - "url": " https://rseng.github.io/software/repository/github/fjankowsk/scatfit", - "content": "Scattering fits of Fast Radio Burst and pulsar data." + "github/entangled/entangled": { + "id": "github/entangled/entangled", + "title": "github/entangled/entangled", + "url": " https://rseng.github.io/software/repository/github/entangled/entangled", + "content": "bi-directional tangle daemon for literate programming" }, - "github/palumbom/grass": { - "id": "github/palumbom/grass", - "title": "github/palumbom/grass", - "url": " https://rseng.github.io/software/repository/github/palumbom/grass", - "content": "A testbed for stellar granulation in exoplanet RV searches. " + "github/pyccel/pyccel": { + "id": "github/pyccel/pyccel", + "title": "github/pyccel/pyccel", + "url": " https://rseng.github.io/software/repository/github/pyccel/pyccel", + "content": "Python extension language using accelerators" }, - "github/idruglab/hignn": { - "id": "github/idruglab/hignn", - "title": "github/idruglab/hignn", - "url": " https://rseng.github.io/software/repository/github/idruglab/hignn", - "content": "Code for "HiGNN: A Hierarchical Informative Graph Neural Network for Molecular Property Prediction Equipped with Feature-Wise Attention"" + "github/birnstiel/two-pop-py": { + "id": "github/birnstiel/two-pop-py", + "title": "github/birnstiel/two-pop-py", + "url": " https://rseng.github.io/software/repository/github/birnstiel/two-pop-py", + "content": "Implementation of the 2-population model for dust evolution in protoplanetary disks after Birnstiel, Klahr, & Ercolano, A&A 2012" }, - "github/Pizzuti92/MG-MAMPOSSt": { - "id": "github/Pizzuti92/MG-MAMPOSSt", - "title": "github/Pizzuti92/MG-MAMPOSSt", - "url": " https://rseng.github.io/software/repository/github/Pizzuti92/MG-MAMPOSSt", - "content": "MG-MAMPOSSt is a FORTRAN code that extended the MAMPOSSt algorithm of G. Mamon, A. Biviano and G. Boué, that performs Bayesian fits of models of mass and velocity anisotropy profiles to the distribution of tracers in projected phase space, to handle modified gravity models and constrain its parameters. The new version implements two distinct types of gravity modifications, namely general chameleon (including $f(\mathcal{R})$ models) and beyond Horndeski gravity (Vainshtein screening)." + "github/teuben/nemo": { + "id": "github/teuben/nemo", + "title": "github/teuben/nemo", + "url": " https://rseng.github.io/software/repository/github/teuben/nemo", + "content": "a Stellar Dynamics Toolbox (Not Everybody Must Observe)" }, - "github/jspsych/jspsych": { - "id": "github/jspsych/jspsych", - "title": "github/jspsych/jspsych", - "url": " https://rseng.github.io/software/repository/github/jspsych/jspsych", - "content": "Create behavioral experiments in a browser using JavaScript" + "github/teuben/QAC": { + "id": "github/teuben/QAC", + "title": "github/teuben/QAC", + "url": " https://rseng.github.io/software/repository/github/teuben/QAC", + "content": "Quick Array Combinations: front end to CASA to run tp2vis, feather and various array combination methods" }, - "github/AntonelliLab/seqcap_processor": { - "id": "github/AntonelliLab/seqcap_processor", - "title": "github/AntonelliLab/seqcap_processor", - "url": " https://rseng.github.io/software/repository/github/AntonelliLab/seqcap_processor", - "content": "Bioinformatic pipeline for processing Sequence Capture data for Phylogenetics" + "github/teuben/DataComb": { + "id": "github/teuben/DataComb", + "title": "github/teuben/DataComb", + "url": " https://rseng.github.io/software/repository/github/teuben/DataComb", + "content": "Code for the DataComb paper" }, - "github/lazzati-astro/MCRaT": { - "id": "github/lazzati-astro/MCRaT", - "title": "github/lazzati-astro/MCRaT", - "url": " https://rseng.github.io/software/repository/github/lazzati-astro/MCRaT", - "content": "Monte Carlo Radiation Transfer Through an Astrophysical Jet" + "github/olivecha/guitarsounds": { + "id": "github/olivecha/guitarsounds", + "title": "github/olivecha/guitarsounds", + "url": " https://rseng.github.io/software/repository/github/olivecha/guitarsounds", + "content": "python library to analyse guitar sounds" }, - 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Python Package for Plasma Diagnostics and Abundance Analysis" }, - "github/FrancesBW/bellamy": { - "id": "github/FrancesBW/bellamy", - "title": "github/FrancesBW/bellamy", - "url": " https://rseng.github.io/software/repository/github/FrancesBW/bellamy", + "github/JunTaoLuo/mctreesearch4j": { + "id": "github/JunTaoLuo/mctreesearch4j", + "title": "github/JunTaoLuo/mctreesearch4j", + "url": " https://rseng.github.io/software/repository/github/JunTaoLuo/mctreesearch4j", "content": "None" }, - "github/scottleedavis/googleearthtoolbox": { - "id": "github/scottleedavis/googleearthtoolbox", - "title": "github/scottleedavis/googleearthtoolbox", - "url": " https://rseng.github.io/software/repository/github/scottleedavis/googleearthtoolbox", - "content": "Leverages the intuitive interactive virtual globe interface provided by Google Earth, providing programatic tools useful in spatio-temporal analysis." + "github/bokeh/bokeh": { + "id": "github/bokeh/bokeh", + "title": "github/bokeh/bokeh", + "url": " https://rseng.github.io/software/repository/github/bokeh/bokeh", + "content": "Interactive Data Visualization in the browser, from Python" }, - 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"github/AIgnesti/PT-REX": { - "id": "github/AIgnesti/PT-REX", - "title": "github/AIgnesti/PT-REX", - "url": " https://rseng.github.io/software/repository/github/AIgnesti/PT-REX", - "content": "None" + "github/davidsoergel/rtax": { + "id": "github/davidsoergel/rtax", + "title": "github/davidsoergel/rtax", + "url": " https://rseng.github.io/software/repository/github/davidsoergel/rtax", + "content": "Rapid and accurate taxonomic classification of short paired-end sequence reads from the 16S ribosomal RNA gene." + }, + "github/R-Vessel-X/SlicerRVXLiverSegmentation": { + "id": "github/R-Vessel-X/SlicerRVXLiverSegmentation", + "title": "github/R-Vessel-X/SlicerRVXLiverSegmentation", + "url": " https://rseng.github.io/software/repository/github/R-Vessel-X/SlicerRVXLiverSegmentation", + "content": "3D Slicer plugin for Liver Anatomy Annotation by R-Vessel-X" + }, + "github/rmjarvis/TreeCorr": { + "id": "github/rmjarvis/TreeCorr", + "title": "github/rmjarvis/TreeCorr", + "url": " https://rseng.github.io/software/repository/github/rmjarvis/TreeCorr", + "content": "Code for efficiently computing 2-point and 3-point correlation functions. For documentation, go to" + }, + "github/rmjarvis/Piff": { + "id": "github/rmjarvis/Piff", + "title": "github/rmjarvis/Piff", + "url": " https://rseng.github.io/software/repository/github/rmjarvis/Piff", + "content": "PSFs In the Full FOV. A software package for modeling the point-spread function (PSF) across the full field of view (FOV). Documentation:" }, - "github/fredericlemoine/goalign": { - "id": "github/fredericlemoine/goalign", - "title": "github/fredericlemoine/goalign", - "url": " https://rseng.github.io/software/repository/github/fredericlemoine/goalign", - "content": "Goalign is a set of command line tools and an API to manipulate multiple alignments. It is implemented in Go language." + "github/alekseyzimin/ufasta": { + "id": "github/alekseyzimin/ufasta", + "title": "github/alekseyzimin/ufasta", + "url": " https://rseng.github.io/software/repository/github/alekseyzimin/ufasta", + "content": "Utility to manipulate fasta files" }, - "github/teamPSG/kNN_Sleep_Scorer_kNNSS": { - "id": "github/teamPSG/kNN_Sleep_Scorer_kNNSS", - "title": "github/teamPSG/kNN_Sleep_Scorer_kNNSS", - "url": " https://rseng.github.io/software/repository/github/teamPSG/kNN_Sleep_Scorer_kNNSS", - "content": "A matlab package for automated sleep scoring using the k-nearest neighbors algorithm" + "github/uedaLabR/nanoDoc": { + "id": "github/uedaLabR/nanoDoc", + "title": "github/uedaLabR/nanoDoc", + "url": " https://rseng.github.io/software/repository/github/uedaLabR/nanoDoc", + "content": "RNA modification detection using Nanopore raw reads with Deep One Class classification" }, - "github/seamplex/feenox": { - "id": "github/seamplex/feenox", - "title": "github/seamplex/feenox", - "url": " https://rseng.github.io/software/repository/github/seamplex/feenox", - "content": "Cloud-first free no-fee no-X uniX-like finite-element(ish) computational engineering tool" + "github/NiallJeffrey/DeepMass": { + "id": "github/NiallJeffrey/DeepMass", + "title": "github/NiallJeffrey/DeepMass", + "url": " https://rseng.github.io/software/repository/github/NiallJeffrey/DeepMass", + "content": "Cosmological map inference with deep learning" }, - "github/nathanael-fijalkow/DeepSynth": { - "id": "github/nathanael-fijalkow/DeepSynth", - "title": "github/nathanael-fijalkow/DeepSynth", - "url": " https://rseng.github.io/software/repository/github/nathanael-fijalkow/DeepSynth", - "content": "General-purpose program synthesiser" + "github/NiallJeffrey/BornRaytrace": { + "id": "github/NiallJeffrey/BornRaytrace", + "title": "github/NiallJeffrey/BornRaytrace", + "url": " https://rseng.github.io/software/repository/github/NiallJeffrey/BornRaytrace", + "content": "BornRaytrace: simulating weak gravitational lensing effects" }, - "github/yangxiaolinyn/Lemon": { - "id": "github/yangxiaolinyn/Lemon", - "title": "github/yangxiaolinyn/Lemon", - "url": " https://rseng.github.io/software/repository/github/yangxiaolinyn/Lemon", + "github/sheydenreich/threepoint": { + "id": "github/sheydenreich/threepoint", + "title": "github/sheydenreich/threepoint", + "url": " https://rseng.github.io/software/repository/github/sheydenreich/threepoint", "content": "None" }, - "github/HannahMDoherty/ChemGAPP": { - "id": "github/HannahMDoherty/ChemGAPP", - "title": "github/HannahMDoherty/ChemGAPP", - "url": " https://rseng.github.io/software/repository/github/HannahMDoherty/ChemGAPP", - "content": "A package and series of Streamlit apps for analysing chemical genomic screen data" + "github/dkirkby/gphist": { + "id": "github/dkirkby/gphist", + "title": "github/dkirkby/gphist", + "url": " https://rseng.github.io/software/repository/github/dkirkby/gphist", + "content": "Cosmological expansion history inference using Gaussian processes" }, - "github/MannLabs/alphapept": { - "id": "github/MannLabs/alphapept", - "title": "github/MannLabs/alphapept", - "url": " https://rseng.github.io/software/repository/github/MannLabs/alphapept", - "content": "A modular, python-based framework for mass spectrometry. Powered by nbdev." + "github/wtsi-hpag/HiLine": { + "id": "github/wtsi-hpag/HiLine", + "title": "github/wtsi-hpag/HiLine", + "url": " https://rseng.github.io/software/repository/github/wtsi-hpag/HiLine", + "content": "HiC alignment and classification pipeline" }, - "github/stefanradev93/BayesFlow": { - "id": "github/stefanradev93/BayesFlow", - "title": "github/stefanradev93/BayesFlow", - "url": " https://rseng.github.io/software/repository/github/stefanradev93/BayesFlow", - "content": "A Python library for amortized Bayesian workflows using generative neural networks." + "github/dfm/corner.py": { + "id": "github/dfm/corner.py", + "title": "github/dfm/corner.py", + "url": " https://rseng.github.io/software/repository/github/dfm/corner.py", + "content": "Make some beautiful corner plots" }, - "github/ec363/fpcountr": { - "id": "github/ec363/fpcountr", - "title": "github/ec363/fpcountr", - "url": " https://rseng.github.io/software/repository/github/ec363/fpcountr", - "content": "Fluorescent protein calibration for plate readers" + "github/dfm/celerite": { + "id": "github/dfm/celerite", + "title": "github/dfm/celerite", + "url": " https://rseng.github.io/software/repository/github/dfm/celerite", + "content": "Scalable 1D Gaussian Processes in C++, Python, and Julia" }, - 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"github/jiffyclub/palettable": { - "id": "github/jiffyclub/palettable", - "title": "github/jiffyclub/palettable", - "url": " https://rseng.github.io/software/repository/github/jiffyclub/palettable", - "content": "Color palettes for Python" + "github/dfm/photodynam": { + "id": "github/dfm/photodynam", + "title": "github/dfm/photodynam", + "url": " https://rseng.github.io/software/repository/github/dfm/photodynam", + "content": "Photodynamical code for fitting the light curves of multiple body systems written by Josh Carter" }, - "github/Dfupa/meTAline": { - "id": "github/Dfupa/meTAline", - "title": "github/Dfupa/meTAline", - "url": " https://rseng.github.io/software/repository/github/Dfupa/meTAline", - "content": "WGS pipeline implementation in Snakemake" + "github/mrirecon/view": { + "id": "github/mrirecon/view", + "title": "github/mrirecon/view", + "url": " https://rseng.github.io/software/repository/github/mrirecon/view", + "content": "Image Viewer for BART" }, - "github/viromelab/tracespipe": { - "id": "github/viromelab/tracespipe", - "title": "github/viromelab/tracespipe", - "url": " https://rseng.github.io/software/repository/github/viromelab/tracespipe", - "content": "Reconstruction and analysis of viral and host genomes at multi-organ level" + "github/mrirecon/bart": { + "id": "github/mrirecon/bart", + "title": "github/mrirecon/bart", + "url": " https://rseng.github.io/software/repository/github/mrirecon/bart", + "content": "BART: Toolbox for Computational Magnetic Resonance Imaging" }, - "github/cosmodesi/pycorr": { - "id": "github/cosmodesi/pycorr", - "title": "github/cosmodesi/pycorr", - "url": " https://rseng.github.io/software/repository/github/cosmodesi/pycorr", - "content": "2-pt correlation function estimation" + "github/jo276/EvapMass": { + "id": "github/jo276/EvapMass", + "title": "github/jo276/EvapMass", + "url": " https://rseng.github.io/software/repository/github/jo276/EvapMass", + "content": "None" }, - "github/facom/tidev": { - "id": "github/facom/tidev", - "title": "github/facom/tidev", - "url": " https://rseng.github.io/software/repository/github/facom/tidev", + "github/FunctionalUrology/MLcps": { + "id": "github/FunctionalUrology/MLcps", + "title": "github/FunctionalUrology/MLcps", + "url": " https://rseng.github.io/software/repository/github/FunctionalUrology/MLcps", "content": "None" }, - "github/facom/exorings": { - "id": "github/facom/exorings", - "title": "github/facom/exorings", - "url": " https://rseng.github.io/software/repository/github/facom/exorings", - "content": "Code Repository for Exoring Transit Properties" + "github/pscicluna/precision": { + "id": "github/pscicluna/precision", + "title": "github/pscicluna/precision", + "url": " https://rseng.github.io/software/repository/github/pscicluna/precision", + "content": "A python pipeline to reduce astronomical IR imaging data. Written with SPHERE data in mind, it provides a fast and easy reduction of bright sources suitable for science. While it may not extract the absolute maximum amount of science, the objective is to provide a means to get science-ready data with minimal computing time or human interaction. 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ISSN 0035-8711 " + "github/firedrakeproject/firedrake": { + "id": "github/firedrakeproject/firedrake", + "title": "github/firedrakeproject/firedrake", + "url": " https://rseng.github.io/software/repository/github/firedrakeproject/firedrake", + "content": "Firedrake is an automated system for the portable solution of partial differential equations using the finite element method (FEM)" }, - "github/bxlab/metaWRAP": { - "id": "github/bxlab/metaWRAP", - "title": "github/bxlab/metaWRAP", - "url": " https://rseng.github.io/software/repository/github/bxlab/metaWRAP", - "content": "MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis" + "github/KenethGarcia/ClassiPyGRB": { + "id": "github/KenethGarcia/ClassiPyGRB", + "title": "github/KenethGarcia/ClassiPyGRB", + "url": " https://rseng.github.io/software/repository/github/KenethGarcia/ClassiPyGRB", + "content": "This repository contains all the updates, code, and documentation related to ClassiPyGRB." + }, + "github/research-software-directory/research-software-directory": { + "id": "github/research-software-directory/research-software-directory", + "title": "github/research-software-directory/research-software-directory", + "url": " https://rseng.github.io/software/repository/github/research-software-directory/research-software-directory", + "content": "The Research Software Directory is a content management system that is tailored to software." + }, + "github/AstroAccelerateOrg/astro-accelerate": { + "id": "github/AstroAccelerateOrg/astro-accelerate", + "title": "github/AstroAccelerateOrg/astro-accelerate", + "url": " https://rseng.github.io/software/repository/github/AstroAccelerateOrg/astro-accelerate", + "content": "AstroAccelerate is a many-core accelerated software package for processing time-domain radio-astronomy data." }, - "github/bxlab/bx-python": { - "id": "github/bxlab/bx-python", - "title": "github/bxlab/bx-python", - "url": " https://rseng.github.io/software/repository/github/bxlab/bx-python", - "content": "Tools for manipulating biological data, particularly multiple sequence alignments" + "github/dicompyler/dicompyler-core": { + "id": "github/dicompyler/dicompyler-core", + "title": "github/dicompyler/dicompyler-core", + "url": " https://rseng.github.io/software/repository/github/dicompyler/dicompyler-core", + "content": "A library of core radiation therapy modules for DICOM RT used by dicompyler" }, - "github/hpc4cmb/toast": { - "id": "github/hpc4cmb/toast", - "title": "github/hpc4cmb/toast", - "url": " https://rseng.github.io/software/repository/github/hpc4cmb/toast", - "content": "Time Ordered Astrophysics Scalable Tools" + "github/shaniAmare/long_read_tools": { + "id": "github/shaniAmare/long_read_tools", + "title": "github/shaniAmare/long_read_tools", + "url": " https://rseng.github.io/software/repository/github/shaniAmare/long_read_tools", + "content": "A catalogue of available long read sequencing data analysis tools" }, - "github/s-abbas/robnptests": { - "id": "github/s-abbas/robnptests", - "title": "github/s-abbas/robnptests", - "url": " https://rseng.github.io/software/repository/github/s-abbas/robnptests", - "content": "Robust two-sample tests for the location problem" + "github/PabloVD/HaloGraphNet": { + "id": "github/PabloVD/HaloGraphNet", + "title": "github/PabloVD/HaloGraphNet", + "url": " https://rseng.github.io/software/repository/github/PabloVD/HaloGraphNet", + "content": "Predict halo masses from simulations via graph neural networks" }, - "github/pangeo-data/climpred": { - "id": "github/pangeo-data/climpred", - "title": "github/pangeo-data/climpred", - "url": " https://rseng.github.io/software/repository/github/pangeo-data/climpred", - "content": ":earth_americas: Verification of weather and climate forecasts. :earth_africa:" + "github/PabloVD/21cmDeepLearning": { + "id": "github/PabloVD/21cmDeepLearning", + "title": "github/PabloVD/21cmDeepLearning", + "url": " https://rseng.github.io/software/repository/github/PabloVD/21cmDeepLearning", + "content": "Python codes to extract the matter density field from a 21 cm map." }, - "github/SJTU-CGM/ivTerm": { - "id": "github/SJTU-CGM/ivTerm", - "title": "github/SJTU-CGM/ivTerm", - "url": " https://rseng.github.io/software/repository/github/SJTU-CGM/ivTerm", - "content": "None" + "github/PabloVD/CosmoGraphNet": { + "id": "github/PabloVD/CosmoGraphNet", + "title": "github/PabloVD/CosmoGraphNet", + "url": " https://rseng.github.io/software/repository/github/PabloVD/CosmoGraphNet", + "content": "Graph Neural Networks to predict the cosmological parameters or the galaxy power spectrum from galaxy catalogs." }, - "github/basehc/IPEV": { - "id": "github/basehc/IPEV", - "title": "github/basehc/IPEV", - "url": " https://rseng.github.io/software/repository/github/basehc/IPEV", - "content": "Software tool to identify prokaryotic and eukaryotic virus-derived sequences in virome using deep learning. Used to calculate a set of scores that reflect the probability that input sequence fragments are prokaryotic and eukaryotic viral sequences." + "github/PabloVD/HAYASHI": { + "id": "github/PabloVD/HAYASHI", + "title": "github/PabloVD/HAYASHI", + "url": " https://rseng.github.io/software/repository/github/PabloVD/HAYASHI", + "content": "Python library for 21 cm forest computations." }, - "github/PixelgenTechnologies/pixelator": { - "id": "github/PixelgenTechnologies/pixelator", - "title": "github/PixelgenTechnologies/pixelator", - "url": " https://rseng.github.io/software/repository/github/PixelgenTechnologies/pixelator", - "content": "A command-line tool and library to process and analyze sequencing data from Molecular Pixelation (MPX) assays." + "github/semaphoreP/whereistheplanet": { + "id": "github/semaphoreP/whereistheplanet", + "title": "github/semaphoreP/whereistheplanet", + "url": " https://rseng.github.io/software/repository/github/semaphoreP/whereistheplanet", + "content": "Prediciting the position of exoplanets" }, - "github/ijuric/MAPS": { - "id": "github/ijuric/MAPS", - "title": "github/ijuric/MAPS", - "url": " https://rseng.github.io/software/repository/github/ijuric/MAPS", - "content": "MAPS (Model-based Analysis of PLAC-Seq data) pipeline is a a set of multiple scripts used to analyze PLAC-Seq and HiChIP data." + "github/benlansdell/ethome": { + "id": "github/benlansdell/ethome", + "title": "github/benlansdell/ethome", + "url": " https://rseng.github.io/software/repository/github/benlansdell/ethome", + "content": "Tools for machine learning of animal behavior" }, - "github/bertrandplez/Turbospectrum_NLTE": { - "id": "github/bertrandplez/Turbospectrum_NLTE", - "title": "github/bertrandplez/Turbospectrum_NLTE", - "url": " https://rseng.github.io/software/repository/github/bertrandplez/Turbospectrum_NLTE", - "content": "Turbospectrum v20 with NLTE capability" + "github/niosh-mining/obsplus": { + "id": "github/niosh-mining/obsplus", + "title": "github/niosh-mining/obsplus", + "url": " https://rseng.github.io/software/repository/github/niosh-mining/obsplus", + "content": "A Pandas-Centric ObsPy Expansion Pack" }, - "github/bertrandplez/Turbospectrum2019": { - "id": "github/bertrandplez/Turbospectrum2019", - "title": "github/bertrandplez/Turbospectrum2019", - "url": " https://rseng.github.io/software/repository/github/bertrandplez/Turbospectrum2019", - "content": "synthetic spectrum calculation companion to MARCS" + "github/freesurfer/freesurfer": { + "id": "github/freesurfer/freesurfer", + "title": "github/freesurfer/freesurfer", + "url": " https://rseng.github.io/software/repository/github/freesurfer/freesurfer", + "content": "Neuroimaging analysis and visualization suite" }, - "github/Starfish-develop/Starfish": { - "id": "github/Starfish-develop/Starfish", - "title": "github/Starfish-develop/Starfish", - "url": " https://rseng.github.io/software/repository/github/Starfish-develop/Starfish", - "content": "Tools for Flexible Spectroscopic Inference" + "github/Higgins00/TESS-Localize": { + "id": "github/Higgins00/TESS-Localize", + "title": "github/Higgins00/TESS-Localize", + "url": " https://rseng.github.io/software/repository/github/Higgins00/TESS-Localize", + "content": "Code for localizing variable star signatures in TESS Photometry" }, - "github/amkozlov/raxml-ng": { - "id": "github/amkozlov/raxml-ng", - "title": "github/amkozlov/raxml-ng", - "url": " https://rseng.github.io/software/repository/github/amkozlov/raxml-ng", - "content": "RAxML Next Generation: faster, easier-to-use and more flexible" + "github/0x0f0f0f/Metatheory.jl": { + "id": "github/0x0f0f0f/Metatheory.jl", + "title": "github/0x0f0f0f/Metatheory.jl", + "url": " https://rseng.github.io/software/repository/github/0x0f0f0f/Metatheory.jl", + "content": "General purpose metaprogramming and algebraic computation library for the Julia programming language" }, - "github/netrias/rnassist": { - "id": "github/netrias/rnassist", - "title": "github/netrias/rnassist", - "url": " https://rseng.github.io/software/repository/github/netrias/rnassist", - "content": "None" + "github/Ashod/garli": { + "id": "github/Ashod/garli", + "title": "github/Ashod/garli", + "url": " https://rseng.github.io/software/repository/github/Ashod/garli", + "content": "Phylogenetic analysis of molecular sequence data using the maximum-likelihood criterion" }, - "github/adithirgis/pollucheck": { - "id": "github/adithirgis/pollucheck", - "title": "github/adithirgis/pollucheck", - "url": " https://rseng.github.io/software/repository/github/adithirgis/pollucheck", - "content": "This application helps exploring the open source air quality data." + "github/villrv/SuperRAENN": { + "id": "github/villrv/SuperRAENN", + "title": "github/villrv/SuperRAENN", + "url": " https://rseng.github.io/software/repository/github/villrv/SuperRAENN", + "content": "A recurrent autoencoder neural network-based classifier for SN light curves." }, - "github/dpryan79/libBigWig": { - "id": "github/dpryan79/libBigWig", - "title": "github/dpryan79/libBigWig", - "url": " https://rseng.github.io/software/repository/github/dpryan79/libBigWig", - "content": "A C library for handling bigWig files" + "github/atmos-cloud-sim-uj/PyMPDATA": { + "id": "github/atmos-cloud-sim-uj/PyMPDATA", + "title": "github/atmos-cloud-sim-uj/PyMPDATA", + "url": " https://rseng.github.io/software/repository/github/atmos-cloud-sim-uj/PyMPDATA", + "content": "Numba-accelerated Pythonic implementation of MPDATA with examples in Python, Julia and Matlab" }, - "github/dpryan79/pyBigWig": { - "id": "github/dpryan79/pyBigWig", - "title": "github/dpryan79/pyBigWig", - "url": " https://rseng.github.io/software/repository/github/dpryan79/pyBigWig", - "content": "A python extension for quick access to bigWig and bigBed files" + "github/atmos-cloud-sim-uj/PySDM": { + "id": "github/atmos-cloud-sim-uj/PySDM", + "title": "github/atmos-cloud-sim-uj/PySDM", + "url": " https://rseng.github.io/software/repository/github/atmos-cloud-sim-uj/PySDM", + "content": "Pythonic particle-based (super-droplet) warm-rain/aqueous-chemistry cloud microphysics package with box, parcel & 1D/2D prescribed-flow examples in Python, Julia and Matlab" }, - "github/dpryan79/MethylDackel": { - "id": "github/dpryan79/MethylDackel", - "title": "github/dpryan79/MethylDackel", - "url": " https://rseng.github.io/software/repository/github/dpryan79/MethylDackel", - "content": "A (mostly) universal methylation extractor for BS-seq experiments." + "github/Varnani/pywd2015-qt5": { + "id": "github/Varnani/pywd2015-qt5", + "title": "github/Varnani/pywd2015-qt5", + "url": " https://rseng.github.io/software/repository/github/Varnani/pywd2015-qt5", + "content": "A Qt5 GUI written in Python for Wilson - Devinney eclipsing binary modeling software." }, - "github/STOmics/EAGS": { - "id": "github/STOmics/EAGS", - "title": "github/STOmics/EAGS", - "url": " https://rseng.github.io/software/repository/github/STOmics/EAGS", - "content": "EAGS:efficient and adaptive Gaussian smoothing" + "github/tekpinar/correlationplus": { + "id": "github/tekpinar/correlationplus", + "title": "github/tekpinar/correlationplus", + "url": " https://rseng.github.io/software/repository/github/tekpinar/correlationplus", + "content": "A Python package to calculate, visualize and analyze dynamical correlations of proteins." }, - "github/MichielCottaar/velbin": { - "id": "github/MichielCottaar/velbin", - "title": "github/MichielCottaar/velbin", - "url": " https://rseng.github.io/software/repository/github/MichielCottaar/velbin", - "content": "No relation to the Russian village" + "github/Blosc/c-blosc": { + "id": "github/Blosc/c-blosc", + "title": "github/Blosc/c-blosc", + "url": " https://rseng.github.io/software/repository/github/Blosc/c-blosc", + "content": "A blocking, shuffling and loss-less compression library that can be faster than `memcpy()`." }, - "github/brandonckelly/carma_pack": { - "id": "github/brandonckelly/carma_pack", - "title": "github/brandonckelly/carma_pack", - "url": " https://rseng.github.io/software/repository/github/brandonckelly/carma_pack", - "content": "MCMC Sampler for Performing Bayesian Inference on Continuous Time Autoregressive Models." + "github/Ouranosinc/xclim": { + "id": "github/Ouranosinc/xclim", + "title": "github/Ouranosinc/xclim", + "url": " https://rseng.github.io/software/repository/github/Ouranosinc/xclim", + "content": "Library of derived climate variables, ie climate indicators, based on xarray. " }, - "github/iipharma/pharmamind-molminer": { - "id": "github/iipharma/pharmamind-molminer", - "title": "github/iipharma/pharmamind-molminer", - "url": " https://rseng.github.io/software/repository/github/iipharma/pharmamind-molminer", - "content": "PharmaMind® is an innovative drug discovery platform that integrates advanced artificial intelligence and computational simulation design techniques, which is suitable for real-world novel drug R&D." + "github/scipion-em/scipion-em-continuousflex": { + "id": "github/scipion-em/scipion-em-continuousflex", + "title": "github/scipion-em/scipion-em-continuousflex", + "url": " https://rseng.github.io/software/repository/github/scipion-em/scipion-em-continuousflex", + "content": "Plugin for continuous conformational flexibility analysis containing HEMNMA, StructMap, HEMNMA-3D and TomoFlow for in vitro and in situ cryo-EM/ET." }, - "github/DSIMB/medusa": { - "id": "github/DSIMB/medusa", - "title": "github/DSIMB/medusa", - "url": " https://rseng.github.io/software/repository/github/DSIMB/medusa", - "content": "A Deep Learning based protein flexibility prediction tool." + "github/ggciag/mandyoc": { + "id": "github/ggciag/mandyoc", + "title": "github/ggciag/mandyoc", + "url": " https://rseng.github.io/software/repository/github/ggciag/mandyoc", + "content": "MANDYOC is a finite element code written on top of the PETSc library to simulate thermo-chemical convection of the Earth's mantle" }, - "github/girder/viime": { - "id": "github/girder/viime", - "title": "github/girder/viime", - "url": " https://rseng.github.io/software/repository/github/girder/viime", - "content": "None" + "github/genouest/biomaj-daemon": { + "id": "github/genouest/biomaj-daemon", + "title": "github/genouest/biomaj-daemon", + "url": " https://rseng.github.io/software/repository/github/genouest/biomaj-daemon", + "content": "micro service to manage biomaj client requests and bank updates" }, - "github/davi-rodrigues/CCBH-Numerics": { - "id": "github/davi-rodrigues/CCBH-Numerics", - "title": "github/davi-rodrigues/CCBH-Numerics", - "url": " https://rseng.github.io/software/repository/github/davi-rodrigues/CCBH-Numerics", - "content": "Using gravitational wave data, CCBH-Numerics computes the probability of the existence of a single cosmologically coupled black hole with a formation mass below a specified threshold. This tool was developed alongside the paper by Amendola, Rodrigues, Kumar, and Quartin, published in MNRAS in 2024" + "github/genouest/biomaj-cli": { + "id": "github/genouest/biomaj-cli", + "title": "github/genouest/biomaj-cli", + "url": " https://rseng.github.io/software/repository/github/genouest/biomaj-cli", + "content": "CLI for BioMAJ" }, - "github/davi-rodrigues/NAVanalysis": { - "id": "github/davi-rodrigues/NAVanalysis", - "title": "github/davi-rodrigues/NAVanalysis", - "url": " https://rseng.github.io/software/repository/github/davi-rodrigues/NAVanalysis", - "content": "Normalized Additional Velocity analysis" + "github/surhudm/savitzky_golay_with_errors": { + "id": "github/surhudm/savitzky_golay_with_errors", + "title": "github/surhudm/savitzky_golay_with_errors", + "url": " https://rseng.github.io/software/repository/github/surhudm/savitzky_golay_with_errors", + "content": "Improving the Savitzky-Golay filtering in the presence of noisy data" + }, + "github/surhudm/aum": { + "id": "github/surhudm/aum", + "title": "github/surhudm/aum", + "url": " https://rseng.github.io/software/repository/github/surhudm/aum", + "content": "aum" }, - "github/TingMAC/FrMLNet": { - "id": "github/TingMAC/FrMLNet", - "title": "github/TingMAC/FrMLNet", - "url": " https://rseng.github.io/software/repository/github/TingMAC/FrMLNet", - "content": "This is a implementation of training code of this paper “FrMLNet: Framelet-based Multi-level Network for Pansharpening”" + "github/zgazak/TAP": { + "id": "github/zgazak/TAP", + "title": "github/zgazak/TAP", + "url": " https://rseng.github.io/software/repository/github/zgazak/TAP", + "content": "Transit Analysis Package for IDL" }, - "github/champsproject/ldds": { - "id": "github/champsproject/ldds", - "title": "github/champsproject/ldds", - "url": " https://rseng.github.io/software/repository/github/champsproject/ldds", - "content": "Python package for computing and visualizing Lagrangian Descriptors in Dynamical Systems" + "github/zblz/naima": { + "id": "github/zblz/naima", + "title": "github/zblz/naima", + "url": " https://rseng.github.io/software/repository/github/zblz/naima", + "content": "Derivation of non-thermal particle distributions through MCMC spectral fitting" }, - "github/kambrian/SubGen": { - "id": "github/kambrian/SubGen", - "title": "github/kambrian/SubGen", - "url": " https://rseng.github.io/software/repository/github/kambrian/SubGen", - "content": "a fast subhalo sampler" + "github/EskelandLab/ShinyArchRUiO": { + "id": "github/EskelandLab/ShinyArchRUiO", + "title": "github/EskelandLab/ShinyArchRUiO", + "url": " https://rseng.github.io/software/repository/github/EskelandLab/ShinyArchRUiO", + "content": "None" }, - "github/atomec-project/atoMEC": { - "id": "github/atomec-project/atoMEC", - "title": "github/atomec-project/atoMEC", - "url": " https://rseng.github.io/software/repository/github/atomec-project/atoMEC", - "content": "Python-based average-atom code for simulations of high energy density phenomena such as in warm dense matter." + "github/e-merlin/eMERLIN_CASA_pipeline": { + "id": "github/e-merlin/eMERLIN_CASA_pipeline", + "title": "github/e-merlin/eMERLIN_CASA_pipeline", + "url": " https://rseng.github.io/software/repository/github/e-merlin/eMERLIN_CASA_pipeline", + "content": "This is CASA eMERLIN pipeline to calibrate data from the e-MERLIN array. Please fork the repository before making any changes and read the Coding Practices page in the wiki. Please add issues with the pipeline in the issues tab." }, - "github/kdmurray91/axe": { - "id": "github/kdmurray91/axe", - "title": "github/kdmurray91/axe", - "url": " https://rseng.github.io/software/repository/github/kdmurray91/axe", - "content": "Rapid competitive read demulitplexer. Made with tries." + "github/dgerosa/gwdet": { + "id": "github/dgerosa/gwdet", + "title": "github/dgerosa/gwdet", + "url": " https://rseng.github.io/software/repository/github/dgerosa/gwdet", + "content": "Detectability of gravitational-wave signals from compact binary coalescences" }, - "github/kdmurray91/libqcpp": { - "id": "github/kdmurray91/libqcpp", - "title": "github/kdmurray91/libqcpp", - "url": " https://rseng.github.io/software/repository/github/kdmurray91/libqcpp", - "content": "libqc++: C++11 library for next-gen sequence quality control and assessment." + "github/dgerosa/spops": { + "id": "github/dgerosa/spops", + "title": "github/dgerosa/spops", + "url": " https://rseng.github.io/software/repository/github/dgerosa/spops", + "content": "Spinning black-hole binary POPulation Synthesis" }, - "github/kdmurray91/libqes": { - "id": "github/kdmurray91/libqes", - "title": "github/kdmurray91/libqes", - "url": " https://rseng.github.io/software/repository/github/kdmurray91/libqes", - "content": "A small C library, with a bioinformatic focus. Optimised for speed and a clean API" + "github/dgerosa/surrkick": { + "id": "github/dgerosa/surrkick", + "title": "github/dgerosa/surrkick", + "url": " https://rseng.github.io/software/repository/github/dgerosa/surrkick", + "content": "Black-hole kicks from numerical-relativity surrogate models" }, - "github/connor-lab/vapor": { - "id": "github/connor-lab/vapor", - "title": "github/connor-lab/vapor", - "url": " https://rseng.github.io/software/repository/github/connor-lab/vapor", - "content": "is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis." + "github/mcfrith/tandem-genotypes": { + "id": "github/mcfrith/tandem-genotypes", + "title": "github/mcfrith/tandem-genotypes", + "url": " https://rseng.github.io/software/repository/github/mcfrith/tandem-genotypes", + "content": "compare lengths of duplications in DNA sequences" }, - "github/networkx/networkx": { - "id": "github/networkx/networkx", - "title": "github/networkx/networkx", - "url": " https://rseng.github.io/software/repository/github/networkx/networkx", - "content": "Network Analysis in Python" + "github/mcfrith/dnarrange": { + "id": "github/mcfrith/dnarrange", + "title": "github/mcfrith/dnarrange", + "url": " https://rseng.github.io/software/repository/github/mcfrith/dnarrange", + "content": "Method to find rearrangements in long DNA reads relative to a genome seq" }, - "github/DJArmstrong/TransitSOM": { - "id": "github/DJArmstrong/TransitSOM", - "title": "github/DJArmstrong/TransitSOM", - "url": " https://rseng.github.io/software/repository/github/DJArmstrong/TransitSOM", - "content": "A Self-Organising Map for Kepler and K2 Transits" + "github/hotokezaka/HeatingRate": { + "id": "github/hotokezaka/HeatingRate", + "title": "github/hotokezaka/HeatingRate", + "url": " https://rseng.github.io/software/repository/github/hotokezaka/HeatingRate", + "content": "None" }, - "github/Yash-10/beta-sgp": { - "id": "github/Yash-10/beta-sgp", - "title": "github/Yash-10/beta-sgp", - "url": " https://rseng.github.io/software/repository/github/Yash-10/beta-sgp", - "content": "Scaled Gradient Projection (SGP) algorithm with beta divergence" + "github/JuliaOcean/PlanktonIndividuals.jl": { + "id": "github/JuliaOcean/PlanktonIndividuals.jl", + "title": "github/JuliaOcean/PlanktonIndividuals.jl", + "url": " https://rseng.github.io/software/repository/github/JuliaOcean/PlanktonIndividuals.jl", + "content": "This package simulates the behaviors of an ensemble of phytoplankton individuals." }, - "github/Yash-10/Periodogram-Comparison-Optimize-Planet-Detection": { - "id": "github/Yash-10/Periodogram-Comparison-Optimize-Planet-Detection", - "title": "github/Yash-10/Periodogram-Comparison-Optimize-Planet-Detection", - "url": " https://rseng.github.io/software/repository/github/Yash-10/Periodogram-Comparison-Optimize-Planet-Detection", - "content": "Extreme Value Theory for comparing periodograms: Optimizing future transiting exoplanet surveys" + "github/JuliaOcean/AIBECS.jl": { + "id": "github/JuliaOcean/AIBECS.jl", + "title": "github/JuliaOcean/AIBECS.jl", + "url": " https://rseng.github.io/software/repository/github/JuliaOcean/AIBECS.jl", + "content": "The ideal tool for exploring global marine biogeochemical cycles." }, - "github/oliveirara/polyMV": { - "id": "github/oliveirara/polyMV", - "title": "github/oliveirara/polyMV", - "url": " https://rseng.github.io/software/repository/github/oliveirara/polyMV", - "content": "Python package that converts multipolar coefficients into Multipole Vectors and Fréchet Vectors" + "github/sparks-baird/xtal2png": { + "id": "github/sparks-baird/xtal2png", + "title": "github/sparks-baird/xtal2png", + "url": " https://rseng.github.io/software/repository/github/sparks-baird/xtal2png", + "content": "Encode/decode a crystal structure to/from a grayscale PNG image for direct use with image-based machine learning models such as Palette." }, - "github/EbmeyerSt/GEnView": { - "id": "github/EbmeyerSt/GEnView", - "title": "github/EbmeyerSt/GEnView", - "url": " https://rseng.github.io/software/repository/github/EbmeyerSt/GEnView", - "content": "GEnView - A phylogeny based comparative genomics software to analyze the genetic environment of genes" + "github/radifar/PyPLIF-HIPPOS": { + "id": "github/radifar/PyPLIF-HIPPOS", + "title": "github/radifar/PyPLIF-HIPPOS", + "url": " https://rseng.github.io/software/repository/github/radifar/PyPLIF-HIPPOS", + "content": "HIPPOS Is PyPLIF On Steroids. A Molecular Interaction Fingerprinting Tool for Docking Results of Autodock Vina and PLANTS" }, - "github/DochtermannLab/BehavioralHeritability": { - "id": "github/DochtermannLab/BehavioralHeritability", - "title": "github/DochtermannLab/BehavioralHeritability", - "url": " https://rseng.github.io/software/repository/github/DochtermannLab/BehavioralHeritability", + "github/semiautomaticgit/SemiAutomaticClassificationPlugin": { + "id": "github/semiautomaticgit/SemiAutomaticClassificationPlugin", + "title": "github/semiautomaticgit/SemiAutomaticClassificationPlugin", + "url": " https://rseng.github.io/software/repository/github/semiautomaticgit/SemiAutomaticClassificationPlugin", "content": "None" }, - "github/DochtermannLab/G-PopComparison": { - "id": "github/DochtermannLab/G-PopComparison", - "title": "github/DochtermannLab/G-PopComparison", - "url": " https://rseng.github.io/software/repository/github/DochtermannLab/G-PopComparison", - "content": "None" + "github/brentp/mosdepth": { + "id": "github/brentp/mosdepth", + "title": "github/brentp/mosdepth", + "url": " https://rseng.github.io/software/repository/github/brentp/mosdepth", + "content": "fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing" }, - 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"github/jmejia8/Metaheuristics.jl": { - "id": "github/jmejia8/Metaheuristics.jl", - "title": "github/jmejia8/Metaheuristics.jl", - "url": " https://rseng.github.io/software/repository/github/jmejia8/Metaheuristics.jl", - "content": "High-performance metaheuristics for optimization coded purely in Julia." + "github/brentp/goleft": { + "id": "github/brentp/goleft", + "title": "github/brentp/goleft", + "url": " https://rseng.github.io/software/repository/github/brentp/goleft", + "content": "goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary" }, - "github/arabic-digital-humanities/adhtools": { - "id": "github/arabic-digital-humanities/adhtools", - "title": "github/arabic-digital-humanities/adhtools", - "url": " https://rseng.github.io/software/repository/github/arabic-digital-humanities/adhtools", - "content": "Scripts for manipulating Arabic texts" + "github/brentp/nim-lapper": { + "id": "github/brentp/nim-lapper", + "title": "github/brentp/nim-lapper", + "url": " https://rseng.github.io/software/repository/github/brentp/nim-lapper", + "content": "fast easy interval overlapping for nim-lang" }, - "github/SDXorg/pysd": { - "id": "github/SDXorg/pysd", - "title": "github/SDXorg/pysd", - "url": " https://rseng.github.io/software/repository/github/SDXorg/pysd", - "content": "System Dynamics Modeling in Python" + "github/brentp/geneimpacts": { + "id": "github/brentp/geneimpacts", + "title": "github/brentp/geneimpacts", + "url": " https://rseng.github.io/software/repository/github/brentp/geneimpacts", + "content": "prioritize effects of variant annotations from VEP, SnpEff, et al." }, - "github/geoelements/gns": { - "id": "github/geoelements/gns", - "title": "github/geoelements/gns", - "url": " https://rseng.github.io/software/repository/github/geoelements/gns", - "content": "Graph Network Simulator" + "github/brentp/smoove": { + "id": "github/brentp/smoove", + "title": "github/brentp/smoove", + "url": " https://rseng.github.io/software/repository/github/brentp/smoove", + "content": "structural variant calling and genotyping with existing tools, but, smoothly." }, - "github/RajLabMSSM/echolocatoR": { - "id": "github/RajLabMSSM/echolocatoR", - "title": "github/RajLabMSSM/echolocatoR", - "url": " https://rseng.github.io/software/repository/github/RajLabMSSM/echolocatoR", - "content": "Automated statistical and functional fine-mapping pipeline with extensive API access to datasets." + "github/brentp/somalier": { + "id": "github/brentp/somalier", + "title": "github/brentp/somalier", + "url": " https://rseng.github.io/software/repository/github/brentp/somalier", + "content": "fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... 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A simple tool do evaluate variant predictors" }, - "github/samb8s/PsrPopPy": { - "id": "github/samb8s/PsrPopPy", - "title": "github/samb8s/PsrPopPy", - "url": " https://rseng.github.io/software/repository/github/samb8s/PsrPopPy", - "content": "Python implementation of PSRPOP, designed to be run from the command line or from Python scripts/interpreter" + "github/nye17/javelin": { + "id": "github/nye17/javelin", + "title": "github/nye17/javelin", + "url": " https://rseng.github.io/software/repository/github/nye17/javelin", + "content": "JAVELIN is now working under Python 3!" }, - "github/iraf-community/iraf": { - "id": "github/iraf-community/iraf", - "title": "github/iraf-community/iraf", - "url": " https://rseng.github.io/software/repository/github/iraf-community/iraf", - "content": "IRAF - Image Reduction and Analysis Facility" + "github/aL3x-O-o-Hung/CAT-Net": { + "id": "github/aL3x-O-o-Hung/CAT-Net", + "title": "github/aL3x-O-o-Hung/CAT-Net", + "url": " https://rseng.github.io/software/repository/github/aL3x-O-o-Hung/CAT-Net", + "content": "None" }, - 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Its development has been motivated by the WP3 Benchmarking (PRUF) project, which aims to provide a reference implementation for plant-level performance assessment." }, - "github/mkenworthy/exorings": { - "id": "github/mkenworthy/exorings", - "title": "github/mkenworthy/exorings", - "url": " https://rseng.github.io/software/repository/github/mkenworthy/exorings", - "content": "Tools for fitting and displaying giant extrasolar planet ring systems." + "github/NREL/graph-env": { + "id": "github/NREL/graph-env", + "title": "github/NREL/graph-env", + "url": " https://rseng.github.io/software/repository/github/NREL/graph-env", + "content": "Reinforcement learning for combinatorial optimization over directed graphs" }, - "github/MichaelAbdul-Masih/SPAMMS": { - "id": "github/MichaelAbdul-Masih/SPAMMS", - "title": "github/MichaelAbdul-Masih/SPAMMS", - "url": " https://rseng.github.io/software/repository/github/MichaelAbdul-Masih/SPAMMS", - "content": "None" + "github/phylo42/RAPPAS": { + "id": "github/phylo42/RAPPAS", + "title": "github/phylo42/RAPPAS", + "url": " https://rseng.github.io/software/repository/github/phylo42/RAPPAS", + "content": "Rapid, Alignment-free, Phylogenetic Placement via Ancestral Sequences" }, - 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"github/BartoszBartmanski/StoSpa2": { - "id": "github/BartoszBartmanski/StoSpa2", - "title": "github/BartoszBartmanski/StoSpa2", - "url": " https://rseng.github.io/software/repository/github/BartoszBartmanski/StoSpa2", - "content": "A C++ software package for stochastic simulations of spatially extended systems" + "github/jmschrei/pomegranate": { + "id": "github/jmschrei/pomegranate", + "title": "github/jmschrei/pomegranate", + "url": " https://rseng.github.io/software/repository/github/jmschrei/pomegranate", + "content": "Fast, flexible and easy to use probabilistic modelling in Python." }, - "github/illumina/pyflow": { - "id": "github/illumina/pyflow", - "title": "github/illumina/pyflow", - "url": " https://rseng.github.io/software/repository/github/illumina/pyflow", - "content": "A lightweight parallel task engine" + "github/VALENCE-software/VALENCE": { + "id": "github/VALENCE-software/VALENCE", + "title": "github/VALENCE-software/VALENCE", + "url": " https://rseng.github.io/software/repository/github/VALENCE-software/VALENCE", + "content": "quantum chemistry software" }, - "github/iric-soft/km": { - "id": "github/iric-soft/km", - "title": "github/iric-soft/km", - "url": " https://rseng.github.io/software/repository/github/iric-soft/km", - "content": "km : a software for RNA-seq investigation using k-mer decomposition" + "github/plazar/coast_guard": { + "id": "github/plazar/coast_guard", + "title": "github/plazar/coast_guard", + "url": " https://rseng.github.io/software/repository/github/plazar/coast_guard", + "content": "A python/PSRCHIVE-based timing pipeline for reducing Effelsberg data." }, - "github/espnet/espnet": { - "id": "github/espnet/espnet", - "title": "github/espnet/espnet", - "url": " https://rseng.github.io/software/repository/github/espnet/espnet", - "content": "End-to-End Speech Processing Toolkit" + "github/plazar/TOASTER": { + "id": "github/plazar/TOASTER", + "title": "github/plazar/TOASTER", + "url": " https://rseng.github.io/software/repository/github/plazar/TOASTER", + "content": "A framework for generating, storing and tracking high-precision TOAs for PTAs as well as observation meta data and processing details." }, - "github/statOmics/satuRnPaper": { - "id": "github/statOmics/satuRnPaper", - "title": "github/statOmics/satuRnPaper", - "url": " https://rseng.github.io/software/repository/github/statOmics/satuRnPaper", - "content": "Github repository associated with the publication of *satuRn: Scalable Analysis of Differential Transcript Usage for Bulk and Single-cell RNA-sequencing Applications*" + "github/PabloMSanAla/fabada": { + "id": "github/PabloMSanAla/fabada", + "title": "github/PabloMSanAla/fabada", + "url": " https://rseng.github.io/software/repository/github/PabloMSanAla/fabada", + "content": "Fully Adaptive Bayesian Algorithm for Data Analysis (FABADA) is a new approach of noise reduction methods. In this repository is shown the package developed for this new method based on \citepaper." }, - "github/statOmics/tradeSeqPaper": { - "id": "github/statOmics/tradeSeqPaper", - "title": "github/statOmics/tradeSeqPaper", - "url": " https://rseng.github.io/software/repository/github/statOmics/tradeSeqPaper", - "content": "Scripts to reproduce analyses of tradeSeq paper." + "github/TheFischerLab/FLEXR": { + "id": "github/TheFischerLab/FLEXR", + "title": "github/TheFischerLab/FLEXR", + "url": " https://rseng.github.io/software/repository/github/TheFischerLab/FLEXR", + "content": "Multi-conformer modeling of crystallographic protein structures" }, - "github/tcassanelli/pywpf": { - "id": "github/tcassanelli/pywpf", - "title": "github/tcassanelli/pywpf", - "url": " https://rseng.github.io/software/repository/github/tcassanelli/pywpf", - "content": "The purpose of this program is to see the effectivity and efficiency that a PCA folding analysis has compared to the Epoch Folding, which is the standard used for pulsar period computations." + "github/B-UMMI/chewBBACA": { + "id": "github/B-UMMI/chewBBACA", + "title": "github/B-UMMI/chewBBACA", + "url": " https://rseng.github.io/software/repository/github/B-UMMI/chewBBACA", + "content": "A complete suite for gene-by-gene schema creation and strain identification." }, - "github/user29A/CCDLAB": { - "id": "github/user29A/CCDLAB", - "title": "github/user29A/CCDLAB", - "url": " https://rseng.github.io/software/repository/github/user29A/CCDLAB", - "content": "FITS image interaction, world coordinate solving, point source extraction, photometry, etc. See the github Wiki link below for more info. If you require CCDLAB for UVIT, please ensure you have the UVIT Calibration Database which you can find at the CCDLAB Wiki link below." + "github/barbagroup/geoclaw-landspill": { + "id": "github/barbagroup/geoclaw-landspill", + "title": "github/barbagroup/geoclaw-landspill", + "url": " https://rseng.github.io/software/repository/github/barbagroup/geoclaw-landspill", + "content": "An oil land-spill and overland flow simulator for pipeline rupture events" }, - "github/user29A/JPFITS": { - "id": "github/user29A/JPFITS", - "title": "github/user29A/JPFITS", - "url": " https://rseng.github.io/software/repository/github/user29A/JPFITS", - "content": "FITS File interaction written in Visual Studio C# .Net, compatible across all .Net platforms. JPFITS is not based on any other implementations and is written from the ground-up, consistent with the FITS standard, designed to interact with FITS files as object-oriented structures. See the github Wiki link below for more info." + "github/napakalas/casbert": { + "id": "github/napakalas/casbert", + "title": "github/napakalas/casbert", + "url": " https://rseng.github.io/software/repository/github/napakalas/casbert", + "content": "None" }, - "github/user29A/fastrometry": { - "id": "github/user29A/fastrometry", - "title": "github/user29A/fastrometry", - "url": " https://rseng.github.io/software/repository/github/user29A/fastrometry", - "content": "Fast Automatic World Coordinate Solution Solver. See the github Wiki link below for more info." + "github/gdrouart/MrMoose": { + "id": "github/gdrouart/MrMoose", + "title": "github/gdrouart/MrMoose", + "url": " https://rseng.github.io/software/repository/github/gdrouart/MrMoose", + "content": "MrMoose is a Spectral Energy Distribution fitting procedure using a Bayesian framework. In a nutshell, this code allows to fit user-defined models onto a set of multi-wavelength data, making use of spatial information and upper-limits with a consistent treatment. The code is highly flexible to allow its use for sources with complex structures." }, - "github/Midnighter/dependency-info": { - "id": "github/Midnighter/dependency-info", - "title": "github/Midnighter/dependency-info", - "url": " https://rseng.github.io/software/repository/github/Midnighter/dependency-info", - "content": "Retrieve and print Python package dependencies." + "github/mes5k/amap-align": { + "id": "github/mes5k/amap-align", + "title": "github/mes5k/amap-align", + "url": " https://rseng.github.io/software/repository/github/mes5k/amap-align", + "content": "Automatically exported from code.google.com/p/amap-align" }, - "github/NctuICLab/PredCRP": { - "id": "github/NctuICLab/PredCRP", - "title": "github/NctuICLab/PredCRP", - "url": " https://rseng.github.io/software/repository/github/NctuICLab/PredCRP", - "content": "Predicting the regulatory role of CRP transcription factor in Escherichia coli " + "github/matteobreschi/bajes": { + "id": "github/matteobreschi/bajes", + "title": "github/matteobreschi/bajes", + "url": " https://rseng.github.io/software/repository/github/matteobreschi/bajes", + "content": "Bayesian Jenaer software" }, - "github/nansencenter/DAPPER": { - "id": "github/nansencenter/DAPPER", - "title": "github/nansencenter/DAPPER", - "url": " https://rseng.github.io/software/repository/github/nansencenter/DAPPER", - "content": "Data Assimilation with Python: a Package for Experimental Research" + "github/thomasorb/orcs": { + "id": "github/thomasorb/orcs", + "title": "github/thomasorb/orcs", + "url": " https://rseng.github.io/software/repository/github/thomasorb/orcs", + "content": "ORCS is an analysis engine for SITELLE spectral cubes." }, - "github/rajeshmondal18/FoF-Halo-finder": { - "id": "github/rajeshmondal18/FoF-Halo-finder", - "title": "github/rajeshmondal18/FoF-Halo-finder", - "url": " https://rseng.github.io/software/repository/github/rajeshmondal18/FoF-Halo-finder", - "content": "A code to identify the location and size of the gravitationally collapsed dark matter halos." + "github/thomasorb/orbs": { + "id": "github/thomasorb/orbs", + "title": "github/thomasorb/orbs", + "url": " https://rseng.github.io/software/repository/github/thomasorb/orbs", + "content": "ORBS is the data reduction pipeline for SITELLE" }, - "github/rajeshmondal18/ReionYuga": { - "id": "github/rajeshmondal18/ReionYuga", - "title": "github/rajeshmondal18/ReionYuga", - "url": " https://rseng.github.io/software/repository/github/rajeshmondal18/ReionYuga", - "content": "A semi-numerical code to generate the Epoch of Reionization (EoR) neutral Hydrogen (HI) field." + "github/mlower/rmnest": { + "id": "github/mlower/rmnest", + "title": "github/mlower/rmnest", + "url": " https://rseng.github.io/software/repository/github/mlower/rmnest", + "content": "A standard (and generalised) rotation measures fitting package written in Python." }, - "github/rajeshmondal18/DviSukta": { - "id": "github/rajeshmondal18/DviSukta", - "title": "github/rajeshmondal18/DviSukta", - "url": " https://rseng.github.io/software/repository/github/rajeshmondal18/DviSukta", - "content": "A direct estimator of the bispectrum" + "github/algolab/shark": { + "id": "github/algolab/shark", + "title": "github/algolab/shark", + "url": " https://rseng.github.io/software/repository/github/algolab/shark", + "content": "Mapping-free software for fishing relevant reads in an RNA-Seq sample" }, - "github/rajeshmondal18/N-body": { - "id": "github/rajeshmondal18/N-body", - "title": "github/rajeshmondal18/N-body", - "url": " https://rseng.github.io/software/repository/github/rajeshmondal18/N-body", - "content": "A code to compute the non-linear evolution of the cosmological matter density contrast." + "github/vcftools/index.html": { + "id": "github/vcftools/index.html", + "title": "github/vcftools/index.html", + "url": " https://rseng.github.io/software/repository/github/vcftools/index.html", + "content": "a program package designed to provide easily accessible methods for working with complex genetic variation data in the form of VCF files, such as those generated by the 1000 Genomes Project." }, - "github/rajeshmondal18/MAPS": { - "id": "github/rajeshmondal18/MAPS", - "title": "github/rajeshmondal18/MAPS", - "url": " https://rseng.github.io/software/repository/github/rajeshmondal18/MAPS", - "content": "The Multi-frequency Angular Power Spectrum (MAPS) estimator" + "github/daissi/thesias": { + "id": "github/daissi/thesias", + "title": "github/daissi/thesias", + "url": " https://rseng.github.io/software/repository/github/daissi/thesias", + "content": "THESIAS: Testing Haplotype Effects In Association Studies" }, - "github/lmcinnes/umap": { - "id": "github/lmcinnes/umap", - "title": "github/lmcinnes/umap", - "url": " https://rseng.github.io/software/repository/github/lmcinnes/umap", - "content": "Uniform Manifold Approximation and Projection" + "github/OSS-Lab/ChemChaste": { + "id": "github/OSS-Lab/ChemChaste", + "title": "github/OSS-Lab/ChemChaste", + "url": " https://rseng.github.io/software/repository/github/OSS-Lab/ChemChaste", + "content": "None" }, - "github/ghislainv/forestatrisk": { - "id": "github/ghislainv/forestatrisk", - "title": "github/ghislainv/forestatrisk", - "url": " https://rseng.github.io/software/repository/github/ghislainv/forestatrisk", - "content": ":package: :snake: Python package to model and forecast the risk of deforestation" + "github/ConorMacBride/mcalf": { + "id": "github/ConorMacBride/mcalf", + "title": "github/ConorMacBride/mcalf", + "url": " https://rseng.github.io/software/repository/github/ConorMacBride/mcalf", + "content": "MCALF: Multi-Component Atmospheric Line Fitting" }, - "github/LeandroOrdonez/explora-vr-dash-client": { - "id": "github/LeandroOrdonez/explora-vr-dash-client", - "title": "github/LeandroOrdonez/explora-vr-dash-client", - "url": " https://rseng.github.io/software/repository/github/LeandroOrdonez/explora-vr-dash-client", + "github/AshleySpindler/AstroVaDEr-Public": { + "id": "github/AshleySpindler/AstroVaDEr-Public", + "title": "github/AshleySpindler/AstroVaDEr-Public", + "url": " https://rseng.github.io/software/repository/github/AshleySpindler/AstroVaDEr-Public", "content": "None" }, - "github/RussellJurek/busy-function-fitting": { - "id": "github/RussellJurek/busy-function-fitting", - "title": "github/RussellJurek/busy-function-fitting", - "url": " https://rseng.github.io/software/repository/github/RussellJurek/busy-function-fitting", - "content": "A C/C++ library and Python module that allows users to fit the Busy Function (Westmeier, Jurek, Obreschkow, Koribalski & Staveley-Smith 2013) to data. Previously available at code.google.com/p/busy-function-fitting" + "github/artic-network/readucks": { + "id": "github/artic-network/readucks", + "title": "github/artic-network/readucks", + "url": " https://rseng.github.io/software/repository/github/artic-network/readucks", + "content": "Nanopore read de-multiplexer" }, - "github/ColemanRHarris/mxnorm": { - "id": "github/ColemanRHarris/mxnorm", - "title": "github/ColemanRHarris/mxnorm", - "url": " https://rseng.github.io/software/repository/github/ColemanRHarris/mxnorm", - "content": "R package to normalize multiplexed imaging data." + "github/artic-network/fieldbioinformatics": { + "id": "github/artic-network/fieldbioinformatics", + "title": "github/artic-network/fieldbioinformatics", + "url": " https://rseng.github.io/software/repository/github/artic-network/fieldbioinformatics", + "content": "The ARTIC field bioinformatics pipeline" }, - "github/SMI/SmiServices": { - "id": "github/SMI/SmiServices", - "title": "github/SMI/SmiServices", - "url": " https://rseng.github.io/software/repository/github/SMI/SmiServices", - "content": "Scale-able loading, linking and anonymisation of DICOM images for healthcare research environments (e.g. Safe Havens)" + "github/sarrvesh/cuFFS": { + "id": "github/sarrvesh/cuFFS", + "title": "github/sarrvesh/cuFFS", + "url": " https://rseng.github.io/software/repository/github/sarrvesh/cuFFS", + "content": "A GPU-accelerated Rotation Measure Synthesis code" }, - "github/jordanlab/STing": { - "id": "github/jordanlab/STing", - "title": "github/jordanlab/STing", - "url": " https://rseng.github.io/software/repository/github/jordanlab/STing", - "content": "Ultrafast sequence typing and gene detection from NGS raw reads" + "github/kutaslab/fitgrid": { + "id": "github/kutaslab/fitgrid", + "title": "github/kutaslab/fitgrid", + "url": " https://rseng.github.io/software/repository/github/kutaslab/fitgrid", + "content": "Multichannel event-related time-series regression modeling for EEG, MEG, and sensor array data" }, - "github/JixingGE/GGCHEMPY": { - "id": "github/JixingGE/GGCHEMPY", - "title": "github/JixingGE/GGCHEMPY", - "url": " https://rseng.github.io/software/repository/github/JixingGE/GGCHEMPY", - "content": "Gas-grain chemical code for interstellar medium in pure Python" + "github/morispi/LRez": { + "id": "github/morispi/LRez", + "title": "github/morispi/LRez", + "url": " https://rseng.github.io/software/repository/github/morispi/LRez", + "content": "Standalone tool and library allowing to work with barcoded linked-reads" }, - "github/joergbuchwald/joss_ogs6py_VTUinterface": { - "id": "github/joergbuchwald/joss_ogs6py_VTUinterface", - "title": "github/joergbuchwald/joss_ogs6py_VTUinterface", - "url": " https://rseng.github.io/software/repository/github/joergbuchwald/joss_ogs6py_VTUinterface", + "github/opengenomebrowser/opengenomebrowser": { + "id": "github/opengenomebrowser/opengenomebrowser", + "title": "github/opengenomebrowser/opengenomebrowser", + "url": " https://rseng.github.io/software/repository/github/opengenomebrowser/opengenomebrowser", "content": "None" }, - "github/Chenmi0619/GALMoss": { - "id": "github/Chenmi0619/GALMoss", - "title": "github/Chenmi0619/GALMoss", - "url": " https://rseng.github.io/software/repository/github/Chenmi0619/GALMoss", - "content": "a galaxy surface bightness fitting code via gradient descent" + "github/mlhutchins/LWPC": { + "id": "github/mlhutchins/LWPC", + "title": "github/mlhutchins/LWPC", + "url": " https://rseng.github.io/software/repository/github/mlhutchins/LWPC", + "content": "Version 2.1 of the U.S. Navy Long Wave Propagation Capability code with alterations for running as a MATLAB function. The altered version has most warning and error reporting removed." }, - "github/mtsch/Ripserer.jl": { - "id": "github/mtsch/Ripserer.jl", - "title": "github/mtsch/Ripserer.jl", - "url": " https://rseng.github.io/software/repository/github/mtsch/Ripserer.jl", - "content": "Ripser and Ripserer" + "github/rpoleski/MulensModel": { + "id": "github/rpoleski/MulensModel", + "title": "github/rpoleski/MulensModel", + "url": " https://rseng.github.io/software/repository/github/rpoleski/MulensModel", + "content": "Microlensing Modelling package" }, - "github/davidsoergel/rtax": { - "id": "github/davidsoergel/rtax", - "title": "github/davidsoergel/rtax", - "url": " https://rseng.github.io/software/repository/github/davidsoergel/rtax", - "content": "Rapid and accurate taxonomic classification of short paired-end sequence reads from the 16S ribosomal RNA gene." + "github/rhysf/HaplotypeTools": { + "id": "github/rhysf/HaplotypeTools", + "title": "github/rhysf/HaplotypeTools", + "url": " https://rseng.github.io/software/repository/github/rhysf/HaplotypeTools", + "content": "A toolkit for identifying recombination and recombinant genotypes" }, - "github/bencebeky/spotrod": { - "id": "github/bencebeky/spotrod", - "title": "github/bencebeky/spotrod", - "url": " https://rseng.github.io/software/repository/github/bencebeky/spotrod", - "content": "A semi-analytic model for transits of spotted stars -- C implementation and Python API" + "github/sjteresi/TE_Density": { + "id": "github/sjteresi/TE_Density", + "title": "github/sjteresi/TE_Density", + "url": " https://rseng.github.io/software/repository/github/sjteresi/TE_Density", + "content": "Python script calculating transposable element density for all genes in a genome. Publication: https://mobilednajournal.biomedcentral.com/articles/10.1186/s13100-022-00264-4" }, - "github/jstuecker/adiabatic-tides": { - "id": "github/jstuecker/adiabatic-tides", - "title": "github/jstuecker/adiabatic-tides", - "url": " https://rseng.github.io/software/repository/github/jstuecker/adiabatic-tides", - "content": "Code for evaluating the tidal stripping of dark matter (sub)haloes in the adiabatic limit" + "github/tcherninceline/PPInteractions": { + "id": "github/tcherninceline/PPInteractions", + "title": "github/tcherninceline/PPInteractions", + "url": " https://rseng.github.io/software/repository/github/tcherninceline/PPInteractions", + "content": "None" }, - "github/ComtekAdvancedStructures/cmstatr": { - "id": "github/ComtekAdvancedStructures/cmstatr", - "title": "github/ComtekAdvancedStructures/cmstatr", - "url": " https://rseng.github.io/software/repository/github/ComtekAdvancedStructures/cmstatr", - "content": "An R Package for Statistical Analysis of Composite Material Data" + "github/graphnet-team/graphnet": { + "id": "github/graphnet-team/graphnet", + "title": "github/graphnet-team/graphnet", + "url": " https://rseng.github.io/software/repository/github/graphnet-team/graphnet", + "content": "Graph neural networks for neutrino telescope event reconstruction" }, - "github/SuLab/Wikidata-phenomizer": { - "id": "github/SuLab/Wikidata-phenomizer", - "title": "github/SuLab/Wikidata-phenomizer", - "url": " https://rseng.github.io/software/repository/github/SuLab/Wikidata-phenomizer", - "content": "Incorporate wikidata statements into phenomizer" + "github/bxlab/bx-python": { + "id": "github/bxlab/bx-python", + "title": "github/bxlab/bx-python", + "url": " https://rseng.github.io/software/repository/github/bxlab/bx-python", + "content": "Tools for manipulating biological data, particularly multiple sequence alignments" }, - "github/PeterDenton/ANA": { - "id": "github/PeterDenton/ANA", - "title": "github/PeterDenton/ANA", - "url": " https://rseng.github.io/software/repository/github/PeterDenton/ANA", - "content": "Astrophysical Neutrino Anisotropy" + "github/bxlab/metaWRAP": { + "id": "github/bxlab/metaWRAP", + "title": "github/bxlab/metaWRAP", + "url": " https://rseng.github.io/software/repository/github/bxlab/metaWRAP", + "content": "MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis" }, - "github/cedrus-opensource/pyxid": { - "id": "github/cedrus-opensource/pyxid", - "title": "github/cedrus-opensource/pyxid", - "url": " https://rseng.github.io/software/repository/github/cedrus-opensource/pyxid", - "content": "Pure python library for communicating with Cedrus XID devices" + "github/mjuric/galfast": { + "id": "github/mjuric/galfast", + "title": "github/mjuric/galfast", + "url": " https://rseng.github.io/software/repository/github/mjuric/galfast", + "content": "Milky Way Mock Catalog Generator" }, - "github/mwanakijiji/rrlfe": { - "id": "github/mwanakijiji/rrlfe", - "title": "github/mwanakijiji/rrlfe", - "url": " https://rseng.github.io/software/repository/github/mwanakijiji/rrlfe", - "content": "None" + "github/nu-radio/NuRadioMC": { + "id": "github/nu-radio/NuRadioMC", + "title": "github/nu-radio/NuRadioMC", + "url": " https://rseng.github.io/software/repository/github/nu-radio/NuRadioMC", + "content": "A Monte Carlo simulation package for radio neutrino detectors" }, - "github/tanhevg/GpABC.jl": { - "id": "github/tanhevg/GpABC.jl", - "title": "github/tanhevg/GpABC.jl", - "url": " https://rseng.github.io/software/repository/github/tanhevg/GpABC.jl", - "content": "None" + "github/MikkelSchubert/adapterremoval": { + "id": "github/MikkelSchubert/adapterremoval", + "title": "github/MikkelSchubert/adapterremoval", + "url": " https://rseng.github.io/software/repository/github/MikkelSchubert/adapterremoval", + "content": "AdapterRemoval v2 - rapid adapter trimming, identification, and read merging" }, - "github/jmcbroome/BTE": { - "id": "github/jmcbroome/BTE", - "title": "github/jmcbroome/BTE", - "url": " https://rseng.github.io/software/repository/github/jmcbroome/BTE", - "content": "Cython API for the Mutation Annotated Tree (MAT) Online Phylogenetics Toolkit" + "github/tofflemire/saphires": { + "id": "github/tofflemire/saphires", + "title": "github/tofflemire/saphires", + "url": " https://rseng.github.io/software/repository/github/tofflemire/saphires", + "content": "Analysis tools for stellar spectroscopy" }, - "github/yungkipreos/Min-CaLM": { - "id": "github/yungkipreos/Min-CaLM", - "title": "github/yungkipreos/Min-CaLM", - "url": " https://rseng.github.io/software/repository/github/yungkipreos/Min-CaLM", - "content": "This python package can perform automated mineral compositional analysis on debris disk spectra. It will determine which minerals are present and what their relative abundances are within the debris disk. This code is used in a paper that has been submitted to the American Journal of Undergraduate Research (AJUR), titled "An Unbiased Mineral Compositional Analysis Technique for Debris Disks" by Yung Kipreos and Dr. Inseok Song.." + "github/JLiangLab/TransVW": { + "id": "github/JLiangLab/TransVW", + "title": "github/JLiangLab/TransVW", + "url": " https://rseng.github.io/software/repository/github/JLiangLab/TransVW", + "content": "Official Keras & PyTorch Implementation and Pre-trained Models for TransVW" }, - "github/anuwu/GOTHIC": { - "id": "github/anuwu/GOTHIC", - "title": "github/anuwu/GOTHIC", - "url": " https://rseng.github.io/software/repository/github/anuwu/GOTHIC", - "content": "Double Nuclei Galaxy Finder from SDSS. Check https://arxiv.org/abs/2011.12177" + "github/lantunes/cellpylib": { + "id": "github/lantunes/cellpylib", + "title": "github/lantunes/cellpylib", + "url": " https://rseng.github.io/software/repository/github/lantunes/cellpylib", + "content": "A library for working with Cellular Automata, for Python." }, - "github/anuwu/DAGN-Blindtest": { - "id": "github/anuwu/DAGN-Blindtest", - "title": "github/anuwu/DAGN-Blindtest", - "url": " https://rseng.github.io/software/repository/github/anuwu/DAGN-Blindtest", - "content": "Double Nuclei Galaxy Finder from SDSS. Check https://arxiv.org/abs/2011.12177" + "github/rramadeu/AGHmatrix": { + "id": "github/rramadeu/AGHmatrix", + "title": "github/rramadeu/AGHmatrix", + "url": " https://rseng.github.io/software/repository/github/rramadeu/AGHmatrix", + "content": "An R package to compute relationship matrices for diploid and autopolyploid species" }, - "github/sing-group/my-brain-seq": { - "id": "github/sing-group/my-brain-seq", - "title": "github/sing-group/my-brain-seq", - "url": " https://rseng.github.io/software/repository/github/sing-group/my-brain-seq", - "content": "myBrain-Seq: a Compi pipeline for miRNA-Seq data analysis in neuropsychiatry" + "github/wdecoster/nanopack": { + "id": "github/wdecoster/nanopack", + "title": "github/wdecoster/nanopack", + "url": " https://rseng.github.io/software/repository/github/wdecoster/nanopack", + "content": "Easily install all nanopack scripts together" }, - "github/sing-group/seda": { - "id": "github/sing-group/seda", - "title": "github/sing-group/seda", - "url": " https://rseng.github.io/software/repository/github/sing-group/seda", - "content": "SEquence DAtaset builder" + "github/wdecoster/nano-snakemake": { + "id": "github/wdecoster/nano-snakemake", + "title": "github/wdecoster/nano-snakemake", + "url": " https://rseng.github.io/software/repository/github/wdecoster/nano-snakemake", + "content": "A snakemake pipeline for SV analysis from nanopore genome sequencing" }, - "github/dansarie/sboxgates": { - "id": "github/dansarie/sboxgates", - "title": "github/dansarie/sboxgates", - "url": " https://rseng.github.io/software/repository/github/dansarie/sboxgates", - "content": "Program for finding low gate count implementations of S-boxes." + "github/wdecoster/nanoget": { + "id": "github/wdecoster/nanoget", + "title": "github/wdecoster/nanoget", + "url": " https://rseng.github.io/software/repository/github/wdecoster/nanoget", + "content": "Functions to extract information from Oxford Nanopore sequencing data and alignments" }, - "github/bolverk/huji-rich": { - "id": "github/bolverk/huji-rich", - "title": "github/bolverk/huji-rich", - "url": " https://rseng.github.io/software/repository/github/bolverk/huji-rich", - "content": "A hydrodynamic simulation on a moving mesh" + "github/wdecoster/nanofilt": { + "id": "github/wdecoster/nanofilt", + "title": "github/wdecoster/nanofilt", + "url": " https://rseng.github.io/software/repository/github/wdecoster/nanofilt", + "content": "Filtering and trimming of long read sequencing data" }, - "github/dpalmasan/TRUNAJOD2.0": { - "id": "github/dpalmasan/TRUNAJOD2.0", - "title": "github/dpalmasan/TRUNAJOD2.0", - "url": " https://rseng.github.io/software/repository/github/dpalmasan/TRUNAJOD2.0", - "content": "An easy-to-use library to extract indices from texts." + "github/wdecoster/nanolyse": { + "id": "github/wdecoster/nanolyse", + "title": "github/wdecoster/nanolyse", + "url": " https://rseng.github.io/software/repository/github/wdecoster/nanolyse", + "content": "Remove lambda phage reads from a fastq file" }, - "github/abacusorg/zeldovich-PLT": { - "id": "github/abacusorg/zeldovich-PLT", - "title": "github/abacusorg/zeldovich-PLT", - "url": " https://rseng.github.io/software/repository/github/abacusorg/zeldovich-PLT", - "content": "Generates initial conditions for cosmological N-body simulations, optionally applying Particle Linear Theory corrections." + "github/wdecoster/chopper": { + "id": "github/wdecoster/chopper", + "title": "github/wdecoster/chopper", + "url": " https://rseng.github.io/software/repository/github/wdecoster/chopper", + "content": "Rust implementation of NanoFilt+NanoLyse, both originally written in Python. This tool, intended for long read sequencing such as PacBio or ONT, filters and trims a fastq file." }, - "github/cmayer/BaitFisher-package": { - "id": "github/cmayer/BaitFisher-package", - "title": "github/cmayer/BaitFisher-package", - "url": " https://rseng.github.io/software/repository/github/cmayer/BaitFisher-package", - "content": "The BaitFisher-package is a software package for designing hybrid enrichment probes. For more information see:" + "github/wdecoster/nanoQC": { + "id": "github/wdecoster/nanoQC", + "title": "github/wdecoster/nanoQC", + "url": " https://rseng.github.io/software/repository/github/wdecoster/nanoQC", + "content": "Quality control tools for nanopore sequencing data" }, - "github/mlaparie/sigh": { - "id": "github/mlaparie/sigh", - "title": "github/mlaparie/sigh", - "url": " https://rseng.github.io/software/repository/github/mlaparie/sigh", - "content": "sigh, a program to cure optimism and automatically scrape worldwide data about reported disaster and perturbation events." + "github/wdecoster/NanoComp": { + "id": "github/wdecoster/NanoComp", + "title": "github/wdecoster/NanoComp", + "url": " https://rseng.github.io/software/repository/github/wdecoster/NanoComp", + "content": "Comparison of multiple long read datasets" }, - "github/mlaparie/phidget-tools": { - "id": "github/mlaparie/phidget-tools", - "title": "github/mlaparie/phidget-tools", - "url": " https://rseng.github.io/software/repository/github/mlaparie/phidget-tools", - "content": "Terminal tools to record/monitor from Phidget 1048_1B USB-thermocouple devices" + "github/wdecoster/NanoPlot": { + "id": "github/wdecoster/NanoPlot", + "title": "github/wdecoster/NanoPlot", + "url": " https://rseng.github.io/software/repository/github/wdecoster/NanoPlot", + "content": "Plotting scripts for long read sequencing data" }, - "github/aconley/simple_cosfitter": { - "id": "github/aconley/simple_cosfitter", - "title": "github/aconley/simple_cosfitter", - "url": " https://rseng.github.io/software/repository/github/aconley/simple_cosfitter", - "content": "Grid based SN cosmology fitting code" + "github/wdecoster/nanomath": { + "id": "github/wdecoster/nanomath", + "title": "github/wdecoster/nanomath", + "url": " https://rseng.github.io/software/repository/github/wdecoster/nanomath", + "content": "A few simple math function for other Oxford Nanopore processing scripts" }, - "github/aconley/mbb_emcee": { - "id": "github/aconley/mbb_emcee", - "title": "github/aconley/mbb_emcee", - "url": " https://rseng.github.io/software/repository/github/aconley/mbb_emcee", - "content": "Modified blackbody MCMC code" + "github/wdecoster/nanostat": { + "id": "github/wdecoster/nanostat", + "title": "github/wdecoster/nanostat", + "url": " https://rseng.github.io/software/repository/github/wdecoster/nanostat", + "content": "Create statistic summary of an Oxford Nanopore read dataset" }, - "github/akcochrane/TEfits": { - "id": "github/akcochrane/TEfits", - "title": "github/akcochrane/TEfits", - "url": " https://rseng.github.io/software/repository/github/akcochrane/TEfits", - "content": "R package for streamlined nonlinear regression" + "github/wdecoster/nanocomp": { + "id": "github/wdecoster/nanocomp", + "title": "github/wdecoster/nanocomp", + "url": " https://rseng.github.io/software/repository/github/wdecoster/nanocomp", + "content": "Comparison of multiple long read datasets" }, - "github/aqlaboratory/openfold": { - "id": "github/aqlaboratory/openfold", - "title": "github/aqlaboratory/openfold", - "url": " https://rseng.github.io/software/repository/github/aqlaboratory/openfold", - "content": "Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2" + "github/trinityrnaseq/wiki": { + "id": "github/trinityrnaseq/wiki", + "title": "github/trinityrnaseq/wiki", + "url": " https://rseng.github.io/software/repository/github/trinityrnaseq/wiki", + "content": "a software package comprised of three independent software modules (Inchworm, Chrysalis, and Butterfly) for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data." }, - "github/mtazzari/uvplot": { - "id": "github/mtazzari/uvplot", - "title": "github/mtazzari/uvplot", - "url": " https://rseng.github.io/software/repository/github/mtazzari/uvplot", - "content": "A simple package to make nice visibility plots and to export visibilites from MS tables" + "github/WorkflowConversion/CTDConverter": { + "id": "github/WorkflowConversion/CTDConverter", + "title": "github/WorkflowConversion/CTDConverter", + "url": " https://rseng.github.io/software/repository/github/WorkflowConversion/CTDConverter", + "content": "Series of python scripts to convert CTD files into other formats such as Galaxy, CWL" }, - "github/mtazzari/galario": { - "id": "github/mtazzari/galario", - "title": "github/mtazzari/galario", - "url": " https://rseng.github.io/software/repository/github/mtazzari/galario", - "content": "Gpu Accelerated Library for Analysing Radio Interferometer Observations" + "github/WorkflowConversion/CTDopts": { + "id": "github/WorkflowConversion/CTDopts", + "title": "github/WorkflowConversion/CTDopts", + "url": " https://rseng.github.io/software/repository/github/WorkflowConversion/CTDopts", + "content": "Gives your command-line tools a CTD-compatible interface" }, - "github/mtazzari/binary": { - "id": "github/mtazzari/binary", - "title": "github/mtazzari/binary", - "url": " https://rseng.github.io/software/repository/github/mtazzari/binary", - "content": "This program computes the evolution of an accretion disc interacting with a binary system. Used in Tazzari, Lodato (2015)." + "github/hsci-r/finnish-media-scrapers": { + "id": "github/hsci-r/finnish-media-scrapers", + "title": "github/hsci-r/finnish-media-scrapers", + "url": " https://rseng.github.io/software/repository/github/hsci-r/finnish-media-scrapers", + "content": "Scrapers for extracting articles from major Finnish journalistic media outlets" + }, + "github/cmzmasek/forester": { + "id": "github/cmzmasek/forester", + "title": "github/cmzmasek/forester", + "url": " https://rseng.github.io/software/repository/github/cmzmasek/forester", + "content": "forester is a collection of open source libraries of Java and Ruby software for phylogenomics and evolutionary biology research" }, - "github/astro-informatics/flaglet-archive": { - "id": "github/astro-informatics/flaglet-archive", - "title": "github/astro-informatics/flaglet-archive", - "url": " https://rseng.github.io/software/repository/github/astro-informatics/flaglet-archive", - "content": "Fast and exact wavelet transform on the ball" + "github/shengjin/Nii": { + "id": "github/shengjin/Nii", + "title": "github/shengjin/Nii", + "url": " https://rseng.github.io/software/repository/github/shengjin/Nii", + "content": "The Nii code" }, - "github/astro-informatics/harmonic": { - "id": "github/astro-informatics/harmonic", - "title": "github/astro-informatics/harmonic", - "url": " https://rseng.github.io/software/repository/github/astro-informatics/harmonic", - "content": "Machine learning assisted marginal likelihood (Bayesian evidence) estimation for Bayesian model selection" + "github/paumard/cubefit": { + "id": "github/paumard/cubefit", + "title": "github/paumard/cubefit", + "url": " https://rseng.github.io/software/repository/github/paumard/cubefit", + "content": "None" }, - "github/astro-informatics/s2": { - "id": "github/astro-informatics/s2", - "title": "github/astro-informatics/s2", - "url": " https://rseng.github.io/software/repository/github/astro-informatics/s2", - "content": "Functions on the sphere" + "github/jolie/tquery": { + "id": "github/jolie/tquery", + "title": "github/jolie/tquery", + "url": " https://rseng.github.io/software/repository/github/jolie/tquery", + "content": "A data-query framework based on a sound variant of the MongoDB aggregation framework" }, - "github/astro-informatics/DarkMappy": { - "id": "github/astro-informatics/DarkMappy", - "title": "github/astro-informatics/DarkMappy", - "url": " https://rseng.github.io/software/repository/github/astro-informatics/DarkMappy", - "content": "Scalable mapping of the dark universe" + "github/UNSW-CEEM/NEMSEER": { + "id": "github/UNSW-CEEM/NEMSEER", + "title": "github/UNSW-CEEM/NEMSEER", + "url": " https://rseng.github.io/software/repository/github/UNSW-CEEM/NEMSEER", + "content": "A package for downloading and handling forecasts for the National Electricity Market (NEM) from the Australian Energy Market Operator (AEMO)." }, - "github/astro-informatics/massmappy": { - "id": "github/astro-informatics/massmappy", - "title": "github/astro-informatics/massmappy", - "url": " https://rseng.github.io/software/repository/github/astro-informatics/massmappy", - "content": "Mapping dark matter on the celestial sphere" + "github/UNSW-CEEM/nempy": { + "id": "github/UNSW-CEEM/nempy", + "title": "github/UNSW-CEEM/nempy", + "url": " https://rseng.github.io/software/repository/github/UNSW-CEEM/nempy", + "content": "A flexible tool kit for modelling Australia's National Electricity Market dispatch procedure." }, - "github/astro-informatics/sleplet": { - "id": "github/astro-informatics/sleplet", - "title": "github/astro-informatics/sleplet", - "url": " https://rseng.github.io/software/repository/github/astro-informatics/sleplet", - "content": "Slepian Scale-Discretised Wavelets" + "github/NeoGeographyToolkit/StereoPipeline": { + "id": "github/NeoGeographyToolkit/StereoPipeline", + "title": "github/NeoGeographyToolkit/StereoPipeline", + "url": " https://rseng.github.io/software/repository/github/NeoGeographyToolkit/StereoPipeline", + "content": "The NASA Ames Stereo Pipeline is a suite of automated geodesy & stereogrammetry tools designed for processing planetary imagery captured from orbiting and landed robotic explorers on other planets." }, - "github/astro-informatics/RequiSim": { - "id": "github/astro-informatics/RequiSim", - "title": "github/astro-informatics/RequiSim", - "url": " https://rseng.github.io/software/repository/github/astro-informatics/RequiSim", - "content": "None" + "github/Alcampopiano/hypothesize": { + "id": "github/Alcampopiano/hypothesize", + "title": "github/Alcampopiano/hypothesize", + "url": " https://rseng.github.io/software/repository/github/Alcampopiano/hypothesize", + "content": "Robust statistics in Python" }, - "github/astro-informatics/flag-archive": { - "id": "github/astro-informatics/flag-archive", - "title": "github/astro-informatics/flag-archive", - "url": " https://rseng.github.io/software/repository/github/astro-informatics/flag-archive", - "content": "Fast Fourier-Laguerre transform on the ball and exact spherical Bessel and Fourier-Bessel transforms" + "github/radio-astro-tools/spectral-cube": { + "id": "github/radio-astro-tools/spectral-cube", + "title": "github/radio-astro-tools/spectral-cube", + "url": " https://rseng.github.io/software/repository/github/radio-astro-tools/spectral-cube", + "content": "Library for reading and analyzing astrophysical spectral data cubes" }, - "github/astro-informatics/comb": { - "id": "github/astro-informatics/comb", - "title": "github/astro-informatics/comb", - "url": " https://rseng.github.io/software/repository/github/astro-informatics/comb", - "content": "Compact object simulations on the sphere" + "github/radio-astro-tools/uvcombine": { + "id": "github/radio-astro-tools/uvcombine", + "title": "github/radio-astro-tools/uvcombine", + "url": " https://rseng.github.io/software/repository/github/radio-astro-tools/uvcombine", + "content": "Combine images made with different resolutions, including the "feathering" technique for interferometry data." }, - "github/astro-informatics/QuantifAI": { - "id": "github/astro-informatics/QuantifAI", - "title": "github/astro-informatics/QuantifAI", - "url": " https://rseng.github.io/software/repository/github/astro-informatics/QuantifAI", - "content": "PyTorch-based RI imaging reconstruction package with scalable Bayesian uncertainty quantification relying on data-driven (learned) priors" + "github/radio-astro-tools/pvextractor": { + "id": "github/radio-astro-tools/pvextractor", + "title": "github/radio-astro-tools/pvextractor", + "url": " https://rseng.github.io/software/repository/github/radio-astro-tools/pvextractor", + "content": "Position-Velocity diagram extract (but it can slice out other things too)" }, - "github/astro-informatics/ssht": { - "id": "github/astro-informatics/ssht", - "title": "github/astro-informatics/ssht", - "url": " https://rseng.github.io/software/repository/github/astro-informatics/ssht", - "content": "Fast and exact spin spherical harmonic transforms" + "github/taoliu/MACS": { + "id": "github/taoliu/MACS", + "title": "github/taoliu/MACS", + "url": " https://rseng.github.io/software/repository/github/taoliu/MACS", + "content": "MACS -- Model-based Analysis of ChIP-Seq" }, - "github/astro-informatics/s2let": { - "id": "github/astro-informatics/s2let", - "title": "github/astro-informatics/s2let", - "url": " https://rseng.github.io/software/repository/github/astro-informatics/s2let", - "content": "Fast wavelet transforms on the sphere." + "github/wilkelab/Opfi": { + "id": "github/wilkelab/Opfi", + "title": "github/wilkelab/Opfi", + "url": " https://rseng.github.io/software/repository/github/wilkelab/Opfi", + "content": "A Python package for discovery, annotation, and analysis of gene clusters in genomics or metagenomics data sets." }, - "github/HITS-AIN/PINK": { - "id": "github/HITS-AIN/PINK", - "title": "github/HITS-AIN/PINK", - "url": " https://rseng.github.io/software/repository/github/HITS-AIN/PINK", - "content": "Parallelized rotation and flipping INvariant Kohonen maps" + "github/s-goldman/Dusty-Evolved-Star-Kit": { + "id": "github/s-goldman/Dusty-Evolved-Star-Kit", + "title": "github/s-goldman/Dusty-Evolved-Star-Kit", + "url": " https://rseng.github.io/software/repository/github/s-goldman/Dusty-Evolved-Star-Kit", + "content": "SED-fitting python package for fitting evolved stars" }, - "github/HITS-AIN/GPCC.jl": { - "id": "github/HITS-AIN/GPCC.jl", - "title": "github/HITS-AIN/GPCC.jl", - "url": " https://rseng.github.io/software/repository/github/HITS-AIN/GPCC.jl", - "content": "Gaussian process cross correlation" + "github/mjshao06/pdifFinder": { + "id": "github/mjshao06/pdifFinder", + "title": "github/mjshao06/pdifFinder", + "url": " https://rseng.github.io/software/repository/github/mjshao06/pdifFinder", + "content": "None" }, - "github/phenology/cgc": { - "id": "github/phenology/cgc", - "title": "github/phenology/cgc", - "url": " https://rseng.github.io/software/repository/github/phenology/cgc", - "content": "A clustering tool for geospatial applications" + "github/gnudatalanguage/gdl": { + "id": "github/gnudatalanguage/gdl", + "title": "github/gnudatalanguage/gdl", + "url": " https://rseng.github.io/software/repository/github/gnudatalanguage/gdl", + "content": "GDL - GNU Data Language" }, - "github/chadagreene/Tide-Model-Driver": { - "id": "github/chadagreene/Tide-Model-Driver", - "title": "github/chadagreene/Tide-Model-Driver", - "url": " https://rseng.github.io/software/repository/github/chadagreene/Tide-Model-Driver", - "content": "Tide Model Driver for MATLAB, version 3.0" + "github/dbuscher/pois": { + "id": "github/dbuscher/pois", + "title": "github/dbuscher/pois", + "url": " https://rseng.github.io/software/repository/github/dbuscher/pois", + "content": "Python framework simulating the data from a ground-based optical interferometer" }, - "github/cov-lineages/pangoLEARN": { - "id": "github/cov-lineages/pangoLEARN", - "title": "github/cov-lineages/pangoLEARN", - "url": " https://rseng.github.io/software/repository/github/cov-lineages/pangoLEARN", - "content": "Store of the trained model for pangolin to access." + "github/lrnv/Copulas.jl": { + "id": "github/lrnv/Copulas.jl", + "title": "github/lrnv/Copulas.jl", + "url": " https://rseng.github.io/software/repository/github/lrnv/Copulas.jl", + "content": "A fully `Distributions.jl`-compliant copula package" }, - "github/cov-lineages/pangolin": { - "id": "github/cov-lineages/pangolin", - "title": "github/cov-lineages/pangolin", - "url": " https://rseng.github.io/software/repository/github/cov-lineages/pangolin", - "content": "Software package for assigning SARS-CoV-2 genome sequences to global lineages." + "github/lrnv/cort": { + "id": "github/lrnv/cort", + "title": "github/lrnv/cort", + "url": " https://rseng.github.io/software/repository/github/lrnv/cort", + "content": "Classes and Tools For Some Empirical and Non-parametrical Copula Models." }, - "github/songningqiang/CosmoLED": { - "id": "github/songningqiang/CosmoLED", - "title": "github/songningqiang/CosmoLED", - "url": " https://rseng.github.io/software/repository/github/songningqiang/CosmoLED", - "content": "None" + "github/lukapecnik/NiaAML": { + "id": "github/lukapecnik/NiaAML", + "title": "github/lukapecnik/NiaAML", + "url": " https://rseng.github.io/software/repository/github/lukapecnik/NiaAML", + "content": "Python automated machine learning framework." }, - "github/Bgi-LUSH/GPMeta": { - "id": "github/Bgi-LUSH/GPMeta", - "title": "github/Bgi-LUSH/GPMeta", - "url": " https://rseng.github.io/software/repository/github/Bgi-LUSH/GPMeta", - "content": "A GPU-accelerated method for ultrarapid pathogen identification from metagenomic sequences." + "github/AP6YC/ClusterValidityIndices.jl": { + "id": "github/AP6YC/ClusterValidityIndices.jl", + "title": "github/AP6YC/ClusterValidityIndices.jl", + "url": " https://rseng.github.io/software/repository/github/AP6YC/ClusterValidityIndices.jl", + "content": "A Julia package for Cluster Validity Indices (CVIs)." }, - "github/optuna/optuna": { - "id": "github/optuna/optuna", - "title": "github/optuna/optuna", - "url": " https://rseng.github.io/software/repository/github/optuna/optuna", - "content": "A hyperparameter optimization framework" + "github/AP6YC/AdaptiveResonance.jl": { + "id": "github/AP6YC/AdaptiveResonance.jl", + "title": "github/AP6YC/AdaptiveResonance.jl", + "url": " https://rseng.github.io/software/repository/github/AP6YC/AdaptiveResonance.jl", + "content": "A Julia package for Adaptive Resonance Theory (ART) algorithms." }, - "github/Bonfanti88/MCMCI": { - "id": "github/Bonfanti88/MCMCI", - "title": "github/Bonfanti88/MCMCI", - "url": " https://rseng.github.io/software/repository/github/Bonfanti88/MCMCI", - "content": "A code to fully characterise an exoplanetary system (Bonfanti & Gillon, 2020)" + "github/grburgess/ronswanson": { + "id": "github/grburgess/ronswanson", + "title": "github/grburgess/ronswanson", + "url": " https://rseng.github.io/software/repository/github/grburgess/ronswanson", + "content": "Ron Swanson builds tables for 3ML" }, - "github/scikit-image/scikit-image": { - "id": "github/scikit-image/scikit-image", - "title": "github/scikit-image/scikit-image", - "url": " https://rseng.github.io/software/repository/github/scikit-image/scikit-image", - "content": "Image processing in Python" + "github/grburgess/popsynth": { + "id": "github/grburgess/popsynth", + "title": "github/grburgess/popsynth", + "url": " https://rseng.github.io/software/repository/github/grburgess/popsynth", + "content": "A generic flux/parameter population synthesis code" }, - "github/acerbilab/pybads": { - "id": "github/acerbilab/pybads", - "title": "github/acerbilab/pybads", - "url": " https://rseng.github.io/software/repository/github/acerbilab/pybads", - "content": "PyBADS: Bayesian Adaptive Direct Search optimization algorithm for model fitting in Python" + "github/matiscke/lcps": { + "id": "github/matiscke/lcps", + "title": "github/matiscke/lcps", + "url": " https://rseng.github.io/software/repository/github/matiscke/lcps", + "content": "A tool for pre-selecting light curves with possible transit signatures" }, - "github/carlodev/SyntheticEddyMethod.jl": { - "id": "github/carlodev/SyntheticEddyMethod.jl", - "title": "github/carlodev/SyntheticEddyMethod.jl", - "url": " https://rseng.github.io/software/repository/github/carlodev/SyntheticEddyMethod.jl", - "content": "None" + "github/Jashcraf/poke": { + "id": "github/Jashcraf/poke", + "title": "github/Jashcraf/poke", + "url": " https://rseng.github.io/software/repository/github/Jashcraf/poke", + "content": "Poke (pronounced poh-keh) is a Polarization Ray Tracing and Gaussian Beamlet module for Python" }, - "github/mortonne/psifr": { - "id": "github/mortonne/psifr", - "title": "github/mortonne/psifr", - "url": " https://rseng.github.io/software/repository/github/mortonne/psifr", - "content": "Psifr: Analysis and visualization of free recall data" + "github/fripon/freeture": { + "id": "github/fripon/freeture", + "title": "github/fripon/freeture", + "url": " https://rseng.github.io/software/repository/github/fripon/freeture", + "content": "A Free software to capTure meteors " }, - "github/shihyuntang/igrins_rv": { - "id": "github/shihyuntang/igrins_rv", - "title": "github/shihyuntang/igrins_rv", - "url": " https://rseng.github.io/software/repository/github/shihyuntang/igrins_rv", - "content": "Welcome to IGRINS RV, a open source pipeline for extracting radial velocity (RV) for the Immersion GRating INfrared Spectrometer (IGRINS) instrument. Please contact asa.stahl@rice.edu or sytang@lowell.edu for more detail." + "github/anuwu/DAGN-Blindtest": { + "id": "github/anuwu/DAGN-Blindtest", + "title": "github/anuwu/DAGN-Blindtest", + "url": " https://rseng.github.io/software/repository/github/anuwu/DAGN-Blindtest", + "content": "Double Nuclei Galaxy Finder from SDSS. Check https://arxiv.org/abs/2011.12177" }, - "github/SSAGESproject/SSAGES": { - "id": "github/SSAGESproject/SSAGES", - "title": "github/SSAGESproject/SSAGES", - "url": " https://rseng.github.io/software/repository/github/SSAGESproject/SSAGES", - "content": "Software Suite for Advanced General Ensemble Simulations" + "github/anuwu/GOTHIC": { + "id": "github/anuwu/GOTHIC", + "title": "github/anuwu/GOTHIC", + "url": " https://rseng.github.io/software/repository/github/anuwu/GOTHIC", + "content": "Double Nuclei Galaxy Finder from SDSS. Check https://arxiv.org/abs/2011.12177" }, - "github/daeken/Emokit": { - "id": "github/daeken/Emokit", - "title": "github/daeken/Emokit", - "url": " https://rseng.github.io/software/repository/github/daeken/Emokit", - "content": "Python library for the Emotiv EPOC headset" + "github/nicolet5/DiffCapAnalyzer": { + "id": "github/nicolet5/DiffCapAnalyzer", + "title": "github/nicolet5/DiffCapAnalyzer", + "url": " https://rseng.github.io/software/repository/github/nicolet5/DiffCapAnalyzer", + "content": "A tool for quantitative analysis of differential capacity data! " }, - "github/martinsparre/XSHPipelineManager": { - "id": "github/martinsparre/XSHPipelineManager", - "title": "github/martinsparre/XSHPipelineManager", - "url": " https://rseng.github.io/software/repository/github/martinsparre/XSHPipelineManager", - "content": "A script to run the X-shooter pipeline" + "github/JacobBumgarner/VesselVio": { + "id": "github/JacobBumgarner/VesselVio", + "title": "github/JacobBumgarner/VesselVio", + "url": " https://rseng.github.io/software/repository/github/JacobBumgarner/VesselVio", + "content": "VesselVio is an open-source application for the analysis and visualization of segmented vasculature datasets" }, - "github/holmescao/ANTS_marking_and_analysis_tools": { - "id": "github/holmescao/ANTS_marking_and_analysis_tools", - "title": "github/holmescao/ANTS_marking_and_analysis_tools", - "url": " https://rseng.github.io/software/repository/github/holmescao/ANTS_marking_and_analysis_tools", - "content": "None" + "github/eWaterCycle/jupyterlab_thredds": { + "id": "github/eWaterCycle/jupyterlab_thredds", + "title": "github/eWaterCycle/jupyterlab_thredds", + "url": " https://rseng.github.io/software/repository/github/eWaterCycle/jupyterlab_thredds", + "content": "JupyterLab dataset browser for THREDDS catalog" }, - "github/michaeltouati/ESVM": { - "id": "github/michaeltouati/ESVM", - "title": "github/michaeltouati/ESVM", - "url": " https://rseng.github.io/software/repository/github/michaeltouati/ESVM", - "content": "Finite-volume Vlasov-Maxwell code to study for Plasma Physics simulations" + "github/eWaterCycle/ewatercycle": { + "id": "github/eWaterCycle/ewatercycle", + "title": "github/eWaterCycle/ewatercycle", + "url": " https://rseng.github.io/software/repository/github/eWaterCycle/ewatercycle", + "content": "Python utilities for running hydrological models" }, - "github/jo276/EvapMass": { - "id": "github/jo276/EvapMass", - "title": "github/jo276/EvapMass", - "url": " https://rseng.github.io/software/repository/github/jo276/EvapMass", - "content": "None" + "github/eWaterCycle/grpc4bmi": { + "id": "github/eWaterCycle/grpc4bmi", + "title": "github/eWaterCycle/grpc4bmi", + "url": " https://rseng.github.io/software/repository/github/eWaterCycle/grpc4bmi", + "content": "gRPC wrapper for model with a Basic modeling interface" }, - "github/Punzo/SlicerAstro": { - "id": "github/Punzo/SlicerAstro", - "title": "github/Punzo/SlicerAstro", - "url": " https://rseng.github.io/software/repository/github/Punzo/SlicerAstro", - "content": "Astronomy (HI) extension for 3DSlicer (https://www.slicer.org/)" + "github/eWaterCycle/Cesium-NcWMS": { + "id": "github/eWaterCycle/Cesium-NcWMS", + "title": "github/eWaterCycle/Cesium-NcWMS", + "url": " https://rseng.github.io/software/repository/github/eWaterCycle/Cesium-NcWMS", + "content": "Cesium angular directive with ncwms integration to display netcdf datasets" }, - "github/mgcooper/baseflow": { - "id": "github/mgcooper/baseflow", - "title": "github/mgcooper/baseflow", - "url": " https://rseng.github.io/software/repository/github/mgcooper/baseflow", - "content": "baseflow recession analysis toolbox" + "github/eWaterCycle/setup-singularity": { + "id": "github/eWaterCycle/setup-singularity", + "title": "github/eWaterCycle/setup-singularity", + "url": " https://rseng.github.io/software/repository/github/eWaterCycle/setup-singularity", + "content": "GitHub action to setup singularity" }, - "github/fcastagna/preprofit": { - "id": "github/fcastagna/preprofit", - "title": "github/fcastagna/preprofit", - "url": " https://rseng.github.io/software/repository/github/fcastagna/preprofit", - "content": "Pressure Profile Fitter for galaxy clusters in Python" + "github/eWaterCycle/setup-grpc": { + "id": "github/eWaterCycle/setup-grpc", + "title": "github/eWaterCycle/setup-grpc", + "url": " https://rseng.github.io/software/repository/github/eWaterCycle/setup-grpc", + "content": "GitHub Action to setup gRPC C++ environment" }, - "github/fcastagna/JoXSZ": { - "id": "github/fcastagna/JoXSZ", - "title": "github/fcastagna/JoXSZ", - "url": " https://rseng.github.io/software/repository/github/fcastagna/JoXSZ", - "content": "Joint X-ray and SZ data fitting code for galaxy clusters in Python" + "github/eWaterCycle/eWaterleaf": { + "id": "github/eWaterCycle/eWaterleaf", + "title": "github/eWaterCycle/eWaterleaf", + "url": " https://rseng.github.io/software/repository/github/eWaterCycle/eWaterleaf", + "content": "Simple leaflet-based visualization for the eWaterCycle project" }, - "github/CobayaSampler/cobaya": { - "id": "github/CobayaSampler/cobaya", - "title": "github/CobayaSampler/cobaya", - "url": " https://rseng.github.io/software/repository/github/CobayaSampler/cobaya", - "content": "Code for Bayesian Analysis" + "github/eWaterCycle/experiment-launcher": { + "id": "github/eWaterCycle/experiment-launcher", + "title": "github/eWaterCycle/experiment-launcher", + "url": " https://rseng.github.io/software/repository/github/eWaterCycle/experiment-launcher", + "content": "eWaterCycle Experiment Launcher" }, - "github/yuliang419/AstroNet-Triage": { - "id": "github/yuliang419/AstroNet-Triage", - "title": "github/yuliang419/AstroNet-Triage", - "url": " https://rseng.github.io/software/repository/github/yuliang419/AstroNet-Triage", - "content": "A Neural Network for TESS Light Curve Triage" + "github/yangfangs/KPP": { + "id": "github/yangfangs/KPP", + "title": "github/yangfangs/KPP", + "url": " https://rseng.github.io/software/repository/github/yangfangs/KPP", + "content": "KPP (kmer phylogenetic profile) algorithm" }, - "github/yuliang419/AstroNet-Vetting": { - "id": "github/yuliang419/AstroNet-Vetting", - "title": "github/yuliang419/AstroNet-Vetting", - "url": " https://rseng.github.io/software/repository/github/yuliang419/AstroNet-Vetting", - "content": "A Neural Network for TESS Light Curve Vetting" + "github/yangfangs/test_GFICLEE": { + "id": "github/yangfangs/test_GFICLEE", + "title": "github/yangfangs/test_GFICLEE", + "url": " https://rseng.github.io/software/repository/github/yangfangs/test_GFICLEE", + "content": "test GFICLEE model" }, - "github/chasmani/piecewise-regression": { - "id": "github/chasmani/piecewise-regression", - "title": "github/chasmani/piecewise-regression", - "url": " https://rseng.github.io/software/repository/github/chasmani/piecewise-regression", - "content": "piecewise-regression (aka segmented regression) in python. For fitting straight line models to data with one or more breakpoints where the gradient changes. " + "github/aertslab/pySCENIC": { + "id": "github/aertslab/pySCENIC", + "title": "github/aertslab/pySCENIC", + "url": " https://rseng.github.io/software/repository/github/aertslab/pySCENIC", + "content": "pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data." }, - "github/dawolfgang/MRrelation": { - "id": "github/dawolfgang/MRrelation", - "title": "github/dawolfgang/MRrelation", - "url": " https://rseng.github.io/software/repository/github/dawolfgang/MRrelation", - "content": "None" + "github/SirSharpest/NarrowEscapeSimulator": { + "id": "github/SirSharpest/NarrowEscapeSimulator", + "title": "github/SirSharpest/NarrowEscapeSimulator", + "url": " https://rseng.github.io/software/repository/github/SirSharpest/NarrowEscapeSimulator", + "content": "Developed during my PhD at the John Innes Centre (Norwich Research Park, Doctoral Training Programme). " }, - "github/sbi-dev/sbi": { - "id": "github/sbi-dev/sbi", - "title": "github/sbi-dev/sbi", - "url": " https://rseng.github.io/software/repository/github/sbi-dev/sbi", - "content": "Simulation-based inference toolkit" + "github/rudolffu/pyfosc": { + "id": "github/rudolffu/pyfosc", + "title": "github/rudolffu/pyfosc", + "url": " https://rseng.github.io/software/repository/github/rudolffu/pyfosc", + "content": "PyFOSC is a pipeline toolbox for spectroscopic data reduction written in Python. It can be used for FOSC data from Xinglong/Lijiang 2-meter telescopes." }, - "github/inonchiu/ComEst": { - "id": "github/inonchiu/ComEst", - "title": "github/inonchiu/ComEst", - "url": " https://rseng.github.io/software/repository/github/inonchiu/ComEst", - "content": "ComEst - a completeness estimator" + "github/mroosmalen/nanosv": { + "id": "github/mroosmalen/nanosv", + "title": "github/mroosmalen/nanosv", + "url": " https://rseng.github.io/software/repository/github/mroosmalen/nanosv", + "content": "SV caller for nanopore data" }, - "github/flekschas/regl-scatterplot": { - "id": "github/flekschas/regl-scatterplot", - "title": "github/flekschas/regl-scatterplot", - "url": " https://rseng.github.io/software/repository/github/flekschas/regl-scatterplot", - "content": "Scalable WebGL-based scatter plot library build with Regl" + "github/cjbarrie/academictwitteR": { + "id": "github/cjbarrie/academictwitteR", + "title": "github/cjbarrie/academictwitteR", + "url": " https://rseng.github.io/software/repository/github/cjbarrie/academictwitteR", + "content": "Repo for academictwitteR package to query the Twitter Academic Research Product Track v2 API endpoint." }, - "github/prmunday/Immunolyser": { - "id": "github/prmunday/Immunolyser", - "title": "github/prmunday/Immunolyser", - "url": " https://rseng.github.io/software/repository/github/prmunday/Immunolyser", - "content": "None" + "github/exafmm/exafmm-t": { + "id": "github/exafmm/exafmm-t", + "title": "github/exafmm/exafmm-t", + "url": " https://rseng.github.io/software/repository/github/exafmm/exafmm-t", + "content": "A kernel-independent fast multipole method library with Python interface." }, - "github/CoolWorlds/ExoPriors": { - "id": "github/CoolWorlds/ExoPriors", - "title": "github/CoolWorlds/ExoPriors", - "url": " https://rseng.github.io/software/repository/github/CoolWorlds/ExoPriors", - "content": "Calculate log-likelihood penalties to account for observational bias in exoplanet detection." + "github/VirtualPlanetaryLaboratory/vplanet": { + "id": "github/VirtualPlanetaryLaboratory/vplanet", + "title": "github/VirtualPlanetaryLaboratory/vplanet", + "url": " https://rseng.github.io/software/repository/github/VirtualPlanetaryLaboratory/vplanet", + "content": "The Virtual Planet Simulator" }, - "github/CoolWorlds/exoinformatics": { - "id": "github/CoolWorlds/exoinformatics", - "title": "github/CoolWorlds/exoinformatics", - "url": " https://rseng.github.io/software/repository/github/CoolWorlds/exoinformatics", + "github/VirtualPlanetaryLaboratory/atmos": { + "id": "github/VirtualPlanetaryLaboratory/atmos", + "title": "github/VirtualPlanetaryLaboratory/atmos", + "url": " https://rseng.github.io/software/repository/github/VirtualPlanetaryLaboratory/atmos", "content": "None" }, - "github/MrMinimal64/multivar_horner": { - "id": "github/MrMinimal64/multivar_horner", - "title": "github/MrMinimal64/multivar_horner", - "url": " https://rseng.github.io/software/repository/github/MrMinimal64/multivar_horner", - "content": "python package implementing a multivariate Horner scheme for efficiently evaluating multivariate polynomials " + "github/aprsa/dips": { + "id": "github/aprsa/dips", + "title": "github/aprsa/dips", + "url": " https://rseng.github.io/software/repository/github/aprsa/dips", + "content": "dips: detrending periodic signals in timeseries." }, - "github/eead-csic-compbio/get_homologues": { - "id": "github/eead-csic-compbio/get_homologues", - "title": "github/eead-csic-compbio/get_homologues", - "url": " https://rseng.github.io/software/repository/github/eead-csic-compbio/get_homologues", - "content": "GET_HOMOLOGUES: a versatile software package for pan-genome analysis" + "github/aprsa/ebai": { + "id": "github/aprsa/ebai", + "title": "github/aprsa/ebai", + "url": " https://rseng.github.io/software/repository/github/aprsa/ebai", + "content": "Eclipsing Binaries with Artificial Intelligence" }, - "github/labxscut/ksak": { - "id": "github/labxscut/ksak", - "title": "github/labxscut/ksak", - "url": " https://rseng.github.io/software/repository/github/labxscut/ksak", - "content": "None" + "github/BEAST-Fitting/beast": { + "id": "github/BEAST-Fitting/beast", + "title": "github/BEAST-Fitting/beast", + "url": " https://rseng.github.io/software/repository/github/BEAST-Fitting/beast", + "content": "Bayesian Extinction And Stellar Tool" + }, + "github/bertrandplez/Turbospectrum_NLTE": { + "id": "github/bertrandplez/Turbospectrum_NLTE", + "title": "github/bertrandplez/Turbospectrum_NLTE", + "url": " https://rseng.github.io/software/repository/github/bertrandplez/Turbospectrum_NLTE", + "content": "Turbospectrum v20 with NLTE capability" }, - "github/ablab/TandemTools": { - "id": "github/ablab/TandemTools", - "title": "github/ablab/TandemTools", - "url": " https://rseng.github.io/software/repository/github/ablab/TandemTools", - "content": "Tool for assessing/improving assembly quality in extra-long tandem repeats" + "github/bertrandplez/Turbospectrum2019": { + "id": "github/bertrandplez/Turbospectrum2019", + "title": "github/bertrandplez/Turbospectrum2019", + "url": " https://rseng.github.io/software/repository/github/bertrandplez/Turbospectrum2019", + "content": "synthetic spectrum calculation companion to MARCS" }, - "github/ablab/spades": { - "id": "github/ablab/spades", - "title": "github/ablab/spades", - "url": " https://rseng.github.io/software/repository/github/ablab/spades", - "content": "SPAdes Genome Assembler" + "github/LucaJRossi/NIGO": { + "id": "github/LucaJRossi/NIGO", + "title": "github/LucaJRossi/NIGO", + "url": " https://rseng.github.io/software/repository/github/LucaJRossi/NIGO", + "content": "NIGO: a Numerical Integrator of Galactic Orbits" }, - "github/ablab/nerpa": { - "id": "github/ablab/nerpa", - "title": "github/ablab/nerpa", - "url": " https://rseng.github.io/software/repository/github/ablab/nerpa", + "github/leprojetcastor/castor": { + "id": "github/leprojetcastor/castor", + "title": "github/leprojetcastor/castor", + "url": " https://rseng.github.io/software/repository/github/leprojetcastor/castor", "content": "None" }, - "github/metaOmics/MetaPath": { - "id": "github/metaOmics/MetaPath", - "title": "github/metaOmics/MetaPath", - "url": " https://rseng.github.io/software/repository/github/metaOmics/MetaPath", - "content": "Meta analysis pathway enrichment" + "github/djones1040/PythonPhot": { + "id": "github/djones1040/PythonPhot", + "title": "github/djones1040/PythonPhot", + "url": " https://rseng.github.io/software/repository/github/djones1040/PythonPhot", + "content": "Simple DAOPHOT-type photometry in Python translated from IDL AstroLib photometry algorithms. Please email me with bugs, suggestions, omissions, etc. The code is citable as part of the Astrophysics Source Code Library (http://ascl.net/1501.010)." }, - "github/insightsengineering/rbmi": { - "id": "github/insightsengineering/rbmi", - "title": "github/insightsengineering/rbmi", - "url": " https://rseng.github.io/software/repository/github/insightsengineering/rbmi", - "content": "Reference based multiple imputation R package" + "github/benjaminbolling/RSW": { + "id": "github/benjaminbolling/RSW", + "title": "github/benjaminbolling/RSW", + "url": " https://rseng.github.io/software/repository/github/benjaminbolling/RSW", + "content": "A Computational Approach to Generate Multi-Shift Rotational Workforce Schedules." }, - "github/samhforbes/PupillometryR": { - "id": "github/samhforbes/PupillometryR", - "title": "github/samhforbes/PupillometryR", - "url": " https://rseng.github.io/software/repository/github/samhforbes/PupillometryR", - "content": "An R package for preparing and analysing pupillometry data" + "github/benjaminbolling/DynaGUI": { + "id": "github/benjaminbolling/DynaGUI", + "title": "github/benjaminbolling/DynaGUI", + "url": " https://rseng.github.io/software/repository/github/benjaminbolling/DynaGUI", + "content": "A Dynamic Graphical User Interface package, which gives users a method to construct temporary, permanent and/or a set of GUI:s for users in a simple and fast manner combined with diagnostics tools (with advance 1D and 2D plotting methods)." }, - "github/CHRF-Genomics/Paratype": { - "id": "github/CHRF-Genomics/Paratype", - "title": "github/CHRF-Genomics/Paratype", - "url": " https://rseng.github.io/software/repository/github/CHRF-Genomics/Paratype", - "content": "Assign genotypes to Salmonella Paratyphi A isolates using their whole-genome data." + "github/Shamir-Lab/domino_web": { + "id": "github/Shamir-Lab/domino_web", + "title": "github/Shamir-Lab/domino_web", + "url": " https://rseng.github.io/software/repository/github/Shamir-Lab/domino_web", + "content": "None" }, - "github/ImperialCollegeLondon/champ": { - "id": "github/ImperialCollegeLondon/champ", - "title": "github/ImperialCollegeLondon/champ", - "url": " https://rseng.github.io/software/repository/github/ImperialCollegeLondon/champ", + "github/esquivas/guacho": { + "id": "github/esquivas/guacho", + "title": "github/esquivas/guacho", + "url": " https://rseng.github.io/software/repository/github/esquivas/guacho", + "content": "A 3D uniform mesh parallel HD/MHD code for astrophysics" + }, + "github/wlloyduw/ContainerProfiler": { + "id": "github/wlloyduw/ContainerProfiler", + "title": "github/wlloyduw/ContainerProfiler", + "url": " https://rseng.github.io/software/repository/github/wlloyduw/ContainerProfiler", "content": "None" }, - "github/ImperialCollegeLondon/ICLOCS": { - "id": "github/ImperialCollegeLondon/ICLOCS", - "title": "github/ImperialCollegeLondon/ICLOCS", - "url": " https://rseng.github.io/software/repository/github/ImperialCollegeLondon/ICLOCS", - "content": "Imperial College London Optimal Control Software (ICLOCS)" + "github/esperlman/JetCurry": { + "id": "github/esperlman/JetCurry", + "title": "github/esperlman/JetCurry", + "url": " https://rseng.github.io/software/repository/github/esperlman/JetCurry", + "content": "None" }, - "github/ImperialCollegeLondon/sharpy": { - "id": "github/ImperialCollegeLondon/sharpy", - "title": "github/ImperialCollegeLondon/sharpy", - "url": " https://rseng.github.io/software/repository/github/ImperialCollegeLondon/sharpy", - "content": "Simulation of High Aspect Ratio aeroplanes and wind turbines in Python: a nonlinear aeroelastic code" + "github/AgentM-GEG/residual_feature_extraction": { + "id": "github/AgentM-GEG/residual_feature_extraction", + "title": "github/AgentM-GEG/residual_feature_extraction", + "url": " https://rseng.github.io/software/repository/github/AgentM-GEG/residual_feature_extraction", + "content": "A pipeline that carries out feature extraction of residual substructure within the residual images produced by popular galaxy structural-fitting routines such as GALFIT, GIM2D, etc. This pipeline works on model-subtracted residual images by popular structural fitting routines (e.g., GALFIT, GIM2D, etc) to extract faint low surface brightness features by isolating flux-wise and area-wise significant contiguous pixels regions by rigourous masking routine. This routine accepts the image cubes (original image, model image, residual image) and generates several data products" }, - "github/ImperialCollegeLondon/rcs-pacemakers": { - "id": "github/ImperialCollegeLondon/rcs-pacemakers", - "title": "github/ImperialCollegeLondon/rcs-pacemakers", - "url": " https://rseng.github.io/software/repository/github/ImperialCollegeLondon/rcs-pacemakers", - "content": "Example of GPU-accelerated machine learning on the RCS compute cluster using Jupyter and conda" + "github/DirectDM/directdm-py": { + "id": "github/DirectDM/directdm-py", + "title": "github/DirectDM/directdm-py", + "url": " https://rseng.github.io/software/repository/github/DirectDM/directdm-py", + "content": "Python version of the DirectDM package" }, - "github/ImperialCollegeLondon/UVLM": { - "id": "github/ImperialCollegeLondon/UVLM", - "title": "github/ImperialCollegeLondon/UVLM", - "url": " https://rseng.github.io/software/repository/github/ImperialCollegeLondon/UVLM", - "content": "Unsteady Vortex Lattice Method for Aeroelasticity in C++" + "github/DirectDM/directdm-mma": { + "id": "github/DirectDM/directdm-mma", + "title": "github/DirectDM/directdm-mma", + "url": " https://rseng.github.io/software/repository/github/DirectDM/directdm-mma", + "content": "DirectDM Mathematica package" }, - "github/ImperialCollegeLondon/R2T2": { - "id": "github/ImperialCollegeLondon/R2T2", - "title": "github/ImperialCollegeLondon/R2T2", - "url": " https://rseng.github.io/software/repository/github/ImperialCollegeLondon/R2T2", - "content": "Research References Tracking Tool" + "github/pmeier/pystiche": { + "id": "github/pmeier/pystiche", + "title": "github/pmeier/pystiche", + "url": " https://rseng.github.io/software/repository/github/pmeier/pystiche", + "content": "Framework for Neural Style Transfer (NST) built upon PyTorch" }, - "github/ImperialCollegeLondon/django-drf-filepond": { - "id": "github/ImperialCollegeLondon/django-drf-filepond", - "title": "github/ImperialCollegeLondon/django-drf-filepond", - "url": " https://rseng.github.io/software/repository/github/ImperialCollegeLondon/django-drf-filepond", - "content": "A Django app providing a server implemention for the Filepond file upload library" + "github/WBK-Robotics/pybullet_industrial": { + "id": "github/WBK-Robotics/pybullet_industrial", + "title": "github/WBK-Robotics/pybullet_industrial", + "url": " https://rseng.github.io/software/repository/github/WBK-Robotics/pybullet_industrial", + "content": "A simulation package extending pybullet for industrial robot applications" }, - "github/ImperialCollegeLondon/research-software-directory-data": { - "id": "github/ImperialCollegeLondon/research-software-directory-data", - "title": "github/ImperialCollegeLondon/research-software-directory-data", - "url": " https://rseng.github.io/software/repository/github/ImperialCollegeLondon/research-software-directory-data", - "content": "Imperial College Research Software Directory" + "github/PfizerRD/sit2standpy": { + "id": "github/PfizerRD/sit2standpy", + "title": "github/PfizerRD/sit2standpy", + "url": " https://rseng.github.io/software/repository/github/PfizerRD/sit2standpy", + "content": "Python based module framework for detecting sit-to-stand transitions" }, - "github/ImperialCollegeLondon/hcga": { - "id": "github/ImperialCollegeLondon/hcga", - "title": "github/ImperialCollegeLondon/hcga", - "url": " https://rseng.github.io/software/repository/github/ImperialCollegeLondon/hcga", - "content": "Highly Comparative Graph Analysis - Code for network phenotyping " + "github/PEJpOhno/SMiPoly": { + "id": "github/PEJpOhno/SMiPoly", + "title": "github/PEJpOhno/SMiPoly", + "url": " https://rseng.github.io/software/repository/github/PEJpOhno/SMiPoly", + "content": "rule-based virtual polymer library generator" }, - "github/ImperialCollegeLondon/fractalgenetics": { - "id": "github/ImperialCollegeLondon/fractalgenetics", - "title": "github/ImperialCollegeLondon/fractalgenetics", - "url": " https://rseng.github.io/software/repository/github/ImperialCollegeLondon/fractalgenetics", - "content": "Analysis of the genomic architecture and functional role of myocardial trabeculae" + "github/ggobi/ggobi": { + "id": "github/ggobi/ggobi", + "title": "github/ggobi/ggobi", + "url": " https://rseng.github.io/software/repository/github/ggobi/ggobi", + "content": "High dimensional data vis" }, - "github/ImperialCollegeLondon/sap-voicebox": { - "id": "github/ImperialCollegeLondon/sap-voicebox", - "title": "github/ImperialCollegeLondon/sap-voicebox", - "url": " https://rseng.github.io/software/repository/github/ImperialCollegeLondon/sap-voicebox", - "content": "Speech Processing Toolbox for MATLAB" + "github/spectrapepper/spectrapepper": { + "id": "github/spectrapepper/spectrapepper", + "title": "github/spectrapepper/spectrapepper", + "url": " https://rseng.github.io/software/repository/github/spectrapepper/spectrapepper", + "content": "A Python package for advanced processing and combinatorial analysis of spectroscopy data." }, - "github/ImperialCollegeLondon/rcs_cluster_scripts": { - "id": "github/ImperialCollegeLondon/rcs_cluster_scripts", - "title": "github/ImperialCollegeLondon/rcs_cluster_scripts", - "url": " https://rseng.github.io/software/repository/github/ImperialCollegeLondon/rcs_cluster_scripts", - "content": "A collection of handy scripts for use with the Imperial College Research Computing Service cluster" + "github/londumas/redvsblue": { + "id": "github/londumas/redvsblue", + "title": "github/londumas/redvsblue", + "url": " https://rseng.github.io/software/repository/github/londumas/redvsblue", + "content": "Quasar and emission line precise redshift fitting from prior" }, - "github/ImperialCollegeLondon/pytest_template_application": { - "id": "github/ImperialCollegeLondon/pytest_template_application", - "title": "github/ImperialCollegeLondon/pytest_template_application", - "url": " https://rseng.github.io/software/repository/github/ImperialCollegeLondon/pytest_template_application", - "content": "Python application template with automated QA and Docker image publishing" + "github/amrex-astro/MAESTRO": { + "id": "github/amrex-astro/MAESTRO", + "title": "github/amrex-astro/MAESTRO", + "url": " https://rseng.github.io/software/repository/github/amrex-astro/MAESTRO", + "content": "A low Mach number stellar hydrodynamics code" }, - "github/ImperialCollegeLondon/WInc3D": { - "id": "github/ImperialCollegeLondon/WInc3D", - "title": "github/ImperialCollegeLondon/WInc3D", - "url": " https://rseng.github.io/software/repository/github/ImperialCollegeLondon/WInc3D", - "content": "Wind Farm Simulator" + "github/amrex-astro/Castro": { + "id": "github/amrex-astro/Castro", + "title": "github/amrex-astro/Castro", + "url": " https://rseng.github.io/software/repository/github/amrex-astro/Castro", + "content": "An adaptive mesh, astrophysical compressible (radiation-, magneto-) hydrodynamics simulation code for massively parallel CPU and GPU architectures." }, - "github/ImperialCollegeLondon/magda_tools": { - "id": "github/ImperialCollegeLondon/magda_tools", - "title": "github/ImperialCollegeLondon/magda_tools", - "url": " https://rseng.github.io/software/repository/github/ImperialCollegeLondon/magda_tools", - "content": "A collection of tools for working with MAGDA data files" + "github/amrex-astro/Nyx": { + "id": "github/amrex-astro/Nyx", + "title": "github/amrex-astro/Nyx", + "url": " https://rseng.github.io/software/repository/github/amrex-astro/Nyx", + "content": "An adaptive mesh, N-body hydro cosmological simulation code" }, - "github/ImperialCollegeLondon/epidemia": { - "id": "github/ImperialCollegeLondon/epidemia", - "title": "github/ImperialCollegeLondon/epidemia", - "url": " https://rseng.github.io/software/repository/github/ImperialCollegeLondon/epidemia", - "content": "epidemia package" + "github/QibangLiu/PDLSM-FEM_mpi": { + "id": "github/QibangLiu/PDLSM-FEM_mpi", + "title": "github/QibangLiu/PDLSM-FEM_mpi", + "url": " https://rseng.github.io/software/repository/github/QibangLiu/PDLSM-FEM_mpi", + "content": "PDLSM-FEM solver is a parallel implementation of (adaptively) coupled peridynamics least squares minimization and finite element method (PDLSM-FEM) in 2D and 3D using MPI parallelism. This cross-platform solver is written in a C++ language and includes implicit static, explicit dynamic, and implicit dynamic solvers for structure analysis under displacement or traction loading." }, - "github/ImperialCollegeLondon/safedata": { - "id": "github/ImperialCollegeLondon/safedata", - "title": "github/ImperialCollegeLondon/safedata", - "url": " https://rseng.github.io/software/repository/github/ImperialCollegeLondon/safedata", - "content": "An R package for discovering and using data from the SAFE Project" + "github/yuhuan-wu/mobilesal": { + "id": "github/yuhuan-wu/mobilesal", + "title": "github/yuhuan-wu/mobilesal", + "url": " https://rseng.github.io/software/repository/github/yuhuan-wu/mobilesal", + "content": "[IEEE TPAMI21] MobileSal: Extremely Efficient RGB-D Salient Object Detection [PyTorch & Jittor]" + }, + "github/lehtiolab/msstitch": { + "id": "github/lehtiolab/msstitch", + "title": "github/lehtiolab/msstitch", + "url": " https://rseng.github.io/software/repository/github/lehtiolab/msstitch", + "content": "MS proteomics post-processing utilities" + }, + "github/CadenArmstrong/simuTrans": { + "id": "github/CadenArmstrong/simuTrans", + "title": "github/CadenArmstrong/simuTrans", + "url": " https://rseng.github.io/software/repository/github/CadenArmstrong/simuTrans", + "content": "Exoplanet transit simulator." }, - "github/ImperialCollegeLondon/adam": { - "id": "github/ImperialCollegeLondon/adam", - "title": "github/ImperialCollegeLondon/adam", - "url": " https://rseng.github.io/software/repository/github/ImperialCollegeLondon/adam", - "content": "None" + "github/CEMeNT-PSAAP/MCDC": { + "id": "github/CEMeNT-PSAAP/MCDC", + "title": "github/CEMeNT-PSAAP/MCDC", + "url": " https://rseng.github.io/software/repository/github/CEMeNT-PSAAP/MCDC", + "content": "MC/DC: Monte Carlo Dynamic Code" }, - "github/ImperialCollegeLondon/covid19model": { - "id": "github/ImperialCollegeLondon/covid19model", - "title": "github/ImperialCollegeLondon/covid19model", - "url": " https://rseng.github.io/software/repository/github/ImperialCollegeLondon/covid19model", - "content": "Code for modelling estimated deaths and cases for COVID19. 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We recommend using Apache 2.2 or later, PHP 5.3 or later and MySQL 5.5 or later." + "github/smirarab/pasta": { + "id": "github/smirarab/pasta", + "title": "github/smirarab/pasta", + "url": " https://rseng.github.io/software/repository/github/smirarab/pasta", + "content": "PASTA (Practical Alignment using SATe and Transitivity) " }, - "github/mfruzan/HaploMaker": { - "id": "github/mfruzan/HaploMaker", - "title": "github/mfruzan/HaploMaker", - "url": " https://rseng.github.io/software/repository/github/mfruzan/HaploMaker", - "content": "None" + "github/smirarab/sepp": { + "id": "github/smirarab/sepp", + "title": "github/smirarab/sepp", + "url": " https://rseng.github.io/software/repository/github/smirarab/sepp", + "content": "Ensemble of HMM methods (SEPP, TIPP, UPP)" }, - "github/octapps/octapps": { - "id": "github/octapps/octapps", - "title": "github/octapps/octapps", - "url": " https://rseng.github.io/software/repository/github/octapps/octapps", - "content": "Library of Octave functions for continuous gravitational-wave data analysis" + "github/MatthijsHak/MetalDock": { + "id": "github/MatthijsHak/MetalDock", + "title": "github/MatthijsHak/MetalDock", + "url": " https://rseng.github.io/software/repository/github/MatthijsHak/MetalDock", + "content": "Dock organometallic compounds to proteins/DNA/biomolecules" }, - 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"title": "github/spacetelescope/hst_cosmic_rays", - "url": " https://rseng.github.io/software/repository/github/spacetelescope/hst_cosmic_rays", + "github/nlesc-sherlock/Rig": { + "id": "github/nlesc-sherlock/Rig", + "title": "github/nlesc-sherlock/Rig", + "url": " https://rseng.github.io/software/repository/github/nlesc-sherlock/Rig", "content": "None" }, - "github/ruizengalways/FOD-Net": { - "id": "github/ruizengalways/FOD-Net", - "title": "github/ruizengalways/FOD-Net", - "url": " https://rseng.github.io/software/repository/github/ruizengalways/FOD-Net", - "content": "FOD-Net: A Deep Learning Method for Fiber Orientation Distribution Angular Super Resolution" - }, - "github/mtlam/PyPulse": { - "id": "github/mtlam/PyPulse", - "title": "github/mtlam/PyPulse", - "url": " https://rseng.github.io/software/repository/github/mtlam/PyPulse", - "content": "Python package for handling and analyzing PSRFITS files" + "github/sonny-harman/snowball": { + "id": "github/sonny-harman/snowball", + "title": "github/sonny-harman/snowball", + "url": " https://rseng.github.io/software/repository/github/sonny-harman/snowball", + "content": "Generalizable atmospheric mass loss calculator" }, - 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Batteries included :)" }, - "github/SegataLab/lefse": { - "id": "github/SegataLab/lefse", - "title": "github/SegataLab/lefse", - "url": " https://rseng.github.io/software/repository/github/SegataLab/lefse", - "content": "determine features of organisms, clades, taxonomic units, genes" + "github/hansenjohnson/WhaleMap": { + "id": "github/hansenjohnson/WhaleMap", + "title": "github/hansenjohnson/WhaleMap", + "url": " https://rseng.github.io/software/repository/github/hansenjohnson/WhaleMap", + "content": "Collate and visualize whale survey results in the NW Atlantic" }, - "github/Pranab-JD/LeXInt": { - "id": "github/Pranab-JD/LeXInt", - "title": "github/Pranab-JD/LeXInt", - "url": " https://rseng.github.io/software/repository/github/Pranab-JD/LeXInt", - "content": "Leja Exponential Integrators" + "github/jbytecode/LinRegOutliers": { + "id": "github/jbytecode/LinRegOutliers", + "title": "github/jbytecode/LinRegOutliers", + "url": " https://rseng.github.io/software/repository/github/jbytecode/LinRegOutliers", + "content": "Direct and robust methods for outlier detection in linear regression" }, - 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"content": "LD Score Regression (LDSC)" - }, - "github/GabrielaCR/AGNfitter": { - "id": "github/GabrielaCR/AGNfitter", - "title": "github/GabrielaCR/AGNfitter", - "url": " https://rseng.github.io/software/repository/github/GabrielaCR/AGNfitter", - "content": "SED-fitting code for AGN and galaxies from a MCMC approach" - }, - "github/pilon/wiki": { - "id": "github/pilon/wiki", - "title": "github/pilon/wiki", - "url": " https://rseng.github.io/software/repository/github/pilon/wiki", - "content": "Pilon is a software tool which can be used to automatically improve draft assemblies and find variation among strains, including large event detection." - }, - "github/ryanhausen/fitsmap": { - "id": "github/ryanhausen/fitsmap", - "title": "github/ryanhausen/fitsmap", - "url": " https://rseng.github.io/software/repository/github/ryanhausen/fitsmap", - "content": "FitsMap: A Simple, Lightweight Tool For Displaying Interactive Astronomical Image and Catalog Data" - }, - "github/askap-craco/CELEBI": { - "id": "github/askap-craco/CELEBI", - "title": "github/askap-craco/CELEBI", - "url": " https://rseng.github.io/software/repository/github/askap-craco/CELEBI", - "content": "The CRAFT Effortless Localisation and Enhanced Burst Inspection Pipeline" - }, - "github/vprusso/toqito": { - "id": "github/vprusso/toqito", - "title": "github/vprusso/toqito", - "url": " https://rseng.github.io/software/repository/github/vprusso/toqito", - "content": "|toqito> (Theory of Quantum Information Toolkit) in Python :snake:" + "github/GabrieleParimbelli/COLIBRI": { + "id": "github/GabrieleParimbelli/COLIBRI", + "title": "github/GabrieleParimbelli/COLIBRI", + "url": " https://rseng.github.io/software/repository/github/GabrieleParimbelli/COLIBRI", + "content": "Cosmology libraries in Python" }, - "github/lyf222/alpconv": { - "id": "github/lyf222/alpconv", - "title": "github/lyf222/alpconv", - "url": " https://rseng.github.io/software/repository/github/lyf222/alpconv", - "content": "calculating alp-photon conversion" + "github/etempel/Bisous": { + "id": "github/etempel/Bisous", + "title": "github/etempel/Bisous", + "url": " https://rseng.github.io/software/repository/github/etempel/Bisous", + "content": "None" }, - 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"github/pysam-developers/pysam": { - "id": "github/pysam-developers/pysam", - "title": "github/pysam-developers/pysam", - "url": " https://rseng.github.io/software/repository/github/pysam-developers/pysam", - "content": "Pysam is a Python module for reading and manipulating SAM/BAM/VCF/BCF files. It's a lightweight wrapper of the htslib C-API, the same one that powers samtools, bcftools, and tabix." + "github/Trovemaster/exocross": { + "id": "github/Trovemaster/exocross", + "title": "github/Trovemaster/exocross", + "url": " https://rseng.github.io/software/repository/github/Trovemaster/exocross", + "content": "Fortran 2003 code to generate molecular spectra, partition functions, lifetimes, cooling functions etc using ExoMol line lists" }, - "github/nnssa/gallumi_public": { - "id": "github/nnssa/gallumi_public", - "title": "github/nnssa/gallumi_public", - "url": " https://rseng.github.io/software/repository/github/nnssa/gallumi_public", - "content": "A Galaxy Luminosity Function Pipeline for Cosmology and Astrophysics" + "github/Trovemaster/TROVE": { + "id": "github/Trovemaster/TROVE", + "title": "github/Trovemaster/TROVE", + "url": " https://rseng.github.io/software/repository/github/Trovemaster/TROVE", + "content": "Theoretical ROVibrational Energies: A variational program for accurate nuclear motion calculations" }, - "github/BioinfoUNIBA/REDItools2": { - "id": "github/BioinfoUNIBA/REDItools2", - "title": "github/BioinfoUNIBA/REDItools2", - "url": " https://rseng.github.io/software/repository/github/BioinfoUNIBA/REDItools2", - "content": "None" + "github/PolymerGuy/recolo": { + "id": "github/PolymerGuy/recolo", + "title": "github/PolymerGuy/recolo", + "url": " https://rseng.github.io/software/repository/github/PolymerGuy/recolo", + "content": "Load reconstuction using virtual fields" }, - "github/msyazwanfaid/hilalpy": { - "id": "github/msyazwanfaid/hilalpy", - "title": "github/msyazwanfaid/hilalpy", - "url": " https://rseng.github.io/software/repository/github/msyazwanfaid/hilalpy", - "content": "A package to analyse the data of Moon sighting for lunar crescent visibility criterion" + "github/RitchieLab/hudson": { + "id": "github/RitchieLab/hudson", + "title": "github/RitchieLab/hudson", + "url": " https://rseng.github.io/software/repository/github/RitchieLab/hudson", + "content": "An R package for creating mirrored Manhattan plots" }, - "github/msyazwanfaid/Authentication-Algorithm-for-New-Moon-Visibility-Report": { - "id": "github/msyazwanfaid/Authentication-Algorithm-for-New-Moon-Visibility-Report", - "title": "github/msyazwanfaid/Authentication-Algorithm-for-New-Moon-Visibility-Report", - "url": " https://rseng.github.io/software/repository/github/msyazwanfaid/Authentication-Algorithm-for-New-Moon-Visibility-Report", - "content": "Authentication Algorithm for New Moon Visibility Report" + "github/imperialchem/mrd-demo": { + "id": "github/imperialchem/mrd-demo", + "title": "github/imperialchem/mrd-demo", + "url": " https://rseng.github.io/software/repository/github/imperialchem/mrd-demo", + "content": "Demonstration of classical molecular reaction dynamics for a tri-atomic system" }, - "github/reneheller/pile-up": { - "id": "github/reneheller/pile-up", - "title": "github/reneheller/pile-up", - "url": " https://rseng.github.io/software/repository/github/reneheller/pile-up", - "content": "A gnuplot script for Monte Carlo simulations of disk and stellar tidal torques acting on hot Jupiters" + "github/bioAI-Oslo/Spikeometric": { + "id": "github/bioAI-Oslo/Spikeometric", + "title": "github/bioAI-Oslo/Spikeometric", + "url": " https://rseng.github.io/software/repository/github/bioAI-Oslo/Spikeometric", + "content": "Spiking Neural Network Simulator based on Generalized Linear Models" }, - "github/icb-dcm/pyabc": { - "id": "github/icb-dcm/pyabc", - "title": "github/icb-dcm/pyabc", - "url": " https://rseng.github.io/software/repository/github/icb-dcm/pyabc", - "content": "distributed, likelihood-free inference" + "github/aibhleog/baryon-sweep": { + "id": "github/aibhleog/baryon-sweep", + "title": "github/aibhleog/baryon-sweep", + "url": " https://rseng.github.io/software/repository/github/aibhleog/baryon-sweep", + "content": "a custom outlier rejection algorithm for JWST/NIRSpec IFS data, described in Hutchison et al. (submitted to PASP)" }, - "github/xiaotiand/FunFor": { - "id": "github/xiaotiand/FunFor", - "title": "github/xiaotiand/FunFor", - "url": " https://rseng.github.io/software/repository/github/xiaotiand/FunFor", - "content": "FunFor R package" + "github/li-yangyang/lotus": { + "id": "github/li-yangyang/lotus", + "title": "github/li-yangyang/lotus", + "url": " https://rseng.github.io/software/repository/github/li-yangyang/lotus", + "content": "Fast tool for 1D Non-LTE stellar parameter determination via Equivalent Width method" }, - "github/Parsl/parsl": { - "id": "github/Parsl/parsl", - "title": "github/Parsl/parsl", - "url": " https://rseng.github.io/software/repository/github/Parsl/parsl", - "content": "Parsl - Parallel Scripting Library" + "github/Climdyn/qgs": { + "id": "github/Climdyn/qgs", + "title": "github/Climdyn/qgs", + "url": " https://rseng.github.io/software/repository/github/Climdyn/qgs", + "content": "A 2-layer quasi-geostrophic atmospheric model in Python. Can be coupled to a simple land or shallow-water ocean component." }, - "github/galaxyproject/ansible-tiaas2": { - "id": "github/galaxyproject/ansible-tiaas2", - "title": "github/galaxyproject/ansible-tiaas2", - "url": " https://rseng.github.io/software/repository/github/galaxyproject/ansible-tiaas2", - "content": "Ansible role for deploying TIaaS2" + "github/OwenWard/ppdiag": { + "id": "github/OwenWard/ppdiag", + "title": "github/OwenWard/ppdiag", + "url": " https://rseng.github.io/software/repository/github/OwenWard/ppdiag", + "content": "None" }, - "github/galaxyproject/galaxy-lib": { - "id": "github/galaxyproject/galaxy-lib", - "title": "github/galaxyproject/galaxy-lib", - "url": " https://rseng.github.io/software/repository/github/galaxyproject/galaxy-lib", - "content": "Subset of Galaxy (http://galaxyproject.org/) core code designed to be used as a library." + "github/kushaltirumala/WaldoInSky": { + "id": "github/kushaltirumala/WaldoInSky", + "title": "github/kushaltirumala/WaldoInSky", + "url": " https://rseng.github.io/software/repository/github/kushaltirumala/WaldoInSky", + "content": "Code Repository for `Where is Waldo (and his friends)? A comparison of anomaly detection algorithms for time-domain astronomy`" }, - "github/davidgardenier/frbcat": { - "id": "github/davidgardenier/frbcat", - "title": "github/davidgardenier/frbcat", - "url": " https://rseng.github.io/software/repository/github/davidgardenier/frbcat", - "content": "Query Fast Radio Burst catalogues" + "github/cmayer/BaitFisher-package": { + "id": "github/cmayer/BaitFisher-package", + "title": "github/cmayer/BaitFisher-package", + "url": " https://rseng.github.io/software/repository/github/cmayer/BaitFisher-package", + "content": "The BaitFisher-package is a software package for designing hybrid enrichment probes. For more information see:" }, - "github/davidgardenier/frbpoppy": { - "id": "github/davidgardenier/frbpoppy", - "title": "github/davidgardenier/frbpoppy", - "url": " https://rseng.github.io/software/repository/github/davidgardenier/frbpoppy", - "content": "Fast Radio Burst Population Synthesis in Python" + "github/MNiwano/Eclaire": { + "id": "github/MNiwano/Eclaire", + "title": "github/MNiwano/Eclaire", + "url": " https://rseng.github.io/software/repository/github/MNiwano/Eclaire", + "content": "Python package using GPU via CUDA for astronomical image reduction" }, - "github/linDing-groups/Deep-4mCW2V": { - "id": "github/linDing-groups/Deep-4mCW2V", - "title": "github/linDing-groups/Deep-4mCW2V", - "url": " https://rseng.github.io/software/repository/github/linDing-groups/Deep-4mCW2V", - "content": "A sequence-based deep learning approach to predict N4-methylcytosine sites in Escherichia coli " + "github/agreenbaum/ImPlaneIA": { + "id": "github/agreenbaum/ImPlaneIA", + "title": "github/agreenbaum/ImPlaneIA", + "url": " https://rseng.github.io/software/repository/github/agreenbaum/ImPlaneIA", + "content": "Tools for fitting (image plane fringes), calibrating, and analyzing NRM data across multiple instruments and modes" }, - "github/wiki/Install-macs2": { - "id": "github/wiki/Install-macs2", - "title": "github/wiki/Install-macs2", - "url": " https://rseng.github.io/software/repository/github/wiki/Install-macs2", - "content": "(Model Based Analysis of ChIP-Seq data) a novel algorithm for identifying transcript factor binding sites." + "github/agreenbaum/gsgs": { + "id": "github/agreenbaum/gsgs", + "title": "github/agreenbaum/gsgs", + "url": " https://rseng.github.io/software/repository/github/agreenbaum/gsgs", + "content": "gsgs does phase retrieval on images given an estimate of the pupil phase, like one from a non-redundant mask " }, - "github/EliabCanul/nauyaca": { - "id": "github/EliabCanul/nauyaca", - "title": "github/EliabCanul/nauyaca", - "url": " https://rseng.github.io/software/repository/github/EliabCanul/nauyaca", - "content": "Nauyaca is a tool to determine planetary masses and orbital elements through the fitting of observed mid-transit times, from a N-body approach." + "github/beckrob/Photo-z-SQL": { + "id": "github/beckrob/Photo-z-SQL", + "title": "github/beckrob/Photo-z-SQL", + "url": " https://rseng.github.io/software/repository/github/beckrob/Photo-z-SQL", + "content": "C# template-based photometric redshift estimation framework" }, - "github/christophuv/PeakBot_example": { - "id": "github/christophuv/PeakBot_example", - "title": "github/christophuv/PeakBot_example", - "url": " https://rseng.github.io/software/repository/github/christophuv/PeakBot_example", - "content": "Example scripts on how to use PeakBot" + "github/qutip/qutip": { + "id": "github/qutip/qutip", + "title": "github/qutip/qutip", + "url": " https://rseng.github.io/software/repository/github/qutip/qutip", + "content": "QuTiP: Quantum Toolbox in Python" }, - "github/nombac/optab": { - "id": "github/nombac/optab", - "title": "github/nombac/optab", - "url": " https://rseng.github.io/software/repository/github/nombac/optab", - "content": "Public Fortran90 code package for generating ideal-gas opacity tables" + "github/ofionnad/radiowinds": { + "id": "github/ofionnad/radiowinds", + "title": "github/ofionnad/radiowinds", + "url": " https://rseng.github.io/software/repository/github/ofionnad/radiowinds", + "content": "Calculate the thermal bremsstrahlung emission from stellar winds" }, - "github/openmsi/openmsistream": { - "id": "github/openmsi/openmsistream", - "title": "github/openmsi/openmsistream", - "url": " https://rseng.github.io/software/repository/github/openmsi/openmsistream", - "content": "Materials data streaming applications, written in Python using Apache Kafka, with a focus on deployment in laboratory environments" + "github/single-cell-genetics/cellsnp-lite": { + "id": "github/single-cell-genetics/cellsnp-lite", + "title": "github/single-cell-genetics/cellsnp-lite", + "url": " https://rseng.github.io/software/repository/github/single-cell-genetics/cellsnp-lite", + "content": "Efficient genotyping bi-allelic SNPs on single cells" }, - "github/pepamengual/UEP": { - "id": "github/pepamengual/UEP", - "title": "github/pepamengual/UEP", - "url": " https://rseng.github.io/software/repository/github/pepamengual/UEP", - "content": "None" + "github/soylentdeen/CounterPoint": { + "id": "github/soylentdeen/CounterPoint", + "title": "github/soylentdeen/CounterPoint", + "url": " https://rseng.github.io/software/repository/github/soylentdeen/CounterPoint", + "content": "Python Companion to MoogStokes" }, - "github/qmarcou/IGoR": { - "id": "github/qmarcou/IGoR", - "title": "github/qmarcou/IGoR", - "url": " https://rseng.github.io/software/repository/github/qmarcou/IGoR", - "content": "IGoR is a C++ software designed to infer V(D)J recombination related processes from sequencing data. Find full documentation at:" + "github/soylentdeen/MoogStokes": { + "id": "github/soylentdeen/MoogStokes", + "title": "github/soylentdeen/MoogStokes", + "url": " https://rseng.github.io/software/repository/github/soylentdeen/MoogStokes", + "content": "Artisanal Zeeman Radiative Transfer" }, - "github/ArgoCanada/argodata": { - "id": "github/ArgoCanada/argodata", - "title": "github/ArgoCanada/argodata", - "url": " https://rseng.github.io/software/repository/github/ArgoCanada/argodata", - "content": "Download Argo Ocean Float Data" + "github/wokast/RePrimAnd": { + "id": "github/wokast/RePrimAnd", + "title": "github/wokast/RePrimAnd", + "url": " https://rseng.github.io/software/repository/github/wokast/RePrimAnd", + "content": "Support library providing EOS and primitive recovery framework for general relativistic ideal MHD" }, - "github/WBK-Robotics/pybullet_industrial": { - "id": "github/WBK-Robotics/pybullet_industrial", - "title": "github/WBK-Robotics/pybullet_industrial", - "url": " https://rseng.github.io/software/repository/github/WBK-Robotics/pybullet_industrial", - "content": "A simulation package extending pybullet for industrial robot applications" + "github/wokast/PyCactus": { + "id": "github/wokast/PyCactus", + "title": "github/wokast/PyCactus", + "url": " https://rseng.github.io/software/repository/github/wokast/PyCactus", + "content": "Python packages for post-processing Cactus computational toolkit simulation data" }, - "github/GRTLCollaboration/GRChombo": { - "id": "github/GRTLCollaboration/GRChombo", - "title": "github/GRTLCollaboration/GRChombo", - "url": " https://rseng.github.io/software/repository/github/GRTLCollaboration/GRChombo", - "content": "An AMR based open-source code for numerical relativity simulations." + "github/johnveitch/cpnest": { + "id": "github/johnveitch/cpnest", + "title": "github/johnveitch/cpnest", + "url": " https://rseng.github.io/software/repository/github/johnveitch/cpnest", + "content": "Parallel nested sampling" }, - "github/GRTLCollaboration/GRFolres": { - "id": "github/GRTLCollaboration/GRFolres", - "title": "github/GRTLCollaboration/GRFolres", - "url": " https://rseng.github.io/software/repository/github/GRTLCollaboration/GRFolres", - "content": "Extension to GRChombo for Modified Gravity simulations" + "github/biosimulations/Biosimulations": { + "id": "github/biosimulations/Biosimulations", + "title": "github/biosimulations/Biosimulations", + "url": " https://rseng.github.io/software/repository/github/biosimulations/Biosimulations", + "content": "Platform for sharing and reusing biomodeling studies including models, simulations, and visualizations of their results" }, - "github/tsfloss/DensityFieldTools": { - "id": "github/tsfloss/DensityFieldTools", - "title": "github/tsfloss/DensityFieldTools", - "url": " https://rseng.github.io/software/repository/github/tsfloss/DensityFieldTools", - "content": "Tools for manipulating density fields and measuring power spectra and bispectra" + "github/puregome/notebooks": { + "id": "github/puregome/notebooks", + "title": "github/puregome/notebooks", + "url": " https://rseng.github.io/software/repository/github/puregome/notebooks", + "content": "Notebooks of the PuReGoMe Project of the Netherlands eScience Center and Utrecht University." }, - 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"github/amerand/SPIPS": { - "id": "github/amerand/SPIPS", - "title": "github/amerand/SPIPS", - "url": " https://rseng.github.io/software/repository/github/amerand/SPIPS", - "content": "Spectro-Photo-Interferometry of Pulsating Stars" + "github/benstahl92/deepSIP": { + "id": "github/benstahl92/deepSIP", + "title": "github/benstahl92/deepSIP", + "url": " https://rseng.github.io/software/repository/github/benstahl92/deepSIP", + "content": "Deep Learning of Supernova Ia Parameters" }, - "github/jradcliffe5/multi_self_cal": { - "id": "github/jradcliffe5/multi_self_cal", - "title": "github/jradcliffe5/multi_self_cal", - "url": " https://rseng.github.io/software/repository/github/jradcliffe5/multi_self_cal", - "content": "Multi-Source Self-Calibration is a Parseltongue (Kettenis et al. 2012) script which provides an extra calibration for VLBI data sets that image multiple target source within one observation. More information is in the README & paper Radcliffe et. al 2016. If you use this script please reference Radcliffe et al. 2016 which is the paper that accompanies this release." + "github/hillerlab/GenomeAlignmentTools": { + "id": "github/hillerlab/GenomeAlignmentTools", + "title": "github/hillerlab/GenomeAlignmentTools", + "url": " https://rseng.github.io/software/repository/github/hillerlab/GenomeAlignmentTools", + "content": "Tools for improving the sensitivity and specificity of genome alignments" }, - "github/APGG-Lab/APGG": { - "id": "github/APGG-Lab/APGG", - "title": "github/APGG-Lab/APGG", - "url": " https://rseng.github.io/software/repository/github/APGG-Lab/APGG", - "content": "A Modular Toolkit for Public Goods Game Computation" + "github/mildpiggy/DEP2": { + "id": "github/mildpiggy/DEP2", + "title": "github/mildpiggy/DEP2", + "url": " https://rseng.github.io/software/repository/github/mildpiggy/DEP2", + "content": "An r package for proteomics data Analysis, developed from DEP." }, - "github/wilsonrljr/sysidentpy": { - "id": "github/wilsonrljr/sysidentpy", - "title": "github/wilsonrljr/sysidentpy", - "url": " https://rseng.github.io/software/repository/github/wilsonrljr/sysidentpy", - "content": "A Python package for System Identification using NARMAX models" + "github/bxia888/CEFCIG": { + "id": "github/bxia888/CEFCIG", + "title": "github/bxia888/CEFCIG", + "url": " https://rseng.github.io/software/repository/github/bxia888/CEFCIG", + "content": "CEFCIG (Computational Epigenetic Framework for Cell Identity Gene Discovery)" }, - "github/SWIFTSIM/emulator": { - "id": "github/SWIFTSIM/emulator", - "title": "github/SWIFTSIM/emulator", - "url": " https://rseng.github.io/software/repository/github/SWIFTSIM/emulator", - "content": "The SWIFT simulation cosmological emulator (swift-emulator)" + "github/williamjameshandley/fgivenx": { + "id": "github/williamjameshandley/fgivenx", + "title": "github/williamjameshandley/fgivenx", + "url": " https://rseng.github.io/software/repository/github/williamjameshandley/fgivenx", + "content": "Functional Posterior Plotter" }, - 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"github/naonori/hitomi": { - "id": "github/naonori/hitomi", - "title": "github/naonori/hitomi", - "url": " https://rseng.github.io/software/repository/github/naonori/hitomi", - "content": "Public repository for the Hitomi Code" + "github/mkargo/pipeline": { + "id": "github/mkargo/pipeline", + "title": "github/mkargo/pipeline", + "url": " https://rseng.github.io/software/repository/github/mkargo/pipeline", + "content": "Data reduction pipeline for e-MERLIN" }, - "github/xiaochuanle/MECAT2": { - "id": "github/xiaochuanle/MECAT2", - "title": "github/xiaochuanle/MECAT2", - "url": " https://rseng.github.io/software/repository/github/xiaochuanle/MECAT2", - "content": "ultra-fast and accurate de novo assembly tools for SMRT reads" + "github/MaayanLab/signature-commons-ui": { + "id": "github/MaayanLab/signature-commons-ui", + "title": "github/MaayanLab/signature-commons-ui", + "url": " https://rseng.github.io/software/repository/github/MaayanLab/signature-commons-ui", + "content": "A front-end UI for demoing API integration" }, - "github/eggplantbren/RJObject": { - "id": "github/eggplantbren/RJObject", - "title": "github/eggplantbren/RJObject", - "url": " https://rseng.github.io/software/repository/github/eggplantbren/RJObject", - "content": "General code for birth/death stuff within DNest3" + "github/HERA-Team/aipy": { + "id": "github/HERA-Team/aipy", + "title": "github/HERA-Team/aipy", + "url": " https://rseng.github.io/software/repository/github/HERA-Team/aipy", + "content": "Astronomical Interferometry in PYthon (AIPY)" }, - "github/eggplantbren/Exoplanet": { - "id": "github/eggplantbren/Exoplanet", - "title": "github/eggplantbren/Exoplanet", - "url": " https://rseng.github.io/software/repository/github/eggplantbren/Exoplanet", - "content": "Exoplanet stuff with RJObject and lookup tables" + "github/HERA-Team/matvis": { + "id": "github/HERA-Team/matvis", + "title": "github/HERA-Team/matvis", + "url": " https://rseng.github.io/software/repository/github/HERA-Team/matvis", + "content": "Fast matrix-based visibility simulator" }, - "github/eggplantbren/DNest3": { - "id": "github/eggplantbren/DNest3", - "title": "github/eggplantbren/DNest3", - "url": " https://rseng.github.io/software/repository/github/eggplantbren/DNest3", - "content": "Diffusive Nested Sampling" + "github/HERA-Team/hera_opm": { + "id": "github/HERA-Team/hera_opm", + "title": "github/HERA-Team/hera_opm", + "url": " https://rseng.github.io/software/repository/github/HERA-Team/hera_opm", + "content": "Online processing of HERA data" }, - "github/eggplantbren/RMHB": { - "id": "github/eggplantbren/RMHB", - "title": "github/eggplantbren/RMHB", - "url": " https://rseng.github.io/software/repository/github/eggplantbren/RMHB", - "content": "Source code for 'hierarchical reverberation mapping'" + "github/hjens/lasso_spectra": { + "id": "github/hjens/lasso_spectra", + "title": "github/hjens/lasso_spectra", + "url": " https://rseng.github.io/software/repository/github/hjens/lasso_spectra", + "content": "Functions for predicting properties from galaxy spectra, using Lasso regression" }, - "github/eggplantbren/DNest4": { - "id": "github/eggplantbren/DNest4", - "title": "github/eggplantbren/DNest4", - "url": " https://rseng.github.io/software/repository/github/eggplantbren/DNest4", - "content": "Diffusive Nested Sampling" + "github/rbturnbull/ausdex": { + "id": "github/rbturnbull/ausdex", + "title": "github/rbturnbull/ausdex", + "url": " https://rseng.github.io/software/repository/github/rbturnbull/ausdex", + "content": "A Python package for adjusting Australian dollars for inflation" }, - "github/AstroUGent/shadowfax": { - "id": "github/AstroUGent/shadowfax", - "title": "github/AstroUGent/shadowfax", - "url": " https://rseng.github.io/software/repository/github/AstroUGent/shadowfax", - "content": "A public moving mesh hydrodynamical integration code, including gravity and a collisionless component." + "github/broadinstitute/picard": { + "id": "github/broadinstitute/picard", + "title": "github/broadinstitute/picard", + "url": " https://rseng.github.io/software/repository/github/broadinstitute/picard", + "content": "A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF." }, - "github/TriPed-Robot/TriP": { - "id": "github/TriPed-Robot/TriP", - "title": "github/TriPed-Robot/TriP", - "url": " https://rseng.github.io/software/repository/github/TriPed-Robot/TriP", - "content": "Python package for inverse kinematic calculations of hybrid serial parallel robots" + "github/broadinstitute/wot": { + "id": "github/broadinstitute/wot", + "title": "github/broadinstitute/wot", + "url": " https://rseng.github.io/software/repository/github/broadinstitute/wot", + "content": "A software package for analyzing snapshots of developmental processes" }, - "github/YosefLab/scvi-tools": { - "id": "github/YosefLab/scvi-tools", - "title": "github/YosefLab/scvi-tools", - "url": " https://rseng.github.io/software/repository/github/YosefLab/scvi-tools", - "content": "Deep probabilistic analysis of single-cell omics data" + "github/broadinstitute/Drop-seq": { + "id": "github/broadinstitute/Drop-seq", + "title": "github/broadinstitute/Drop-seq", + "url": " https://rseng.github.io/software/repository/github/broadinstitute/Drop-seq", + "content": "Java tools for analyzing Drop-seq data" }, - "github/dsavransky/EXOSIMS": { - "id": "github/dsavransky/EXOSIMS", - "title": "github/dsavransky/EXOSIMS", - "url": " https://rseng.github.io/software/repository/github/dsavransky/EXOSIMS", - "content": "Simulator for exoplanet direct imaging space missions" + "github/broadinstitute/cromwell": { + "id": "github/broadinstitute/cromwell", + "title": "github/broadinstitute/cromwell", + "url": " https://rseng.github.io/software/repository/github/broadinstitute/cromwell", + "content": "Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments" }, - "github/gwpy/gwpy": { - "id": "github/gwpy/gwpy", - "title": "github/gwpy/gwpy", - "url": " https://rseng.github.io/software/repository/github/gwpy/gwpy", - "content": "Package for analysing and characterising gravitational wave data in python" + "github/broadinstitute/CellBender": { + "id": "github/broadinstitute/CellBender", + "title": "github/broadinstitute/CellBender", + "url": " https://rseng.github.io/software/repository/github/broadinstitute/CellBender", + "content": "a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data." }, - "github/csinva/imodels": { - "id": "github/csinva/imodels", - "title": "github/csinva/imodels", - "url": " https://rseng.github.io/software/repository/github/csinva/imodels", - "content": "Interpretable ML package 🔍 for concise, transparent, and accurate predictive modeling (sklearn-compatible)." + "github/SJ001/AI-Feynman": { + "id": "github/SJ001/AI-Feynman", + "title": "github/SJ001/AI-Feynman", + "url": " https://rseng.github.io/software/repository/github/SJ001/AI-Feynman", + "content": "None" }, - "github/signaturescience/skater": { - "id": "github/signaturescience/skater", - "title": "github/signaturescience/skater", - "url": " https://rseng.github.io/software/repository/github/signaturescience/skater", - "content": "SKATE R Utilities" + "github/nedRad88/SCALAR": { + "id": "github/nedRad88/SCALAR", + "title": "github/nedRad88/SCALAR", + "url": " https://rseng.github.io/software/repository/github/nedRad88/SCALAR", + "content": "SCALAR - Streaming ChALlenge plAtfoRm" }, - "github/cosmoinin/MGPT": { - "id": "github/cosmoinin/MGPT", - "title": "github/cosmoinin/MGPT", - "url": " https://rseng.github.io/software/repository/github/cosmoinin/MGPT", - "content": "Modified gravity perturbation theory code" + "github/TianlaiProject/tlpipe": { + "id": "github/TianlaiProject/tlpipe", + "title": "github/TianlaiProject/tlpipe", + "url": " https://rseng.github.io/software/repository/github/TianlaiProject/tlpipe", + "content": "The Tianlai pipeline." + }, + "github/FitSNAP/FitSNAP": { + "id": "github/FitSNAP/FitSNAP", + "title": "github/FitSNAP/FitSNAP", + "url": " https://rseng.github.io/software/repository/github/FitSNAP/FitSNAP", + "content": "Software for generating SNAP machine-learning interatomic potentials" }, - "github/benedictpaten/marginPhase": { - "id": "github/benedictpaten/marginPhase", - "title": "github/benedictpaten/marginPhase", - "url": " https://rseng.github.io/software/repository/github/benedictpaten/marginPhase", - "content": "simultaneous haplotyping and genotyping" + "github/nbellomo/Multi_CLASS": { + "id": "github/nbellomo/Multi_CLASS", + "title": "github/nbellomo/Multi_CLASS", + "url": " https://rseng.github.io/software/repository/github/nbellomo/Multi_CLASS", + "content": "Public repository of the Multi_CLASS code" }, - "github/jamesaird/FAST": { - "id": "github/jamesaird/FAST", - "title": "github/jamesaird/FAST", - "url": " https://rseng.github.io/software/repository/github/jamesaird/FAST", - "content": "Fitting and Assessment of Synthetic Templates - an IDL-based code that fits stellar population synthesis templates to broadband photometry and/or spectra." + "github/valerio-marra/CalPriorSNIa": { + "id": "github/valerio-marra/CalPriorSNIa", + "title": "github/valerio-marra/CalPriorSNIa", + "url": " https://rseng.github.io/software/repository/github/valerio-marra/CalPriorSNIa", + "content": "Effective calibration prior on the absolute magnitude of Type Ia supernovae" }, - 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"id": "github/BarquistLab/mason_paper", - "title": "github/BarquistLab/mason_paper", - "url": " https://rseng.github.io/software/repository/github/BarquistLab/mason_paper", - "content": "Code and analysis for MASON paper" + "github/tatekawa-astron/PN": { + "id": "github/tatekawa-astron/PN", + "title": "github/tatekawa-astron/PN", + "url": " https://rseng.github.io/software/repository/github/tatekawa-astron/PN", + "content": "None" }, - "github/ruggiero/galstep": { - "id": "github/ruggiero/galstep", - "title": "github/ruggiero/galstep", - "url": " https://rseng.github.io/software/repository/github/ruggiero/galstep", - "content": "Generates initial conditions for a spiral galaxy simulation in a format that can be read in GADGET2 or RAMSES, or alternatively in the HDF5 format." + "github/li-shaochuan/SEDIM": { + "id": "github/li-shaochuan/SEDIM", + "title": "github/li-shaochuan/SEDIM", + "url": " https://rseng.github.io/software/repository/github/li-shaochuan/SEDIM", + "content": "None" }, - 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Professional geographical SIR model with a flexible plugin architecture to support complex scenario modelling" + "github/ismael-mendoza/ShapeMeasurementFisherFormalism": { + "id": "github/ismael-mendoza/ShapeMeasurementFisherFormalism", + "title": "github/ismael-mendoza/ShapeMeasurementFisherFormalism", + "url": " https://rseng.github.io/software/repository/github/ismael-mendoza/ShapeMeasurementFisherFormalism", + "content": "Fisher Formalism for Weak Lensing using 1 or 2 Galsim galaxies." }, - "github/zblz/naima": { - "id": "github/zblz/naima", - "title": "github/zblz/naima", - "url": " https://rseng.github.io/software/repository/github/zblz/naima", - "content": "Derivation of non-thermal particle distributions through MCMC spectral fitting" + "github/jendelel/PrankWebApp": { + "id": "github/jendelel/PrankWebApp", + "title": "github/jendelel/PrankWebApp", + "url": " https://rseng.github.io/software/repository/github/jendelel/PrankWebApp", + "content": "Web application for protein-ligand binding sites analysis and visualization" }, - 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For reconstructing probability distributions using Gaussian processes." + "github/mzechmeister/serval": { + "id": "github/mzechmeister/serval", + "title": "github/mzechmeister/serval", + "url": " https://rseng.github.io/software/repository/github/mzechmeister/serval", + "content": "calculate radial velocities from stellar spectra" + }, + "github/mzechmeister/viper": { + "id": "github/mzechmeister/viper", + "title": "github/mzechmeister/viper", + "url": " https://rseng.github.io/software/repository/github/mzechmeister/viper", + "content": "None" }, - "github/tmcclintock/cluster_toolkit": { - "id": "github/tmcclintock/cluster_toolkit", - "title": "github/tmcclintock/cluster_toolkit", - "url": " https://rseng.github.io/software/repository/github/tmcclintock/cluster_toolkit", - "content": "Tools for analyzing galaxy clusters." + "github/ifilot/edp": { + "id": "github/ifilot/edp", + "title": "github/ifilot/edp", + "url": " https://rseng.github.io/software/repository/github/ifilot/edp", + "content": "Electron Density Plotter" }, - 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The method implements marginalization across a series of models to represent stochastic models for observatory and instrument systematics. This is primarily for HST WFC3, however, may be extened to STIS in the future. " + "github/farhanferoz/MultiNest": { + "id": "github/farhanferoz/MultiNest", + "title": "github/farhanferoz/MultiNest", + "url": " https://rseng.github.io/software/repository/github/farhanferoz/MultiNest", + "content": "MultiNest is a Bayesian inference tool which calculates the evidence and explores the parameter space which may contain multiple posterior modes and pronounced (curving) degeneracies in moderately high dimensions. 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This tool can be used to detect viral infectious diseases, like COVID-19." }, - "github/marbl/Winnowmap": { - "id": "github/marbl/Winnowmap", - "title": "github/marbl/Winnowmap", - "url": " https://rseng.github.io/software/repository/github/marbl/Winnowmap", - "content": "Long read / genome alignment software" + "github/OpenGene/fastp": { + "id": "github/OpenGene/fastp", + "title": "github/OpenGene/fastp", + "url": " https://rseng.github.io/software/repository/github/OpenGene/fastp", + "content": "An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)" }, - "github/marbl/Mash": { - "id": "github/marbl/Mash", - "title": "github/marbl/Mash", - "url": " https://rseng.github.io/software/repository/github/marbl/Mash", - "content": "Fast genome and metagenome distance estimation using MinHash" + "github/ChileanVirtualObservatory/indexing_utfsm": { + "id": "github/ChileanVirtualObservatory/indexing_utfsm", + "title": "github/ChileanVirtualObservatory/indexing_utfsm", + "url": " https://rseng.github.io/software/repository/github/ChileanVirtualObservatory/indexing_utfsm", + "content": "R implementation of RoiSE algorithm" }, - 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"github/danxhuber/evolstate": { - "id": "github/danxhuber/evolstate", - "title": "github/danxhuber/evolstate", - "url": " https://rseng.github.io/software/repository/github/danxhuber/evolstate", - "content": "Assign simple evolutionary states to stars" + "github/idptools/metapredict": { + "id": "github/idptools/metapredict", + "title": "github/idptools/metapredict", + "url": " https://rseng.github.io/software/repository/github/idptools/metapredict", + "content": "A machine learning based protein disorder predictor." }, - "github/UM-Bridge/umbridge": { - "id": "github/UM-Bridge/umbridge", - "title": "github/UM-Bridge/umbridge", - "url": " https://rseng.github.io/software/repository/github/UM-Bridge/umbridge", + "github/sevenstarknight/VariableStarAnalysis": { + "id": "github/sevenstarknight/VariableStarAnalysis", + "title": "github/sevenstarknight/VariableStarAnalysis", + "url": " https://rseng.github.io/software/repository/github/sevenstarknight/VariableStarAnalysis", "content": "None" }, - 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"github/infer-actively/pymdp": { - "id": "github/infer-actively/pymdp", - "title": "github/infer-actively/pymdp", - "url": " https://rseng.github.io/software/repository/github/infer-actively/pymdp", - "content": "A Python implementation of active inference for Markov Decision Processes" + "github/sidchaini/DistClassiPy": { + "id": "github/sidchaini/DistClassiPy", + "title": "github/sidchaini/DistClassiPy", + "url": " https://rseng.github.io/software/repository/github/sidchaini/DistClassiPy", + "content": "A python package for a distance-based classifier which can use several different distance metrics." }, - "github/amkram/shusher": { - "id": "github/amkram/shusher", - "title": "github/amkram/shusher", - "url": " https://rseng.github.io/software/repository/github/amkram/shusher", - "content": "Private, browser-based placement of genome sequences on phylogenetic trees using UShER." + "github/brian-lau/MatlabAUC": { + "id": "github/brian-lau/MatlabAUC", + "title": "github/brian-lau/MatlabAUC", + "url": " https://rseng.github.io/software/repository/github/brian-lau/MatlabAUC", + "content": "Matlab code for the area under the receiver operating curve (AUC) and confidence intervals" }, - 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"github/JulianZDing/UniMAP": { - "id": "github/JulianZDing/UniMAP", - "title": "github/JulianZDing/UniMAP", - "url": " https://rseng.github.io/software/repository/github/JulianZDing/UniMAP", - "content": "None" + "github/auckland-cosmo/interp-mc": { + "id": "github/auckland-cosmo/interp-mc", + "title": "github/auckland-cosmo/interp-mc", + "url": " https://rseng.github.io/software/repository/github/auckland-cosmo/interp-mc", + "content": "Archival patch to CosmoMC for "interp-mc" paper" }, - "github/NSAPH-Software/CRE": { - "id": "github/NSAPH-Software/CRE", - "title": "github/NSAPH-Software/CRE", - "url": " https://rseng.github.io/software/repository/github/NSAPH-Software/CRE", - "content": "The Causal Rule Ensemble Method" + "github/auckland-cosmo/defrost-mpi": { + "id": "github/auckland-cosmo/defrost-mpi", + "title": "github/auckland-cosmo/defrost-mpi", + "url": " https://rseng.github.io/software/repository/github/auckland-cosmo/defrost-mpi", + "content": "MPI version of the defrost code " }, - "github/NSAPH-Software/GPCERF": { - "id": "github/NSAPH-Software/GPCERF", - "title": "github/NSAPH-Software/GPCERF", - "url": " https://rseng.github.io/software/repository/github/NSAPH-Software/GPCERF", - "content": "None" + "github/auckland-cosmo/PyUltraLight": { + "id": "github/auckland-cosmo/PyUltraLight", + "title": "github/auckland-cosmo/PyUltraLight", + "url": " https://rseng.github.io/software/repository/github/auckland-cosmo/PyUltraLight", + "content": "Pseudo-spectral Python code to compute ultralight dark matter dynamics. " }, - "github/demorest/nanopipe": { - "id": "github/demorest/nanopipe", - "title": "github/demorest/nanopipe", - "url": " https://rseng.github.io/software/repository/github/demorest/nanopipe", - "content": "Calibration and TOA generation scripts for NANOGrav data" + "github/ParisAstronomicalDataCentre/OPUS": { + "id": "github/ParisAstronomicalDataCentre/OPUS", + "title": "github/ParisAstronomicalDataCentre/OPUS", + "url": " https://rseng.github.io/software/repository/github/ParisAstronomicalDataCentre/OPUS", + "content": "Observatoire de Paris UWS System (OPUS): UWS web client/server developped at the Paris Astronomical Data Centre." }, - "github/harrispopgen/mutyper": { - "id": "github/harrispopgen/mutyper", - "title": "github/harrispopgen/mutyper", - "url": " https://rseng.github.io/software/repository/github/harrispopgen/mutyper", - "content": "Ancestral k-mer mutation types for SNP data" + "github/TNOCS/csWeb": { + "id": "github/TNOCS/csWeb", + "title": "github/TNOCS/csWeb", + "url": " https://rseng.github.io/software/repository/github/TNOCS/csWeb", + "content": "csWeb, short for common sense Web, is a userfriendly web application for showing (GIS) data on a map. It allows you to apply multiple filters to filter your data, and to style it, so you can immediately see what's important." }, - "github/mathjax/MathJax": { - "id": "github/mathjax/MathJax", - "title": "github/mathjax/MathJax", - "url": " https://rseng.github.io/software/repository/github/mathjax/MathJax", - "content": "Beautiful math in all browsers" + "github/CliMA/EnsembleKalmanProcesses.jl": { + "id": "github/CliMA/EnsembleKalmanProcesses.jl", + "title": "github/CliMA/EnsembleKalmanProcesses.jl", + "url": " https://rseng.github.io/software/repository/github/CliMA/EnsembleKalmanProcesses.jl", + "content": "Implements Optimization and approximate uncertainty quantification algorithms, Ensemble Kalman Inversion, and Ensemble Kalman Processes." }, - "github/casacore/casacore": { - "id": "github/casacore/casacore", - "title": "github/casacore/casacore", - "url": " https://rseng.github.io/software/repository/github/casacore/casacore", - "content": "Suite of C++ libraries for radio astronomy data processing" + "github/AndresRTejedor/Mold": { + "id": "github/AndresRTejedor/Mold", + "title": "github/AndresRTejedor/Mold", + "url": " https://rseng.github.io/software/repository/github/AndresRTejedor/Mold", + "content": "Lammps package including square-like well potential to implement Mold integration and Lattice mold techniques" }, - "github/AndreNicolasChene/DRAGRACES": { - "id": "github/AndreNicolasChene/DRAGRACES", - "title": "github/AndreNicolasChene/DRAGRACES", - "url": " https://rseng.github.io/software/repository/github/AndreNicolasChene/DRAGRACES", - "content": "Reduction pipeline for GRACES spectra (Gemini spectrograph)" + "github/matchms/ms2deepscore": { + "id": "github/matchms/ms2deepscore", + "title": "github/matchms/ms2deepscore", + "url": " https://rseng.github.io/software/repository/github/matchms/ms2deepscore", + "content": "Deep learning similarity measure for comparing MS/MS spectra with respect to their chemical similarity" }, - "github/Griffan/VerifyBamID": { - "id": "github/Griffan/VerifyBamID", - "title": "github/Griffan/VerifyBamID", - "url": " https://rseng.github.io/software/repository/github/Griffan/VerifyBamID", - "content": "VerifyBamID2: A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method." + "github/matchms/matchms": { + "id": "github/matchms/matchms", + "title": "github/matchms/matchms", + "url": " https://rseng.github.io/software/repository/github/matchms/matchms", + "content": "Python library for fuzzy comparison of mass spectrum data and other Python objects" }, - "github/bpp/bpp": { - "id": "github/bpp/bpp", - "title": "github/bpp/bpp", - "url": " https://rseng.github.io/software/repository/github/bpp/bpp", - "content": "implements a versatile high-performance version of the BPP software" + "github/liniguez/Insplico_simulations": { + "id": "github/liniguez/Insplico_simulations", + "title": "github/liniguez/Insplico_simulations", + "url": " https://rseng.github.io/software/repository/github/liniguez/Insplico_simulations", + "content": "None" }, - "github/julblarod/SOPHISM": { - "id": "github/julblarod/SOPHISM", - "title": "github/julblarod/SOPHISM", - "url": " https://rseng.github.io/software/repository/github/julblarod/SOPHISM", - "content": "Repository for software instrument simulator SOPHISM" + "github/nyusngroup/pyMCZ": { + "id": "github/nyusngroup/pyMCZ", + "title": "github/nyusngroup/pyMCZ", + "url": " https://rseng.github.io/software/repository/github/nyusngroup/pyMCZ", + "content": "montecarlo sampling method to calculate metalicity from flux data" }, - "github/diCenzo-GC/Tn-Core-webserver": { - "id": "github/diCenzo-GC/Tn-Core-webserver", - "title": "github/diCenzo-GC/Tn-Core-webserver", - "url": " https://rseng.github.io/software/repository/github/diCenzo-GC/Tn-Core-webserver", - "content": "Help files and sample data for the Tn-Core webserver. The code supporting the web server is also included." + "github/tresoldi/ngesh": { + "id": "github/tresoldi/ngesh", + "title": "github/tresoldi/ngesh", + "url": " https://rseng.github.io/software/repository/github/tresoldi/ngesh", + "content": "A Python library for generating random phylogenetic trees and related data" + }, + "github/jianlin-cheng/DRCon": { + "id": "github/jianlin-cheng/DRCon", + "title": "github/jianlin-cheng/DRCon", + "url": " https://rseng.github.io/software/repository/github/jianlin-cheng/DRCon", + "content": "Deep dilated convolutional residual neural network for predicting interchain contacts of protein homodimers" }, "github/AngryMaciek/hypercomplex": { "id": "github/AngryMaciek/hypercomplex", @@ -14805,569 +14373,617 @@ "url": " https://rseng.github.io/software/repository/github/AngryMaciek/hypercomplex", "content": "Abstract & fast header-only C++ template library for lattice-based cryptosystems in high-dimensional algebras" }, - "github/mbillingr/libgdf": { - "id": "github/mbillingr/libgdf", - "title": "github/mbillingr/libgdf", - "url": " https://rseng.github.io/software/repository/github/mbillingr/libgdf", - "content": "C++ implementation of GDF - "a general dataformat for biosignals" version V2.20." + "github/BenMql/coral": { + "id": "github/BenMql/coral", + "title": "github/BenMql/coral", + "url": " https://rseng.github.io/software/repository/github/BenMql/coral", + "content": "Parallel spectral solver for partial differential equations in the plane layer geometry. " }, - "github/mpi4py/shmem4py": { - "id": "github/mpi4py/shmem4py", - "title": "github/mpi4py/shmem4py", - "url": " https://rseng.github.io/software/repository/github/mpi4py/shmem4py", + "github/david-barnett/microViz": { + "id": "github/david-barnett/microViz", + "title": "github/david-barnett/microViz", + "url": " https://rseng.github.io/software/repository/github/david-barnett/microViz", + "content": "R package for microbiome data visualization. Uses phyloseq, vegan and tidyverse. See website link for docs with visual examples. Docker image available." + }, + "github/ttgump/scDeepCluster_pytorch": { + "id": "github/ttgump/scDeepCluster_pytorch", + "title": "github/ttgump/scDeepCluster_pytorch", + "url": " https://rseng.github.io/software/repository/github/ttgump/scDeepCluster_pytorch", + "content": "Pytorch implementation of scDeepCluster for Single Cell RNA-seq data" + }, + "github/ttgump/scDHMap": { + "id": "github/ttgump/scDHMap", + "title": "github/ttgump/scDHMap", + "url": " https://rseng.github.io/software/repository/github/ttgump/scDHMap", + "content": "Model-based deep hyperbolic manifold learning for visualizing complex hierarchical structures in single-cell genomics data" + }, + "github/snad-space/ztf-viewer": { + "id": "github/snad-space/ztf-viewer", + "title": "github/snad-space/ztf-viewer", + "url": " https://rseng.github.io/software/repository/github/snad-space/ztf-viewer", + "content": "ZTF data releases light curve viewer" + }, + "github/snad-space/coniferest": { + "id": "github/snad-space/coniferest", + "title": "github/snad-space/coniferest", + "url": " https://rseng.github.io/software/repository/github/snad-space/coniferest", "content": "None" }, - 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"title": "github/maxmahlke/ssos", - "url": " https://rseng.github.io/software/repository/github/maxmahlke/ssos", - "content": "Pipeline to recover astrometry and photometry of Solar System Objects in imaging surveys" + "github/jls713/tact": { + "id": "github/jls713/tact", + "title": "github/jls713/tact", + "url": " https://rseng.github.io/software/repository/github/jls713/tact", + "content": "action, angle and frequency estimation using various methods" }, - "github/shangguandong1996/FindIT2": { - "id": "github/shangguandong1996/FindIT2", - "title": "github/shangguandong1996/FindIT2", - "url": " https://rseng.github.io/software/repository/github/shangguandong1996/FindIT2", + "github/aranyics/ReDCM": { + "id": "github/aranyics/ReDCM", + "title": "github/aranyics/ReDCM", + "url": " https://rseng.github.io/software/repository/github/aranyics/ReDCM", + "content": "Reimplementation of DCM12 algorithm in R language" + }, + "github/mmp2/megaman": { + "id": "github/mmp2/megaman", + "title": "github/mmp2/megaman", + "url": " https://rseng.github.io/software/repository/github/mmp2/megaman", + "content": "megaman: Manifold Learning for Millions of Points " + }, + "github/mdsteiner/EFAtools": { + "id": "github/mdsteiner/EFAtools", + "title": "github/mdsteiner/EFAtools", + "url": " https://rseng.github.io/software/repository/github/mdsteiner/EFAtools", "content": "None" }, - "github/daniel-muthukrishna/astrodash": { - "id": "github/daniel-muthukrishna/astrodash", - "title": "github/daniel-muthukrishna/astrodash", - "url": " https://rseng.github.io/software/repository/github/daniel-muthukrishna/astrodash", - "content": "Deep learning for the automated spectral classification of supernovae" + "github/djsutherland/py-sdm": { + "id": "github/djsutherland/py-sdm", + "title": "github/djsutherland/py-sdm", + "url": " https://rseng.github.io/software/repository/github/djsutherland/py-sdm", + "content": "Python implementation of nonparametric nearest-neighbor-based estimators for divergences between distributions." }, - "github/carpenterphysics/DarkFlux": { - "id": "github/carpenterphysics/DarkFlux", - "title": "github/carpenterphysics/DarkFlux", - "url": " https://rseng.github.io/software/repository/github/carpenterphysics/DarkFlux", - "content": "DarkFlux is a tool to compute Dark Matter the Dark Matter annihilation spectrum in Next Generation Dark Matter Models" + "github/sonwell/biotools": { + "id": "github/sonwell/biotools", + "title": "github/sonwell/biotools", + "url": " https://rseng.github.io/software/repository/github/sonwell/biotools", + "content": "A bunch of bioinformatics tools." }, - "github/abinit/abinit": { - "id": "github/abinit/abinit", - "title": "github/abinit/abinit", - "url": " https://rseng.github.io/software/repository/github/abinit/abinit", - "content": "The official github mirror of the Abinit repository. We welcome bug fixes and improvements. Note that most of the active developments are hosted on our https://gitlab.abinit.org/ server. Before embarking on making significant changes, please contact the Abinit group." + "github/kartheikiyer/dense_basis": { + "id": "github/kartheikiyer/dense_basis", + "title": "github/kartheikiyer/dense_basis", + "url": " https://rseng.github.io/software/repository/github/kartheikiyer/dense_basis", + "content": "Dense Basis SED fitting" }, - "github/PeterKamphuis/FAT": { - "id": "github/PeterKamphuis/FAT", - "title": "github/PeterKamphuis/FAT", - "url": " https://rseng.github.io/software/repository/github/PeterKamphuis/FAT", - "content": "An IDL/GDL wrapper to automate TiRiFiC" + "github/tuoyl/tat-pulsar": { + "id": "github/tuoyl/tat-pulsar", + "title": "github/tuoyl/tat-pulsar", + "url": " https://rseng.github.io/software/repository/github/tuoyl/tat-pulsar", + "content": "A Python based pulsar timing analysis tools (TAT)." }, - "github/JensUweUlrich/ReadBouncer": { - "id": "github/JensUweUlrich/ReadBouncer", - "title": "github/JensUweUlrich/ReadBouncer", - "url": " https://rseng.github.io/software/repository/github/JensUweUlrich/ReadBouncer", - 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"content": "lhorizon helps you find things in the Solar System." + "github/ImperialCollegeLondon/research-software-directory-data": { + "id": "github/ImperialCollegeLondon/research-software-directory-data", + "title": "github/ImperialCollegeLondon/research-software-directory-data", + "url": " https://rseng.github.io/software/repository/github/ImperialCollegeLondon/research-software-directory-data", + "content": "Imperial College Research Software Directory" }, - "github/mourisl/Lighter": { - "id": "github/mourisl/Lighter", - "title": "github/mourisl/Lighter", - "url": " https://rseng.github.io/software/repository/github/mourisl/Lighter", - "content": "Fast and memory-efficient sequencing error corrector" + "github/kungfugo/BellDiagonalQudits.jl": { + "id": "github/kungfugo/BellDiagonalQudits.jl", + "title": "github/kungfugo/BellDiagonalQudits.jl", + "url": " https://rseng.github.io/software/repository/github/kungfugo/BellDiagonalQudits.jl", + "content": "None" + }, + "github/CavendishAstrophysics/anmap": { + "id": "github/CavendishAstrophysics/anmap", + "title": "github/CavendishAstrophysics/anmap", + "url": " https://rseng.github.io/software/repository/github/CavendishAstrophysics/anmap", + "content": "MRAO image and data analysis system" }, - 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Uses phyloseq, vegan and tidyverse. See website link for docs with visual examples. Docker image available." + "github/ewatercycle/era5cli": { + "id": "github/ewatercycle/era5cli", + "title": "github/ewatercycle/era5cli", + "url": " https://rseng.github.io/software/repository/github/ewatercycle/era5cli", + "content": "Command Line Interface to download ERA5 from Copernicus Climate Data Service" }, - "github/pikarpov-LANL/Sapsan": { - "id": "github/pikarpov-LANL/Sapsan", - "title": "github/pikarpov-LANL/Sapsan", - "url": " https://rseng.github.io/software/repository/github/pikarpov-LANL/Sapsan", - "content": "ML-based turbulence modeling for astrophysics" + "github/i-VRESSE/pdbtbx-ts": { + "id": "github/i-VRESSE/pdbtbx-ts", + "title": "github/i-VRESSE/pdbtbx-ts", + "url": " https://rseng.github.io/software/repository/github/i-VRESSE/pdbtbx-ts", + "content": "JS wrapper around pdbtbx rust crate" }, - "github/moscibrodzka/ipole": { - "id": "github/moscibrodzka/ipole", - "title": "github/moscibrodzka/ipole", - "url": " https://rseng.github.io/software/repository/github/moscibrodzka/ipole", - "content": "ipole (master, originally published), ipole-v2.0 (v2.0 is more compact with additional features). This is the original repository for the ipole code. " + "github/i-VRESSE/workflow-builder": { + "id": "github/i-VRESSE/workflow-builder", + "title": "github/i-VRESSE/workflow-builder", + "url": " https://rseng.github.io/software/repository/github/i-VRESSE/workflow-builder", + "content": "Graphical interface to build a workflow file" }, - "github/villano-lab/nrCascadeSim": { - "id": "github/villano-lab/nrCascadeSim", - "title": "github/villano-lab/nrCascadeSim", - "url": " https://rseng.github.io/software/repository/github/villano-lab/nrCascadeSim", - "content": "calculating the NR spectrum resulting from neutron-capture cascades." + "github/jakevdp/wpca": { + "id": "github/jakevdp/wpca", + "title": "github/jakevdp/wpca", + "url": " https://rseng.github.io/software/repository/github/jakevdp/wpca", + "content": "Weighted Principal Component Analysis (PCA) in Python" }, - "github/wtraylor/modular_megafauna_model": { - "id": "github/wtraylor/modular_megafauna_model", - "title": "github/wtraylor/modular_megafauna_model", - "url": " https://rseng.github.io/software/repository/github/wtraylor/modular_megafauna_model", - "content": "Extendable, dynamic, process-based herbivore simulator that can be integrated into a dynamic vegetation model. Written as a C++ library." + "github/daiqile96/OTTERS_paper": { + "id": "github/daiqile96/OTTERS_paper", + "title": "github/daiqile96/OTTERS_paper", + "url": " https://rseng.github.io/software/repository/github/daiqile96/OTTERS_paper", + "content": "None" }, - "github/dokester/BayesicFitting": { - "id": "github/dokester/BayesicFitting", - "title": "github/dokester/BayesicFitting", - "url": " https://rseng.github.io/software/repository/github/dokester/BayesicFitting", - "content": "Bayesian fitting package" + "github/anchal-009/SAVED21cm": { + "id": "github/anchal-009/SAVED21cm", + "title": "github/anchal-009/SAVED21cm", + "url": " https://rseng.github.io/software/repository/github/anchal-009/SAVED21cm", + "content": "A toolbox for extracting the 21cm signal from the simulated mock observation for REACH." }, - "github/skovaka/UNCALLED": { - "id": "github/skovaka/UNCALLED", - "title": "github/skovaka/UNCALLED", - "url": " https://rseng.github.io/software/repository/github/skovaka/UNCALLED", - "content": "Raw nanopore signal mapper that enables real-time targeted sequencing" + "github/fstrozzi/Fastool": { + "id": "github/fstrozzi/Fastool", + "title": "github/fstrozzi/Fastool", + "url": " https://rseng.github.io/software/repository/github/fstrozzi/Fastool", + "content": "Simple and quick FastQ and FastA tool for file reading and conversion" }, - "github/amrex-astro/Nyx": { - "id": "github/amrex-astro/Nyx", - "title": "github/amrex-astro/Nyx", - "url": " https://rseng.github.io/software/repository/github/amrex-astro/Nyx", - "content": "An adaptive mesh, N-body hydro cosmological simulation code" + "github/candYgene/pbg-ld": { + "id": "github/candYgene/pbg-ld", + "title": "github/candYgene/pbg-ld", + "url": " https://rseng.github.io/software/repository/github/candYgene/pbg-ld", + "content": "Linked Data Platform for Plant Breeding & Genomics" }, - "github/amrex-astro/MAESTRO": { - "id": "github/amrex-astro/MAESTRO", - "title": "github/amrex-astro/MAESTRO", - "url": " https://rseng.github.io/software/repository/github/amrex-astro/MAESTRO", - "content": "A low Mach number stellar hydrodynamics code" + "github/candYgene/QTM": { + "id": "github/candYgene/QTM", + "title": "github/candYgene/QTM", + "url": " https://rseng.github.io/software/repository/github/candYgene/QTM", + "content": "QTLTableMiner++ tool for mining tables in scientific articles" }, - "github/amrex-astro/Castro": { - "id": "github/amrex-astro/Castro", - "title": "github/amrex-astro/Castro", - "url": " https://rseng.github.io/software/repository/github/amrex-astro/Castro", - "content": "An adaptive mesh, astrophysical compressible (radiation-, magneto-) hydrodynamics simulation code for massively parallel CPU and GPU architectures." + "github/candYgene/siga": { + "id": "github/candYgene/siga", + "title": "github/candYgene/siga", + "url": " https://rseng.github.io/software/repository/github/candYgene/siga", + "content": "Semantically Interoperable Genome Annotations" }, - "github/jaimedelacruz/stic": { - "id": "github/jaimedelacruz/stic", - "title": "github/jaimedelacruz/stic", - "url": " https://rseng.github.io/software/repository/github/jaimedelacruz/stic", - "content": "The Stockholm inversion code" + "github/candYgene/abg-ld": { + "id": "github/candYgene/abg-ld", + "title": "github/candYgene/abg-ld", + "url": " https://rseng.github.io/software/repository/github/candYgene/abg-ld", + "content": "Linked Data Platform for Animal Breeding & Genomics" }, - "github/yuansh3354/CaSee": { - "id": "github/yuansh3354/CaSee", - "title": "github/yuansh3354/CaSee", - "url": " https://rseng.github.io/software/repository/github/yuansh3354/CaSee", - "content": "None" + "github/gabraham/flashpca": { + "id": "github/gabraham/flashpca", + "title": "github/gabraham/flashpca", + "url": " https://rseng.github.io/software/repository/github/gabraham/flashpca", + "content": "Fast Principal Component Analysis of Large-Scale Genome-Wide Data" }, - "github/esquivas/guacho": { - "id": "github/esquivas/guacho", - "title": "github/esquivas/guacho", - "url": " https://rseng.github.io/software/repository/github/esquivas/guacho", - "content": "A 3D uniform mesh parallel HD/MHD code for astrophysics" + "github/caracal-pipeline/caracal": { + "id": "github/caracal-pipeline/caracal", + "title": "github/caracal-pipeline/caracal", + "url": " https://rseng.github.io/software/repository/github/caracal-pipeline/caracal", + "content": "Containerized Automated Radio Astronomy Calibration (CARACal) pipeline " }, - "github/NKI-CCB/PRECISE": { - "id": "github/NKI-CCB/PRECISE", - "title": "github/NKI-CCB/PRECISE", - "url": " https://rseng.github.io/software/repository/github/NKI-CCB/PRECISE", + "github/yair111/AnalyticLC": { + "id": "github/yair111/AnalyticLC", + "title": "github/yair111/AnalyticLC", + "url": " https://rseng.github.io/software/repository/github/yair111/AnalyticLC", "content": "None" }, - "github/DMGW-Goethe/imripy": { - "id": "github/DMGW-Goethe/imripy", - "title": "github/DMGW-Goethe/imripy", - "url": " https://rseng.github.io/software/repository/github/DMGW-Goethe/imripy", - "content": "A python code able to simulate Intermediate Mass Ratio Inspirals (IMRI)" + "github/msaland/THInCR-Suite": { + "id": "github/msaland/THInCR-Suite", + "title": "github/msaland/THInCR-Suite", + "url": " https://rseng.github.io/software/repository/github/msaland/THInCR-Suite", + "content": "None" }, - 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"title": "github/fpavogt/E0102-VR", - "url": " https://rseng.github.io/software/repository/github/fpavogt/E0102-VR", - "content": "An experimental VR application to visualize the 3D map of the oxygen-bright ejecta in SNR 1E 0102.2-7219" + "github/ArisTr/PyRaTE": { + "id": "github/ArisTr/PyRaTE", + "title": "github/ArisTr/PyRaTE", + "url": " https://rseng.github.io/software/repository/github/ArisTr/PyRaTE", + "content": "Python Radiative Transfer Emission Code" }, - "github/adammoss/supernovae": { - "id": "github/adammoss/supernovae", - "title": "github/adammoss/supernovae", - "url": " https://rseng.github.io/software/repository/github/adammoss/supernovae", - "content": "None" + "github/forrest-lab/scMatch": { + "id": "github/forrest-lab/scMatch", + "title": "github/forrest-lab/scMatch", + "url": " https://rseng.github.io/software/repository/github/forrest-lab/scMatch", + "content": "scMatch: a single-cell gene expression profile annotation tool using reference datasets" }, - "github/supernnova/SuperNNova": { - "id": "github/supernnova/SuperNNova", - "title": "github/supernnova/SuperNNova", - "url": " https://rseng.github.io/software/repository/github/supernnova/SuperNNova", - "content": "Open Source Photometric classification https://supernnova.readthedocs.io" + "github/INCF/one_click": { + "id": "github/INCF/one_click", + "title": "github/INCF/one_click", + "url": " https://rseng.github.io/software/repository/github/INCF/one_click", + "content": "One Click Sharing" }, - "github/stermzsofi/TiDE": { - "id": "github/stermzsofi/TiDE", - "title": "github/stermzsofi/TiDE", - "url": " https://rseng.github.io/software/repository/github/stermzsofi/TiDE", - "content": "None" + "github/Goobley/Radynversion": { + "id": "github/Goobley/Radynversion", + "title": "github/Goobley/Radynversion", + "url": " https://rseng.github.io/software/repository/github/Goobley/Radynversion", + "content": "Inverting Solar Flare Observations with Invertible Neural Nets (with RADYN physics) " }, - "github/gtw2i/GA-Galaxy": { - "id": "github/gtw2i/GA-Galaxy", - "title": "github/gtw2i/GA-Galaxy", - "url": " https://rseng.github.io/software/repository/github/gtw2i/GA-Galaxy", + "github/JoeMcEwen/FAST-PT": { + "id": "github/JoeMcEwen/FAST-PT", + "title": "github/JoeMcEwen/FAST-PT", + "url": " https://rseng.github.io/software/repository/github/JoeMcEwen/FAST-PT", "content": "None" }, - "github/aberer/RogueNaRok": { - "id": "github/aberer/RogueNaRok", - "title": "github/aberer/RogueNaRok", - "url": " https://rseng.github.io/software/repository/github/aberer/RogueNaRok", - "content": "A versatile and scalable algorithm for rogue taxon identification. 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(1992) Membrane Protein Structure Prediction: Hydrophobicity Analysis and the 'Positive Inside' (PMID: 1593632)" + }, + "github/martinjameswhite/ZeldovichRecon": { + "id": "github/martinjameswhite/ZeldovichRecon", + "title": "github/martinjameswhite/ZeldovichRecon", + "url": " https://rseng.github.io/software/repository/github/martinjameswhite/ZeldovichRecon", + "content": "Code to compute the post-reconstruction halo correlation function using the Zeldovich approximation." + }, + "github/WatsonLab/MAGpy": { + "id": "github/WatsonLab/MAGpy", + "title": "github/WatsonLab/MAGpy", + "url": " https://rseng.github.io/software/repository/github/WatsonLab/MAGpy", + "content": "Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)" + }, + "github/the-rccg/hw2d": { + "id": "github/the-rccg/hw2d", + "title": "github/the-rccg/hw2d", + "url": " https://rseng.github.io/software/repository/github/the-rccg/hw2d", + "content": "Reference implementation for the Hasegawa-Wakatani model of plasma turbulence inside nuclear fusion reactors in two dimensions" + }, + "github/GRTLCollaboration/GRChombo": { + "id": "github/GRTLCollaboration/GRChombo", + "title": "github/GRTLCollaboration/GRChombo", + "url": " https://rseng.github.io/software/repository/github/GRTLCollaboration/GRChombo", + "content": "An AMR based open-source code for numerical relativity simulations." + }, + "github/GRTLCollaboration/GRFolres": { + "id": "github/GRTLCollaboration/GRFolres", + "title": "github/GRTLCollaboration/GRFolres", + "url": " https://rseng.github.io/software/repository/github/GRTLCollaboration/GRFolres", + "content": "Extension to GRChombo for Modified Gravity simulations" + }, + "github/daniel-muthukrishna/astrodash": { + "id": "github/daniel-muthukrishna/astrodash", + "title": "github/daniel-muthukrishna/astrodash", + "url": " https://rseng.github.io/software/repository/github/daniel-muthukrishna/astrodash", + "content": "Deep learning for the automated spectral classification of supernovae" + }, + "github/cholla-hydro/cholla": { + "id": "github/cholla-hydro/cholla", + "title": "github/cholla-hydro/cholla", + "url": " https://rseng.github.io/software/repository/github/cholla-hydro/cholla", + "content": "A GPU-based hydro code" + }, + "github/QuantumPlasma/SFQEDtoolkit": { + "id": "github/QuantumPlasma/SFQEDtoolkit", + "title": "github/QuantumPlasma/SFQEDtoolkit", + "url": " https://rseng.github.io/software/repository/github/QuantumPlasma/SFQEDtoolkit", + "content": "None" + }, + "github/easystats/effectsize": { + "id": "github/easystats/effectsize", + "title": "github/easystats/effectsize", + "url": " https://rseng.github.io/software/repository/github/easystats/effectsize", + "content": ":dragon: Compute and work with indices of effect size and standardized parameters" + }, + "github/easystats/parameters": { + "id": "github/easystats/parameters", + "title": "github/easystats/parameters", + "url": " https://rseng.github.io/software/repository/github/easystats/parameters", + "content": ":bar_chart: Computation and processing of models' parameters" + }, + "github/easystats/performance": { + "id": "github/easystats/performance", + "title": "github/easystats/performance", + "url": " https://rseng.github.io/software/repository/github/easystats/performance", + "content": ":muscle: Models' quality and performance metrics (R2, ICC, LOO, AIC, BF, ...)" + }, + "github/easystats/correlation": { + "id": "github/easystats/correlation", + "title": "github/easystats/correlation", + "url": " https://rseng.github.io/software/repository/github/easystats/correlation", + "content": ":link: Methods for Correlation Analysis" + }, + "github/gtayana/CVRMS": { + "id": "github/gtayana/CVRMS", + "title": "github/gtayana/CVRMS", + "url": " https://rseng.github.io/software/repository/github/gtayana/CVRMS", + "content": "Marker selection for genome-wide prediction" + }, + "github/EbmeyerSt/GEnView": { + "id": "github/EbmeyerSt/GEnView", + "title": "github/EbmeyerSt/GEnView", + "url": " https://rseng.github.io/software/repository/github/EbmeyerSt/GEnView", + "content": "GEnView - A phylogeny based comparative genomics software to analyze the genetic environment of genes" }, - "github/akleroy/phangs_imaging_scripts": { - "id": "github/akleroy/phangs_imaging_scripts", - "title": "github/akleroy/phangs_imaging_scripts", - "url": " https://rseng.github.io/software/repository/github/akleroy/phangs_imaging_scripts", - "content": "CASA+python imaging and product creation scripts for PHANGS-ALMA" + "github/Yida-Lin/libxdf": { + "id": "github/Yida-Lin/libxdf", + "title": "github/Yida-Lin/libxdf", + "url": " https://rseng.github.io/software/repository/github/Yida-Lin/libxdf", + "content": "C++ library for loading XDF files" }, - "github/pedro-acunha/SHEEP": { - "id": "github/pedro-acunha/SHEEP", - "title": "github/pedro-acunha/SHEEP", - "url": " https://rseng.github.io/software/repository/github/pedro-acunha/SHEEP", - "content": "Machine Learning pipeline to classify astronomical sources into galaxies, quasars and stars using photometric data." + "github/bwkeller/PASTA": { + "id": "github/bwkeller/PASTA", + "title": "github/bwkeller/PASTA", + "url": " https://rseng.github.io/software/repository/github/bwkeller/PASTA", + "content": "Python Astronomical Stacking Tool Array" }, - 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The theoretical foundation for this code is laid out in the paper "Analytic Reflected Lightcurves for Exoplanets" by Hal M. Haggard and Nicolas B. Cowan, which can be found the arXiv." }, - "github/bbbbbbzhou/MDPET": { - "id": "github/bbbbbbzhou/MDPET", - "title": "github/bbbbbbzhou/MDPET", - "url": " https://rseng.github.io/software/repository/github/bbbbbbzhou/MDPET", - "content": "MDPET: A Unified Motion Correction and Denoising Adversarial Network for Low-dose Gated PET (IEEE Transactions on Medical Imaging, 2021)" + "github/openmsi/openmsistream": { + "id": "github/openmsi/openmsistream", + "title": "github/openmsi/openmsistream", + "url": " https://rseng.github.io/software/repository/github/openmsi/openmsistream", + "content": "Materials data streaming applications, written in Python using Apache Kafka, with a focus on deployment in laboratory environments" }, - "github/PanKonstantinos/MEvA-X": { - "id": "github/PanKonstantinos/MEvA-X", - "title": "github/PanKonstantinos/MEvA-X", - "url": " https://rseng.github.io/software/repository/github/PanKonstantinos/MEvA-X", - "content": "Open source Biomarker discovery tool based on multi-objective Evolutionary algorithm and the XGBoost Classifier" + "github/NKI-AI/direct": { + "id": "github/NKI-AI/direct", + "title": "github/NKI-AI/direct", + "url": " https://rseng.github.io/software/repository/github/NKI-AI/direct", + "content": "Deep learning framework for MRI reconstruction" }, - 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"github/davideamato/NAPLES": { - "id": "github/davideamato/NAPLES", - "title": "github/davideamato/NAPLES", - "url": " https://rseng.github.io/software/repository/github/davideamato/NAPLES", - "content": "NAPLES (Numerical Analysis of PLanetary EncounterS) is a Fortran code for the numerical analysis of close encounters in the Circular, Restricted Three-Body Problem using regularized formulations." + "github/SSAGESproject/SSAGES": { + "id": "github/SSAGESproject/SSAGES", + "title": "github/SSAGESproject/SSAGES", + "url": " https://rseng.github.io/software/repository/github/SSAGESproject/SSAGES", + "content": "Software Suite for Advanced General Ensemble Simulations" }, - "github/AndreyTavleev/DiscVerSt": { - "id": "github/AndreyTavleev/DiscVerSt", - "title": "github/AndreyTavleev/DiscVerSt", - "url": " https://rseng.github.io/software/repository/github/AndreyTavleev/DiscVerSt", - "content": "Code calculates vertical structure of accretion discs around neutron stars and black holes." + "github/BorgwardtLab/simbsig": { + "id": "github/BorgwardtLab/simbsig", + "title": "github/BorgwardtLab/simbsig", + "url": " https://rseng.github.io/software/repository/github/BorgwardtLab/simbsig", + "content": "The official implementation for the SIMBSIG package" }, - "github/Filter-Bubble/stroll": { - "id": "github/Filter-Bubble/stroll", - "title": "github/Filter-Bubble/stroll", - "url": " https://rseng.github.io/software/repository/github/Filter-Bubble/stroll", - "content": "Graph based Sematic Role Labeller" + "github/ABard0/MDGF-MCEC": { + "id": "github/ABard0/MDGF-MCEC", + "title": "github/ABard0/MDGF-MCEC", + "url": " https://rseng.github.io/software/repository/github/ABard0/MDGF-MCEC", + "content": "None" }, - "github/Filter-Bubble/e2e-Dutch": { - "id": "github/Filter-Bubble/e2e-Dutch", - "title": "github/Filter-Bubble/e2e-Dutch", - "url": " https://rseng.github.io/software/repository/github/Filter-Bubble/e2e-Dutch", - "content": "Code for e2e coref model in Dutch" + "github/bmorris3/fleck": { + "id": "github/bmorris3/fleck", + "title": "github/bmorris3/fleck", + "url": " https://rseng.github.io/software/repository/github/bmorris3/fleck", + "content": "Fast approximate light curves for starspot rotational modulation" }, - "github/BiocomputeLab/paraSBOLv": { - "id": "github/BiocomputeLab/paraSBOLv", - "title": "github/BiocomputeLab/paraSBOLv", - "url": " https://rseng.github.io/software/repository/github/BiocomputeLab/paraSBOLv", - "content": "A lightweight Python library designed to simplify the development of tools that render SBOL Visual diagrams." + "github/bmorris3/aesop": { + "id": "github/bmorris3/aesop", + "title": "github/bmorris3/aesop", + "url": " https://rseng.github.io/software/repository/github/bmorris3/aesop", + "content": "ARC Echelle Spectroscopic Observation Pipeline (aesop)" }, - "github/magnusmanske/snpomatic": { - "id": "github/magnusmanske/snpomatic", - "title": "github/magnusmanske/snpomatic", - "url": " https://rseng.github.io/software/repository/github/magnusmanske/snpomatic", - "content": "fast, stringent short-read mapping software" + "github/odelaneau/shapeit5": { + "id": "github/odelaneau/shapeit5", + "title": "github/odelaneau/shapeit5", + "url": " https://rseng.github.io/software/repository/github/odelaneau/shapeit5", + "content": "Segmented HAPlotype Estimation and Imputation Tool" }, - "github/MiguelEA/nudec_BSM": { - "id": "github/MiguelEA/nudec_BSM", - "title": "github/MiguelEA/nudec_BSM", - "url": " https://rseng.github.io/software/repository/github/MiguelEA/nudec_BSM", - "content": "Neutrino Decoupling Beyond the Standard Model" + "github/odelaneau/shapeit4": { + "id": "github/odelaneau/shapeit4", + "title": "github/odelaneau/shapeit4", + "url": " https://rseng.github.io/software/repository/github/odelaneau/shapeit4", + "content": "Segmented HAPlotype Estimation and Imputation Tool" }, - "github/sieunhanbom04/support-exploration-matrix-factorization": { - "id": "github/sieunhanbom04/support-exploration-matrix-factorization", - "title": "github/sieunhanbom04/support-exploration-matrix-factorization", - "url": " https://rseng.github.io/software/repository/github/sieunhanbom04/support-exploration-matrix-factorization", - "content": "Code for the paper "Structured support exploration for multi-layer sparse matrix factorization" - ICASSP 2020" + "github/odelaneau/GLIMPSE": { + "id": "github/odelaneau/GLIMPSE", + "title": "github/odelaneau/GLIMPSE", + "url": " https://rseng.github.io/software/repository/github/odelaneau/GLIMPSE", + "content": "Low Coverage Calling of Genotypes" }, - "github/exoclime/HELA": { - "id": "github/exoclime/HELA", - "title": "github/exoclime/HELA", - "url": " https://rseng.github.io/software/repository/github/exoclime/HELA", - "content": "Random Forest retrieval for exoplanet atmospheres" + "github/FDPS/FDPS": { + "id": "github/FDPS/FDPS", + "title": "github/FDPS/FDPS", + "url": " https://rseng.github.io/software/repository/github/FDPS/FDPS", + "content": "Github repository for FDPS" }, - "github/exoclime/HELIOS-K": { - "id": "github/exoclime/HELIOS-K", - "title": "github/exoclime/HELIOS-K", - "url": " https://rseng.github.io/software/repository/github/exoclime/HELIOS-K", - "content": "Ultrafast opacity calculator for exoplanetary atmospheres." + "github/rychallener/ThERESA": { + "id": "github/rychallener/ThERESA", + "title": "github/rychallener/ThERESA", + "url": " https://rseng.github.io/software/repository/github/rychallener/ThERESA", + "content": "3D Exoplanet Cartography" }, - "github/exoclime/THOR": { - "id": "github/exoclime/THOR", - "title": "github/exoclime/THOR", - "url": " https://rseng.github.io/software/repository/github/exoclime/THOR", - "content": "Atmospheric fluid dynamics solver optimized for GPUs." + "github/JannisHoch/copro": { + "id": "github/JannisHoch/copro", + "title": "github/JannisHoch/copro", + "url": " https://rseng.github.io/software/repository/github/JannisHoch/copro", + "content": "(ML) model for computing conflict risk from climate, environmental, and societal drivers." }, - "github/exoclime/VULCAN": { - "id": "github/exoclime/VULCAN", - "title": "github/exoclime/VULCAN", - "url": " https://rseng.github.io/software/repository/github/exoclime/VULCAN", - "content": "Chemical Kinetics For Exoplanetary Atmospheres" + "github/gromacs/gromacs": { + "id": "github/gromacs/gromacs", + "title": "github/gromacs/gromacs", + "url": " https://rseng.github.io/software/repository/github/gromacs/gromacs", + "content": "Public/backup repository of the GROMACS molecular simulation toolkit. Please do not mine the metadata blindly; we use https://gitlab.com/gromacs/gromacs for code review and issue tracking." }, - "github/exoclime/Helios-r2": { - "id": "github/exoclime/Helios-r2", - "title": "github/exoclime/Helios-r2", - "url": " https://rseng.github.io/software/repository/github/exoclime/Helios-r2", - "content": "A Bayesian Nested-Sampling Retrieval Code" + "github/codidact/qpixel": { + "id": "github/codidact/qpixel", + "title": "github/codidact/qpixel", + "url": " https://rseng.github.io/software/repository/github/codidact/qpixel", + "content": "Q&A-based community knowledge-sharing software" }, - "github/exoclime/FastChem": { - "id": "github/exoclime/FastChem", - "title": "github/exoclime/FastChem", - "url": " https://rseng.github.io/software/repository/github/exoclime/FastChem", - "content": "An ultra-fast equilibrium chemistry" + "github/cschreib/egg": { + "id": "github/cschreib/egg", + "title": "github/cschreib/egg", + "url": " https://rseng.github.io/software/repository/github/cschreib/egg", + "content": "Tool to generate fake galaxy catalogs with realistic positions, morphologies and fluxes from the far-ultraviolet to the far-infrared." }, - "github/exoclime/HELIOS": { - "id": "github/exoclime/HELIOS", - "title": "github/exoclime/HELIOS", - "url": " https://rseng.github.io/software/repository/github/exoclime/HELIOS", - "content": "GPU-Accelerated Radiative Transfer Code For Exoplanetary Atmospheres" + "github/QuantEcon/QuantEcon.py": { + "id": "github/QuantEcon/QuantEcon.py", + "title": "github/QuantEcon/QuantEcon.py", + "url": " https://rseng.github.io/software/repository/github/QuantEcon/QuantEcon.py", + "content": "A community based Python library for quantitative economics" }, - "github/mommermi/photometrypipeline": { - "id": "github/mommermi/photometrypipeline", - "title": "github/mommermi/photometrypipeline", - "url": " https://rseng.github.io/software/repository/github/mommermi/photometrypipeline", - "content": "automated photometry pipeline for small to medium-sized observatories" + "github/pangeo-data/climpred": { + "id": "github/pangeo-data/climpred", + "title": "github/pangeo-data/climpred", + "url": " https://rseng.github.io/software/repository/github/pangeo-data/climpred", + "content": ":earth_americas: Verification of weather and climate forecasts. :earth_africa:" }, - "github/watts-dev/watts": { - "id": "github/watts-dev/watts", - "title": "github/watts-dev/watts", - "url": " https://rseng.github.io/software/repository/github/watts-dev/watts", - "content": "Workflow and Template Toolkit for Simulation (WATTS)" + "github/travisseymour/EPICpy": { + "id": "github/travisseymour/EPICpy", + "title": "github/travisseymour/EPICpy", + "url": " https://rseng.github.io/software/repository/github/travisseymour/EPICpy", + "content": "Cross Platform Python Interface for EPIC modeling using C++ EPIClib backend" }, - "github/creanero/locus": { - "id": "github/creanero/locus", - "title": "github/creanero/locus", - "url": " https://rseng.github.io/software/repository/github/creanero/locus", - "content": "code and script for Locus Algorithm" + "github/vsoch/gridtest": { + "id": "github/vsoch/gridtest", + "title": "github/vsoch/gridtest", + "url": " https://rseng.github.io/software/repository/github/vsoch/gridtest", + "content": "grid parameters and testing for Python modules and functions" }, - "github/Heldenkombinat/Logodetect": { - "id": "github/Heldenkombinat/Logodetect", - "title": "github/Heldenkombinat/Logodetect", - "url": " https://rseng.github.io/software/repository/github/Heldenkombinat/Logodetect", - "content": "Find logos in images and videos in just one-shot. Never be embarrassed again to say that you have a small data situation!" + "github/vsoch/citelang": { + "id": "github/vsoch/citelang", + "title": "github/vsoch/citelang", + "url": " https://rseng.github.io/software/repository/github/vsoch/citelang", + "content": "markdown syntax and credit system for software!" }, - "github/FlorianThibord/OptimiR": { - "id": "github/FlorianThibord/OptimiR", - "title": "github/FlorianThibord/OptimiR", - "url": " https://rseng.github.io/software/repository/github/FlorianThibord/OptimiR", - "content": "miRSeq data alignment workflow - integrates genetic information to assess the impact of variants on miRNA expression" + "github/SebOliver/PCA": { + "id": "github/SebOliver/PCA", + "title": "github/SebOliver/PCA", + "url": " https://rseng.github.io/software/repository/github/SebOliver/PCA", + "content": "The folders in this file are those discussed in the paper: "Principal Component Analysis and Radiative Transfer modelling of Spitzer IRS Spectra of Ultra Luminous Infrared Galaxies " Hurley et al. 2012 Monthly Notices of the Royal Astronomical Society, 424 (3). pp. 2069-2078. ISSN 0035-8711 " }, - "github/cboursnell/crb-blast": { - "id": "github/cboursnell/crb-blast", - "title": "github/cboursnell/crb-blast", - "url": " https://rseng.github.io/software/repository/github/cboursnell/crb-blast", - "content": "Conditional Reciprocal Best Blast" + "github/eaobservatory/jcmt_coadd": { + "id": "github/eaobservatory/jcmt_coadd", + "title": "github/eaobservatory/jcmt_coadd", + "url": " https://rseng.github.io/software/repository/github/eaobservatory/jcmt_coadd", + "content": "UKT14 photometry data reduction tool" }, - "github/SJ001/AI-Feynman": { - "id": "github/SJ001/AI-Feynman", - "title": "github/SJ001/AI-Feynman", - "url": " https://rseng.github.io/software/repository/github/SJ001/AI-Feynman", - "content": "None" + "github/dstansby/pfsspy": { + "id": "github/dstansby/pfsspy", + "title": "github/dstansby/pfsspy", + "url": " https://rseng.github.io/software/repository/github/dstansby/pfsspy", + "content": "Potential Field Source Surface model package for Python" }, - "github/kyleaoman/martini": { - "id": "github/kyleaoman/martini", - "title": "github/kyleaoman/martini", - "url": " https://rseng.github.io/software/repository/github/kyleaoman/martini", - "content": "Mock spatially resolved spectral line observations of simulated galaxies. Documentation:" + "github/ebmonson/2DFFTUtils-Module": { + "id": "github/ebmonson/2DFFTUtils-Module", + "title": "github/ebmonson/2DFFTUtils-Module", + "url": " https://rseng.github.io/software/repository/github/ebmonson/2DFFTUtils-Module", + "content": "A Python module implementation of some tasks associated with measuring spiral galaxy pitch angle with 2DFFT. To be merged into the 2dfft_utils repository at a later date. TODO: Rename package and repository to SpiralUtils." }, - "github/tesselle/aion": { - "id": "github/tesselle/aion", - "title": "github/tesselle/aion", - "url": " https://rseng.github.io/software/repository/github/tesselle/aion", - "content": ":stopwatch: Archaeological Time Series" + "github/cogent3/cogent3": { + "id": "github/cogent3/cogent3", + "title": "github/cogent3/cogent3", + "url": " https://rseng.github.io/software/repository/github/cogent3/cogent3", + "content": "Comparative Genomics Toolkit 3" }, - "github/SciOmicsLab/PhenoComb": { - "id": "github/SciOmicsLab/PhenoComb", - "title": "github/SciOmicsLab/PhenoComb", - "url": " https://rseng.github.io/software/repository/github/SciOmicsLab/PhenoComb", - "content": "An R package for combinatorial analysis of phenotypes" + "github/nebblu/ReACT": { + "id": "github/nebblu/ReACT", + "title": "github/nebblu/ReACT", + "url": " https://rseng.github.io/software/repository/github/nebblu/ReACT", + "content": "ReACT public repo" }, - "github/schlafly/crowdsource": { - "id": "github/schlafly/crowdsource", - "title": "github/schlafly/crowdsource", - "url": " https://rseng.github.io/software/repository/github/schlafly/crowdsource", - "content": "Crowded field photometry pipeline" + "github/hydrosolutions/riversCentralAsia": { + "id": "github/hydrosolutions/riversCentralAsia", + "title": "github/hydrosolutions/riversCentralAsia", + "url": " https://rseng.github.io/software/repository/github/hydrosolutions/riversCentralAsia", + "content": "Package with helper functions to load, manage and analyze hydrometeorological data from Central Asia" }, - "github/CIRADA-Tools/RM-Tools": { - "id": "github/CIRADA-Tools/RM-Tools", - "title": "github/CIRADA-Tools/RM-Tools", - "url": " https://rseng.github.io/software/repository/github/CIRADA-Tools/RM-Tools", - "content": "RM-synthesis, RM-clean and QU-fitting on polarised radio spectra" + "github/AlexMikes/AutoFunc": { + "id": "github/AlexMikes/AutoFunc", + "title": "github/AlexMikes/AutoFunc", + "url": " https://rseng.github.io/software/repository/github/AlexMikes/AutoFunc", + "content": "Data Mining for Automated Functional Representations" }, - "github/FSEC-Photovoltaics/pvrpm-lcoe": { - "id": "github/FSEC-Photovoltaics/pvrpm-lcoe", - "title": "github/FSEC-Photovoltaics/pvrpm-lcoe", - "url": " https://rseng.github.io/software/repository/github/FSEC-Photovoltaics/pvrpm-lcoe", - "content": "PV Simulation using SAM and Python" + "github/NLeSC/eAstroViz": { + "id": "github/NLeSC/eAstroViz", + "title": "github/NLeSC/eAstroViz", + "url": " https://rseng.github.io/software/repository/github/NLeSC/eAstroViz", + "content": "None" }, - "github/NorwegianVeterinaryInstitute/ALPPACA": { - "id": "github/NorwegianVeterinaryInstitute/ALPPACA", - "title": "github/NorwegianVeterinaryInstitute/ALPPACA", - "url": " https://rseng.github.io/software/repository/github/NorwegianVeterinaryInstitute/ALPPACA", - "content": "A tooL for Prokaryotic Phylogeny And Clustering Analysis" + "github/NLeSC/nlesc-serverless-boilerplate": { + "id": "github/NLeSC/nlesc-serverless-boilerplate", + "title": "github/NLeSC/nlesc-serverless-boilerplate", + "url": " https://rseng.github.io/software/repository/github/NLeSC/nlesc-serverless-boilerplate", + "content": "An AWS amplify boilerplate web application" }, - "github/bxia888/CEFCIG": { - "id": "github/bxia888/CEFCIG", - "title": "github/bxia888/CEFCIG", - "url": " https://rseng.github.io/software/repository/github/bxia888/CEFCIG", - "content": "CEFCIG (Computational Epigenetic Framework for Cell Identity Gene Discovery)" + "github/NLeSC/root-conda-recipes": { + "id": "github/NLeSC/root-conda-recipes", + "title": "github/NLeSC/root-conda-recipes", + "url": " https://rseng.github.io/software/repository/github/NLeSC/root-conda-recipes", + "content": "Conda recipes for building ROOT 5 and ROOT 6 binaries, root_numpy, rootpy, root_pandas, with both Python 2 and Python 3 support." }, - "github/biomed-AI/GraphBepi": { - "id": "github/biomed-AI/GraphBepi", - "title": "github/biomed-AI/GraphBepi", - "url": " https://rseng.github.io/software/repository/github/biomed-AI/GraphBepi", + "github/NLeSC/UncertaintyVisualization": { + "id": "github/NLeSC/UncertaintyVisualization", + "title": "github/NLeSC/UncertaintyVisualization", + "url": " https://rseng.github.io/software/repository/github/NLeSC/UncertaintyVisualization", "content": "None" }, - "github/djbard/ccogs": { - "id": "github/djbard/ccogs", - "title": "github/djbard/ccogs", - "url": " https://rseng.github.io/software/repository/github/djbard/ccogs", - "content": "Cosmological Calculations on GPUS. A collection of code used to perform calculations use in Cosmology studies and written for GPUs. " - }, - "github/secimTools/SECIMTools": { - "id": "github/secimTools/SECIMTools", - "title": "github/secimTools/SECIMTools", - "url": " https://rseng.github.io/software/repository/github/secimTools/SECIMTools", - "content": "A set of metabolomics tools for use in Galaxy" + "github/NLeSC/Massive-PotreeConverter": { + "id": "github/NLeSC/Massive-PotreeConverter", + "title": "github/NLeSC/Massive-PotreeConverter", + "url": " https://rseng.github.io/software/repository/github/NLeSC/Massive-PotreeConverter", + "content": "Convert massive pointcloud, for example ahn2 (640 Billion points) to potree format." }, - "github/pwry/lextes": { - "id": "github/pwry/lextes", - "title": "github/pwry/lextes", - "url": " https://rseng.github.io/software/repository/github/pwry/lextes", - "content": "PDF link scraper/tester for Schroedinger's Code paper" + "github/NLeSC/Chemical-Analytics-Platform": { + "id": "github/NLeSC/Chemical-Analytics-Platform", + "title": "github/NLeSC/Chemical-Analytics-Platform", + "url": " https://rseng.github.io/software/repository/github/NLeSC/Chemical-Analytics-Platform", + "content": "Scripts to create chemical analytics platform based on Knime" }, - "github/SMTG-UCL/surfaxe": { - "id": "github/SMTG-UCL/surfaxe", - "title": "github/SMTG-UCL/surfaxe", - "url": " https://rseng.github.io/software/repository/github/SMTG-UCL/surfaxe", - "content": "Dealing with slabs for first principles calculations of surfaces" + "github/NLeSC/eEcology-script-wrapper": { + "id": "github/NLeSC/eEcology-script-wrapper", + "title": "github/NLeSC/eEcology-script-wrapper", + "url": " https://rseng.github.io/software/repository/github/NLeSC/eEcology-script-wrapper", + "content": "Web application to make Matlab, R scripts available." }, - "github/SMTG-UCL/ShakeNBreak": { - "id": "github/SMTG-UCL/ShakeNBreak", - "title": "github/SMTG-UCL/ShakeNBreak", - "url": " https://rseng.github.io/software/repository/github/SMTG-UCL/ShakeNBreak", - "content": "Defect structure-searching method employing chemically-guided bond distortions to locate ground-state and metastable structures of point defects in solid materials." + "github/NLeSC/PattyData": { + "id": "github/NLeSC/PattyData", + "title": "github/NLeSC/PattyData", + "url": " https://rseng.github.io/software/repository/github/NLeSC/PattyData", + "content": "None" }, - "github/spacetx/starfish": { - "id": "github/spacetx/starfish", - "title": "github/spacetx/starfish", - "url": " https://rseng.github.io/software/repository/github/spacetx/starfish", - "content": "starfish: unified pipelines for image-based transcriptomics" + "github/NLeSC/noodles": { + "id": "github/NLeSC/noodles", + "title": "github/NLeSC/noodles", + "url": " https://rseng.github.io/software/repository/github/NLeSC/noodles", + "content": "Computational workflow engine, making distributed computing in Python easy!" }, - "github/phylo42/RAPPAS": { - "id": "github/phylo42/RAPPAS", - "title": "github/phylo42/RAPPAS", - "url": " https://rseng.github.io/software/repository/github/phylo42/RAPPAS", - "content": "Rapid, Alignment-free, Phylogenetic Placement via Ancestral Sequences" + "github/NLeSC/SalientDescriptor-matlab": { + "id": "github/NLeSC/SalientDescriptor-matlab", + "title": "github/NLeSC/SalientDescriptor-matlab", + "url": " https://rseng.github.io/software/repository/github/NLeSC/SalientDescriptor-matlab", + "content": "None" }, - "github/PacificBiosciences/pbcore": { - "id": "github/PacificBiosciences/pbcore", - "title": "github/PacificBiosciences/pbcore", - "url": " https://rseng.github.io/software/repository/github/PacificBiosciences/pbcore", - "content": "A Python library for reading and writing PacBio® data files" + "github/NLeSC/spot": { + "id": "github/NLeSC/spot", + "title": "github/NLeSC/spot", + "url": " https://rseng.github.io/software/repository/github/NLeSC/spot", + "content": "Try the demo" }, - "github/PacificBiosciences/pbalign": { - "id": "github/PacificBiosciences/pbalign", - "title": "github/PacificBiosciences/pbalign", - "url": " https://rseng.github.io/software/repository/github/PacificBiosciences/pbalign", - "content": "pbalign aligns PacBio reads to reference sequences, filters aligned reads according to user-specific filtering criteria, and converts the output to either the SAM format or PacBio Compare HDF5 (e.g., .cmp.h5) format. The output Compare HDF5 file will be compatible with Quiver if --forQuiver option is specified." + "github/NLeSC/xtas": { + "id": "github/NLeSC/xtas", + "title": "github/NLeSC/xtas", + "url": " https://rseng.github.io/software/repository/github/NLeSC/xtas", + "content": "Distributed text analysis suite based on Celery" }, - "github/PacificBiosciences/IsoSeq": { - "id": "github/PacificBiosciences/IsoSeq", - "title": "github/PacificBiosciences/IsoSeq", - "url": " https://rseng.github.io/software/repository/github/PacificBiosciences/IsoSeq", - "content": "IsoSeq3 - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads" + "github/NLeSC/xenon-cli": { + "id": "github/NLeSC/xenon-cli", + "title": "github/NLeSC/xenon-cli", + "url": " https://rseng.github.io/software/repository/github/NLeSC/xenon-cli", + "content": "Perform files and jobs operations with Xenon library from command line" }, - "github/PacificBiosciences/pbbioconda": { - "id": "github/PacificBiosciences/pbbioconda", - "title": "github/PacificBiosciences/pbbioconda", - "url": " https://rseng.github.io/software/repository/github/PacificBiosciences/pbbioconda", - "content": "PacBio Secondary Analysis Tools on Bioconda" + "github/NLeSC/esibayes": { + "id": "github/NLeSC/esibayes", + "title": "github/NLeSC/esibayes", + "url": " https://rseng.github.io/software/repository/github/NLeSC/esibayes", + "content": "Optimization and state estimation of dynamic models" }, - "github/PacificBiosciences/FALCON": { - "id": "github/PacificBiosciences/FALCON", - "title": "github/PacificBiosciences/FALCON", - "url": " https://rseng.github.io/software/repository/github/PacificBiosciences/FALCON", - "content": "FALCON: experimental PacBio diploid assembler -- Out-of-date -- Please use a binary release: https://github.com/PacificBiosciences/FALCON_unzip/wiki/Binaries" + "github/NLeSC/EEG-epilepsy-diagnosis": { + "id": "github/NLeSC/EEG-epilepsy-diagnosis", + "title": "github/NLeSC/EEG-epilepsy-diagnosis", + "url": " https://rseng.github.io/software/repository/github/NLeSC/EEG-epilepsy-diagnosis", + "content": "Detection of Epilepsy from EEG data (14 channel x 5 minutes)" }, - "github/PacificBiosciences/kineticsTools": { - "id": "github/PacificBiosciences/kineticsTools", - "title": "github/PacificBiosciences/kineticsTools", - "url": " https://rseng.github.io/software/repository/github/PacificBiosciences/kineticsTools", - "content": "Tools for detecting DNA modifications from single molecule, real-time sequencing data" + "github/NLeSC/ExtJS-DateTime": { + "id": "github/NLeSC/ExtJS-DateTime", + "title": "github/NLeSC/ExtJS-DateTime", + "url": " https://rseng.github.io/software/repository/github/NLeSC/ExtJS-DateTime", + "content": "DateTime input field for Ext JS" }, - "github/PacificBiosciences/minorseq": { - "id": "github/PacificBiosciences/minorseq", - "title": "github/PacificBiosciences/minorseq", - "url": " https://rseng.github.io/software/repository/github/PacificBiosciences/minorseq", - "content": "Minor Variant Calling and Phasing Tools" + "github/NLeSC/pattyvis": { + "id": "github/NLeSC/pattyvis", + "title": "github/NLeSC/pattyvis", + "url": " https://rseng.github.io/software/repository/github/NLeSC/pattyvis", + "content": "Webgl pointcloud visualization of the Via Appia based on potree" }, - "github/PacificBiosciences/pbmm2": { - "id": "github/PacificBiosciences/pbmm2", - "title": "github/PacificBiosciences/pbmm2", - "url": " https://rseng.github.io/software/repository/github/PacificBiosciences/pbmm2", - "content": "A minimap2 frontend for PacBio native data formats" + "github/NLeSC/eEcology-Annotation-WS": { + "id": "github/NLeSC/eEcology-Annotation-WS", + "title": "github/NLeSC/eEcology-Annotation-WS", + "url": " https://rseng.github.io/software/repository/github/NLeSC/eEcology-Annotation-WS", + "content": "Webservice for eEcology Annotation project." }, - "github/PacificBiosciences/pbcopper": { - "id": "github/PacificBiosciences/pbcopper", - "title": "github/PacificBiosciences/pbcopper", - "url": " https://rseng.github.io/software/repository/github/PacificBiosciences/pbcopper", - "content": "Core C++ library for data structures, algorithms, and utilities" + "github/NLeSC/boatswain": { + "id": "github/NLeSC/boatswain", + "title": "github/NLeSC/boatswain", + "url": " https://rseng.github.io/software/repository/github/NLeSC/boatswain", + "content": "A simple build system for docker images" }, - "github/PacificBiosciences/blasr": { - "id": "github/PacificBiosciences/blasr", - "title": "github/PacificBiosciences/blasr", - "url": " https://rseng.github.io/software/repository/github/PacificBiosciences/blasr", - "content": "BLASR (Basic Local Alignment with Successive Refinement) maps Single Molecule Sequencing (SMS) reads that are thousands of bases long, with divergence between the read and genome dominated by insertion and deletion error." + "github/NLeSC/PattyAnalytics": { + "id": "github/NLeSC/PattyAnalytics", + "title": "github/NLeSC/PattyAnalytics", + "url": " https://rseng.github.io/software/repository/github/NLeSC/PattyAnalytics", + "content": "Reusable point cloud analytics software. Includes segmentation, registration, file format conversion. " }, - "github/PacificBiosciences/pbbam": { - "id": "github/PacificBiosciences/pbbam", - "title": "github/PacificBiosciences/pbbam", - "url": " https://rseng.github.io/software/repository/github/PacificBiosciences/pbbam", - "content": "PacBio BAM C++ library" + "github/NLeSC/compressing-the-sky": { + "id": "github/NLeSC/compressing-the-sky", + "title": "github/NLeSC/compressing-the-sky", + "url": " https://rseng.github.io/software/repository/github/NLeSC/compressing-the-sky", + "content": "Compressing the Sky project with CWI DA" }, - "github/lsds/faasm": { - "id": "github/lsds/faasm", - "title": "github/lsds/faasm", - "url": " https://rseng.github.io/software/repository/github/lsds/faasm", - "content": "High-performance stateful serverless runtime based on WebAssembly" + "github/NLeSC/xenon-flow": { + "id": "github/NLeSC/xenon-flow", + "title": "github/NLeSC/xenon-flow", + "url": " https://rseng.github.io/software/repository/github/NLeSC/xenon-flow", + "content": "Run CWL workflows using Xenon" }, - "github/lsds/SEEP": { - "id": "github/lsds/SEEP", - "title": "github/lsds/SEEP", - "url": " https://rseng.github.io/software/repository/github/lsds/SEEP", - "content": "Cluster computing using Stateful Dataflow Graphs" + "github/NLeSC/ShiCo": { + "id": "github/NLeSC/ShiCo", + "title": "github/NLeSC/ShiCo", + "url": " https://rseng.github.io/software/repository/github/NLeSC/ShiCo", + "content": "Netherlands eScience Center - Shifting Concepts Through Time project" }, - "github/lsds/TaLoS": { - "id": "github/lsds/TaLoS", - "title": "github/lsds/TaLoS", - "url": " https://rseng.github.io/software/repository/github/lsds/TaLoS", - "content": "Efficient TLS termination inside Intel SGX enclaves for existing applications" + "github/NLeSC/MAGMa": { + "id": "github/NLeSC/MAGMa", + "title": "github/NLeSC/MAGMa", + "url": " https://rseng.github.io/software/repository/github/NLeSC/MAGMa", + "content": "eMetabolomics project: Mass Annotation based on in silico Generated Metabolites" }, - "github/lsds/KungFu": { - "id": "github/lsds/KungFu", - "title": "github/lsds/KungFu", - "url": " https://rseng.github.io/software/repository/github/lsds/KungFu", - "content": "Fast and Adaptive Distributed Machine Learning for TensorFlow, PyTorch and MindSpore." + "github/NLeSC/case-law-app": { + "id": "github/NLeSC/case-law-app", + "title": "github/NLeSC/case-law-app", + "url": " https://rseng.github.io/software/repository/github/NLeSC/case-law-app", + "content": "None" }, - "github/lsds/Neptune": { - "id": "github/lsds/Neptune", - "title": "github/lsds/Neptune", - "url": " https://rseng.github.io/software/repository/github/lsds/Neptune", - "content": "Neptune Execution Framework for Stream/Batch Spark Applications" + "github/NLeSC/hadrianus-scripts": { + "id": "github/NLeSC/hadrianus-scripts", + "title": "github/NLeSC/hadrianus-scripts", + "url": " https://rseng.github.io/software/repository/github/NLeSC/hadrianus-scripts", + "content": "Scripts used for the Hadrianus project" }, - "github/lsds/Teechain": { - "id": "github/lsds/Teechain", - "title": "github/lsds/Teechain", - "url": " https://rseng.github.io/software/repository/github/lsds/Teechain", - "content": "Teechain: A Secure Payment Network with Asynchronous Blockchain Access" + "github/NLeSC/structure-from-motion": { + "id": "github/NLeSC/structure-from-motion", + "title": "github/NLeSC/structure-from-motion", + "url": " https://rseng.github.io/software/repository/github/NLeSC/structure-from-motion", + "content": "Structure from Motion Pipeline" }, - "github/lsds/sgx-lkl": { - "id": "github/lsds/sgx-lkl", - "title": "github/lsds/sgx-lkl", - "url": " https://rseng.github.io/software/repository/github/lsds/sgx-lkl", - "content": "SGX-LKL Library OS for running Linux applications inside of Intel SGX enclaves" + "github/NLeSC/ahn-pointcloud-viewer-ws": { + "id": "github/NLeSC/ahn-pointcloud-viewer-ws", + "title": "github/NLeSC/ahn-pointcloud-viewer-ws", + "url": " https://rseng.github.io/software/repository/github/NLeSC/ahn-pointcloud-viewer-ws", + "content": "Webservice for ahn pointcloud viewer" }, - "github/lsds/Saber": { - "id": "github/lsds/Saber", - "title": "github/lsds/Saber", - "url": " https://rseng.github.io/software/repository/github/lsds/Saber", - "content": "Window-Based Hybrid CPU/GPU Stream Processing Engine" + "github/NLeSC/eEcology-SMS-reciever": { + "id": "github/NLeSC/eEcology-SMS-reciever", + "title": "github/NLeSC/eEcology-SMS-reciever", + "url": " https://rseng.github.io/software/repository/github/NLeSC/eEcology-SMS-reciever", + "content": "Webservice to store SMS messages into a database table" }, - "github/lsds/LightSaber": { - "id": "github/lsds/LightSaber", - "title": "github/lsds/LightSaber", - "url": " https://rseng.github.io/software/repository/github/lsds/LightSaber", - "content": "Multi-core Window-Based Stream Processing Engine" + "github/NLeSC/python-pcl": { + "id": "github/NLeSC/python-pcl", + "title": "github/NLeSC/python-pcl", + "url": " https://rseng.github.io/software/repository/github/NLeSC/python-pcl", + "content": "Python bindings to the pointcloud library (pcl)" }, - "github/lsds/Crossbow": { - "id": "github/lsds/Crossbow", - "title": "github/lsds/Crossbow", - "url": " https://rseng.github.io/software/repository/github/lsds/Crossbow", - "content": "Crossbow: A Multi-GPU Deep Learning System for Training with Small Batch Sizes" + "github/NLeSC/DiVE": { + "id": "github/NLeSC/DiVE", + "title": "github/NLeSC/DiVE", + "url": " https://rseng.github.io/software/repository/github/NLeSC/DiVE", + "content": "An interactive 3D web viewer of up to million points on one screen that represent data. Provides interaction for viewing high-dimensional data that has been previously embedded in 3D or 2D. Based on graphosaurus.js and three.js. For a Linux release of a complete embedding+visualization pipeline please visit https://github.com/sonjageorgievska/Embed-Dive." }, - "github/parsotat/batanalysis": { - "id": "github/parsotat/batanalysis", - "title": "github/parsotat/batanalysis", - "url": " https://rseng.github.io/software/repository/github/parsotat/batanalysis", - "content": "A python HEASOFT wrapper for processing Swift-BAT data." + "github/NLeSC/litstudy": { + "id": "github/NLeSC/litstudy", + "title": "github/NLeSC/litstudy", + "url": " https://rseng.github.io/software/repository/github/NLeSC/litstudy", + "content": "Using the power of Python and Jupyter notebooks to automate analysis of scientific literature" }, - "github/oliverphilcox/OneLoopBispectrum": { - "id": "github/oliverphilcox/OneLoopBispectrum", - "title": "github/oliverphilcox/OneLoopBispectrum", - "url": " https://rseng.github.io/software/repository/github/oliverphilcox/OneLoopBispectrum", - "content": "Computation of the one-loop bispectrum of galaxies in redshift space" + "github/NLeSC/lokum": { + "id": "github/NLeSC/lokum", + "title": "github/NLeSC/lokum", + "url": " https://rseng.github.io/software/repository/github/NLeSC/lokum", + "content": "Deploy GlusterFS, Docker, Spark and JupyterHub services on bare-metal cluster." + }, + "github/NLeSC/docker-couch-admin": { + "id": "github/NLeSC/docker-couch-admin", + "title": "github/NLeSC/docker-couch-admin", + "url": " https://rseng.github.io/software/repository/github/NLeSC/docker-couch-admin", + "content": "Configures a web service using angular-schema-form and CouchDB" }, - "github/oliverphilcox/HIPSTER": { - "id": "github/oliverphilcox/HIPSTER", - "title": "github/oliverphilcox/HIPSTER", - "url": " https://rseng.github.io/software/repository/github/oliverphilcox/HIPSTER", - "content": "HIPSTER: HIgh-k Power SpecTrum and bispectrum EstimatoR" + "github/NLeSC/osmium": { + "id": "github/NLeSC/osmium", + "title": "github/NLeSC/osmium", + "url": " https://rseng.github.io/software/repository/github/NLeSC/osmium", + "content": "Xenon Job Webservice" }, - "github/oliverphilcox/PolyBin": { - "id": "github/oliverphilcox/PolyBin", - "title": "github/oliverphilcox/PolyBin", - "url": " https://rseng.github.io/software/repository/github/oliverphilcox/PolyBin", - "content": "Binned polyspectrum estimation on the full sky, optionally polarized and mask-deconvolved" + "github/NLeSC/baklava": { + "id": "github/NLeSC/baklava", + "title": "github/NLeSC/baklava", + "url": " https://rseng.github.io/software/repository/github/NLeSC/baklava", + "content": "Deploy a Kubernetes cluster and big data services on the cloud." }, - "github/oliverphilcox/HADES": { - "id": "github/oliverphilcox/HADES", - "title": "github/oliverphilcox/HADES", - "url": " https://rseng.github.io/software/repository/github/oliverphilcox/HADES", - "content": "A Hexadecapolar Analysis for Dust Estimation in Simulations (of CMB B-mode thermal dust emission)" + "github/NLeSC/pycoeman": { + "id": "github/NLeSC/pycoeman", + "title": "github/NLeSC/pycoeman", + "url": " https://rseng.github.io/software/repository/github/NLeSC/pycoeman", + "content": "Python Commands Execution Manager" }, - "github/oliverphilcox/RascalC": { - "id": "github/oliverphilcox/RascalC", - "title": "github/oliverphilcox/RascalC", - "url": " https://rseng.github.io/software/repository/github/oliverphilcox/RascalC", - "content": "RascalC: A Fast Code for Galaxy Covariance Matrix Estimation" + "github/NLeSC/python-template": { + "id": "github/NLeSC/python-template", + "title": "github/NLeSC/python-template", + "url": " https://rseng.github.io/software/repository/github/NLeSC/python-template", + "content": "Netherlands eScience Center Python Template" }, - "github/oliverphilcox/encore": { - "id": "github/oliverphilcox/encore", - "title": "github/oliverphilcox/encore", - "url": " https://rseng.github.io/software/repository/github/oliverphilcox/encore", - "content": "encore: Efficient isotropic 2-, 3-, 4-, 5- and 6-point correlation functions in C++ and CUDA" + "github/NLeSC/fairdatapoint": { + "id": "github/NLeSC/fairdatapoint", + "title": "github/NLeSC/fairdatapoint", + "url": " https://rseng.github.io/software/repository/github/NLeSC/fairdatapoint", + "content": "Provide machine-readable descriptions of your data assets" }, - "github/oliverphilcox/Spectra-Without-Windows": { - "id": "github/oliverphilcox/Spectra-Without-Windows", - "title": "github/oliverphilcox/Spectra-Without-Windows", - "url": " https://rseng.github.io/software/repository/github/oliverphilcox/Spectra-Without-Windows", - "content": "Estimators and data for window-free analysis of power spectra and bispectra" + "github/NLeSC/xenon-grpc": { + "id": "github/NLeSC/xenon-grpc", + "title": "github/NLeSC/xenon-grpc", + "url": " https://rseng.github.io/software/repository/github/NLeSC/xenon-grpc", + "content": "Xenon grpc based server" }, - "github/oliverphilcox/Keplers-Goat-Herd": { - "id": "github/oliverphilcox/Keplers-Goat-Herd", - "title": "github/oliverphilcox/Keplers-Goat-Herd", - "url": " https://rseng.github.io/software/repository/github/oliverphilcox/Keplers-Goat-Herd", - "content": "Solving Kepler's equation via contour integration, implemented in C++" + "github/NLeSC/SalientDetector-python": { + "id": "github/NLeSC/SalientDetector-python", + "title": "github/NLeSC/SalientDetector-python", + "url": " https://rseng.github.io/software/repository/github/NLeSC/SalientDetector-python", + "content": "Python package for Large Scale Imaging research @ NLeSC" }, - "github/Onogi/VIGoR": { - "id": "github/Onogi/VIGoR", - "title": "github/Onogi/VIGoR", - "url": " https://rseng.github.io/software/repository/github/Onogi/VIGoR", - "content": "Variational Bayesian Inference for Genome-Wide Regression" + "github/NLeSC/eEcology-Classification": { + "id": "github/NLeSC/eEcology-Classification", + "title": "github/NLeSC/eEcology-Classification", + "url": " https://rseng.github.io/software/repository/github/NLeSC/eEcology-Classification", + "content": "Classification tool" }, - "github/barbagroup/geoclaw-landspill": { - "id": "github/barbagroup/geoclaw-landspill", - "title": "github/barbagroup/geoclaw-landspill", - "url": " https://rseng.github.io/software/repository/github/barbagroup/geoclaw-landspill", - "content": "An oil land-spill and overland flow simulator for pipeline rupture events" + "github/NLeSC/SalientDetector-matlab": { + "id": "github/NLeSC/SalientDetector-matlab", + "title": "github/NLeSC/SalientDetector-matlab", + "url": " https://rseng.github.io/software/repository/github/NLeSC/SalientDetector-matlab", + "content": "MATLAB Software for Large Scale Imaging research @ NLeSc" }, - "github/peikuan/WBBC": { - "id": "github/peikuan/WBBC", - "title": "github/peikuan/WBBC", - "url": " https://rseng.github.io/software/repository/github/peikuan/WBBC", - "content": "Westlake BioBank for Chinese pilot project" + "github/NLeSC/mcfly": { + "id": "github/NLeSC/mcfly", + "title": "github/NLeSC/mcfly", + "url": " https://rseng.github.io/software/repository/github/NLeSC/mcfly", + "content": "A deep learning tool for time series classification" }, - "github/BradGreig/21CMMC": { - "id": "github/BradGreig/21CMMC", - "title": "github/BradGreig/21CMMC", - "url": " https://rseng.github.io/software/repository/github/BradGreig/21CMMC", - "content": "A parallelised, Monte Carlo Markov Chain analysis tool for the epoch of reionisation (EoR)" + "github/NLeSC/cptm": { + "id": "github/NLeSC/cptm", + "title": "github/NLeSC/cptm", + "url": " https://rseng.github.io/software/repository/github/NLeSC/cptm", + "content": "Cross-Perspective Topic Modeling" }, - "github/philres/catfishq": { - "id": "github/philres/catfishq", - "title": "github/philres/catfishq", - "url": " https://rseng.github.io/software/repository/github/philres/catfishq", - "content": "Cat FASTQ files" + "github/NLeSC/OCTSegmentation": { + "id": "github/NLeSC/OCTSegmentation", + "title": "github/NLeSC/OCTSegmentation", + "url": " https://rseng.github.io/software/repository/github/NLeSC/OCTSegmentation", + "content": "EYR4-OCTSEG " }, - "github/philres/ngmlr": { - "id": "github/philres/ngmlr", - 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In a nutshell, this code allows to fit user-defined models onto a set of multi-wavelength data, making use of spatial information and upper-limits with a consistent treatment. The code is highly flexible to allow its use for sources with complex structures." + "github/era-urban/wrfpy": { + "id": "github/era-urban/wrfpy", + "title": "github/era-urban/wrfpy", + "url": " https://rseng.github.io/software/repository/github/era-urban/wrfpy", + "content": "None" }, - "github/LindleyLentati/Cobra": { - "id": "github/LindleyLentati/Cobra", - "title": "github/LindleyLentati/Cobra", - "url": " https://rseng.github.io/software/repository/github/LindleyLentati/Cobra", - "content": "Bayesian Pulsar Searching" + "github/cosimameyer/overviewR": { + "id": "github/cosimameyer/overviewR", + "title": "github/cosimameyer/overviewR", + "url": " https://rseng.github.io/software/repository/github/cosimameyer/overviewR", + "content": "Easily Extracting Information About Your Data" }, - "github/songweizhi/Binning_refiner": { - "id": "github/songweizhi/Binning_refiner", - "title": "github/songweizhi/Binning_refiner", - "url": " https://rseng.github.io/software/repository/github/songweizhi/Binning_refiner", - "content": "Improving genome bins through the combination of different binning programs " + "github/phenology/cgc": { + "id": "github/phenology/cgc", + "title": "github/phenology/cgc", + "url": " https://rseng.github.io/software/repository/github/phenology/cgc", + "content": "A clustering tool for geospatial applications" }, - "github/ICRAR/shark": { - "id": "github/ICRAR/shark", - "title": "github/ICRAR/shark", - "url": " https://rseng.github.io/software/repository/github/ICRAR/shark", - "content": "None" + "github/julia-wrobel/registr": { + "id": "github/julia-wrobel/registr", + "title": "github/julia-wrobel/registr", + "url": " https://rseng.github.io/software/repository/github/julia-wrobel/registr", + "content": "Register exponential family curves" }, - "github/ICRAR/ProFit": { - "id": "github/ICRAR/ProFit", - "title": "github/ICRAR/ProFit", - "url": " https://rseng.github.io/software/repository/github/ICRAR/ProFit", - "content": "ProFit is a galaxy image bulge-disk decomposition program" + "github/faircloth-lab/phyluce": { + "id": "github/faircloth-lab/phyluce", + "title": "github/faircloth-lab/phyluce", + "url": " https://rseng.github.io/software/repository/github/faircloth-lab/phyluce", + "content": "software for UCE (and general) phylogenomics" }, - "github/ICRAR/libprofit": { - "id": "github/ICRAR/libprofit", - "title": "github/ICRAR/libprofit", - "url": " https://rseng.github.io/software/repository/github/ICRAR/libprofit", - "content": "A C++ library that produces images based on different luminosity profiles" + "github/icecube/toise": { + "id": "github/icecube/toise", + "title": "github/icecube/toise", + "url": " https://rseng.github.io/software/repository/github/icecube/toise", + "content": "Framework to describe the performance of high-energy neutrino detectors" }, - "github/teoxxx/nemiss_proper": { - "id": "github/teoxxx/nemiss_proper", - "title": "github/teoxxx/nemiss_proper", - "url": " https://rseng.github.io/software/repository/github/teoxxx/nemiss_proper", - "content": "nemiss code repo 2023" + "github/icecube/TauRunner": { + "id": "github/icecube/TauRunner", + "title": "github/icecube/TauRunner", + "url": " https://rseng.github.io/software/repository/github/icecube/TauRunner", + "content": "Code to propagate tau neutrinos at very high energies" }, - "github/teoxxx/rlos": { - "id": "github/teoxxx/rlos", - "title": "github/teoxxx/rlos", - "url": " https://rseng.github.io/software/repository/github/teoxxx/rlos", - "content": "RLOS Relativistic Line of Sight, time-resolved imaging of model astrophysical jets" + "github/icecube/FIRESONG": { + "id": "github/icecube/FIRESONG", + "title": "github/icecube/FIRESONG", + "url": " https://rseng.github.io/software/repository/github/icecube/FIRESONG", + "content": "FIRst Extragalactic Simulation Of Neutrino and Gamma-ray" }, - "github/teoxxx/nemiss_pbl": { - "id": "github/teoxxx/nemiss_pbl", - "title": "github/teoxxx/nemiss_pbl", - "url": " https://rseng.github.io/software/repository/github/teoxxx/nemiss_pbl", - "content": "nemiss neutrino emission from hydrocode data describing a simulated stellar binary system" + "github/ratschlab/metagraph": { + "id": "github/ratschlab/metagraph", + "title": "github/ratschlab/metagraph", + "url": " https://rseng.github.io/software/repository/github/ratschlab/metagraph", + "content": "Scalable annotated de Bruijn graphs for DNA indexing, alignment, and assembly" }, - 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This tool can be used to detect viral infectious diseases, like COVID-19." + "github/EISy-as-Py/hardy": { + "id": "github/EISy-as-Py/hardy", + "title": "github/EISy-as-Py/hardy", + "url": " https://rseng.github.io/software/repository/github/EISy-as-Py/hardy", + "content": "Handling Arbitrary Recognition of Data! y not?" }, - "github/rhyspoulton/WhereWolf": { - "id": "github/rhyspoulton/WhereWolf", - "title": "github/rhyspoulton/WhereWolf", - "url": " https://rseng.github.io/software/repository/github/rhyspoulton/WhereWolf", - "content": "Galaxy/(sub)Halo ghosting tool for N-body simulations" + "github/hpparvi/PyTransit": { + "id": "github/hpparvi/PyTransit", + "title": "github/hpparvi/PyTransit", + "url": " https://rseng.github.io/software/repository/github/hpparvi/PyTransit", + "content": "Fast and easy exoplanet transit light curve modelling." + }, + "github/hpparvi/opents": { + "id": "github/hpparvi/opents", + "title": "github/hpparvi/opents", + "url": " https://rseng.github.io/software/repository/github/hpparvi/opents", + "content": "Open exoplanet transit search pipeline" }, - "github/rhyspoulton/OrbWeaver": { - "id": "github/rhyspoulton/OrbWeaver", - "title": "github/rhyspoulton/OrbWeaver", - "url": " https://rseng.github.io/software/repository/github/rhyspoulton/OrbWeaver", - "content": "Galaxy/(sub)halo orbital processing tool" + "github/hpparvi/ldtk": { + "id": "github/hpparvi/ldtk", + "title": "github/hpparvi/ldtk", + "url": " https://rseng.github.io/software/repository/github/hpparvi/ldtk", + "content": "Python toolkit for calculating stellar limb darkening profiles and model-specific coefficients using the stellar atmosphere spectrum library by Husser et al. (2013). Described in Parviainen & Aigrain, MNRAS 453, 3821–3826 (2015)." }, - "github/Shamir-Lab/domino_web": { - "id": "github/Shamir-Lab/domino_web", - "title": "github/Shamir-Lab/domino_web", - "url": " https://rseng.github.io/software/repository/github/Shamir-Lab/domino_web", - "content": "None" + "github/hpparvi/MuSCAT2_transit_pipeline": { + "id": "github/hpparvi/MuSCAT2_transit_pipeline", + "title": "github/hpparvi/MuSCAT2_transit_pipeline", + "url": " https://rseng.github.io/software/repository/github/hpparvi/MuSCAT2_transit_pipeline", + "content": "MuSCAT2 transit analysis pipeline" }, - "github/tool-bin/ukbcc": { - "id": "github/tool-bin/ukbcc", - "title": "github/tool-bin/ukbcc", - "url": " https://rseng.github.io/software/repository/github/tool-bin/ukbcc", - "content": "UKBB Cohort Curator. " + "github/pyvisa/pyvisa": { + "id": "github/pyvisa/pyvisa", + "title": "github/pyvisa/pyvisa", + "url": " https://rseng.github.io/software/repository/github/pyvisa/pyvisa", + "content": "A Python package with bindings to the "Virtual Instrument Software Architecture" VISA library, in order to control measurement devices and test equipment via GPIB, RS232, or USB." }, - "github/rasg-affiliates/healvis": { - "id": "github/rasg-affiliates/healvis", - "title": "github/rasg-affiliates/healvis", - "url": " https://rseng.github.io/software/repository/github/rasg-affiliates/healvis", - "content": "Visibility simulation off of HEALPix shells." + "github/franpoz/SHERLOCK": { + "id": "github/franpoz/SHERLOCK", + "title": "github/franpoz/SHERLOCK", + "url": " https://rseng.github.io/software/repository/github/franpoz/SHERLOCK", + "content": "Easy and versatile open-source code to explore Kepler, K2 and TESS data in the search for exoplanets" }, - "github/cgobat/asymmetric_uncertainty": { - "id": "github/cgobat/asymmetric_uncertainty", - "title": "github/cgobat/asymmetric_uncertainty", - "url": " https://rseng.github.io/software/repository/github/cgobat/asymmetric_uncertainty", - "content": "A package that implements a class to represent numeric quantities with asymmetric uncertainties." + "github/Zafiirah13/meercrab": { + "id": "github/Zafiirah13/meercrab", + "title": "github/Zafiirah13/meercrab", + "url": " https://rseng.github.io/software/repository/github/Zafiirah13/meercrab", + "content": "MeerLICHT Classification of Real And Bogus using deep learning" }, - "github/cpinte/mcfost": { - "id": "github/cpinte/mcfost", - "title": "github/cpinte/mcfost", - "url": " https://rseng.github.io/software/repository/github/cpinte/mcfost", - "content": "MCFOST radiative transfer code" + "github/nhejazi/txshift": { + "id": "github/nhejazi/txshift", + "title": "github/nhejazi/txshift", + "url": " https://rseng.github.io/software/repository/github/nhejazi/txshift", + "content": ":package: :game_die: R/txshift: Efficient Estimation of the Causal Effects of Stochastic Interventions, with Two-Phase Sampling Corrections" }, - 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First cluster_identifier is used to generate soft-clipped read cluster consensus sequences. 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Largely based on the IDL software "VIEW" developed by Giovanni Galizia. Implemented in Python by Ajayrama Kumaraswamy" }, - "github/rajewsky-lab/novosparc": { - "id": "github/rajewsky-lab/novosparc", - "title": "github/rajewsky-lab/novosparc", - "url": " https://rseng.github.io/software/repository/github/rajewsky-lab/novosparc", - "content": "None" + "github/OSeMOSYS/otoole": { + "id": "github/OSeMOSYS/otoole", + "title": "github/OSeMOSYS/otoole", + "url": " https://rseng.github.io/software/repository/github/OSeMOSYS/otoole", + "content": "OSeMOSYS Tools for Energy" }, - "github/rajewsky-lab/spacemake": { - "id": "github/rajewsky-lab/spacemake", - "title": "github/rajewsky-lab/spacemake", - "url": " https://rseng.github.io/software/repository/github/rajewsky-lab/spacemake", + "github/CoolWorlds/exoinformatics": { + "id": "github/CoolWorlds/exoinformatics", + "title": "github/CoolWorlds/exoinformatics", + "url": " https://rseng.github.io/software/repository/github/CoolWorlds/exoinformatics", "content": "None" }, - "github/tofflemire/saphires": { - "id": "github/tofflemire/saphires", - "title": "github/tofflemire/saphires", - "url": " https://rseng.github.io/software/repository/github/tofflemire/saphires", - "content": "Analysis tools for stellar spectroscopy" + "github/CoolWorlds/ExoPriors": { + "id": "github/CoolWorlds/ExoPriors", + "title": "github/CoolWorlds/ExoPriors", + "url": " https://rseng.github.io/software/repository/github/CoolWorlds/ExoPriors", + "content": "Calculate log-likelihood penalties to account for observational bias in exoplanet detection." }, - "github/conda/pycosat": { - "id": "github/conda/pycosat", - "title": "github/conda/pycosat", - "url": " https://rseng.github.io/software/repository/github/conda/pycosat", - "content": "Python bindings to picosat (a SAT solver)" + "github/sagepublishing/rejected_article_tracker_pkg": { + "id": "github/sagepublishing/rejected_article_tracker_pkg", + "title": "github/sagepublishing/rejected_article_tracker_pkg", + "url": " https://rseng.github.io/software/repository/github/sagepublishing/rejected_article_tracker_pkg", + "content": "None" }, - 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"github/ajosephy/Clustering": { - "id": "github/ajosephy/Clustering", - "title": "github/ajosephy/Clustering", - "url": " https://rseng.github.io/software/repository/github/ajosephy/Clustering", - "content": "Modified RRATrap + new DBSCAN codes to cluster single pulse events." + "github/amiralih/MembraneAnalysis.jl": { + "id": "github/amiralih/MembraneAnalysis.jl", + "title": "github/amiralih/MembraneAnalysis.jl", + "url": " https://rseng.github.io/software/repository/github/amiralih/MembraneAnalysis.jl", + "content": "A package for analyzing molecular dynamics simulations of lipid membranes" }, - "github/GreenBankObservatory/gbtgridder": { - "id": "github/GreenBankObservatory/gbtgridder", - "title": "github/GreenBankObservatory/gbtgridder", - "url": " https://rseng.github.io/software/repository/github/GreenBankObservatory/gbtgridder", - "content": "A stand-alone spectral gridder and imager for the Green Bank Telescope" + "github/ylxu05/HN-PPISP": { + "id": "github/ylxu05/HN-PPISP", + "title": "github/ylxu05/HN-PPISP", + "url": " https://rseng.github.io/software/repository/github/ylxu05/HN-PPISP", + "content": "None" }, - "github/Hoohm/CITE-seq-Count": { - "id": "github/Hoohm/CITE-seq-Count", - "title": "github/Hoohm/CITE-seq-Count", - "url": " https://rseng.github.io/software/repository/github/Hoohm/CITE-seq-Count", - "content": "A tool that allows to get UMI counts from a single cell protein assay" + "github/astronomyk/SimCADO": { + "id": "github/astronomyk/SimCADO", + "title": "github/astronomyk/SimCADO", + "url": " https://rseng.github.io/software/repository/github/astronomyk/SimCADO", + "content": "None" }, - "github/Schulik/aiolos": { - "id": "github/Schulik/aiolos", - "title": "github/Schulik/aiolos", - "url": " https://rseng.github.io/software/repository/github/Schulik/aiolos", - "content": "1-D hydrodynamics code for planetary atmosphere accretion and escape simulations" + "github/cloudflex-project/cloudflex": { + "id": "github/cloudflex-project/cloudflex", + "title": "github/cloudflex-project/cloudflex", + "url": " https://rseng.github.io/software/repository/github/cloudflex-project/cloudflex", + "content": "None" + }, + "github/Kamuish/archi": { + "id": "github/Kamuish/archi", + "title": "github/Kamuish/archi", + "url": " https://rseng.github.io/software/repository/github/Kamuish/archi", + "content": "Pipeline to study CHEOPS background stars" + }, + "github/alejandrobll/py-sphviewer": { + "id": "github/alejandrobll/py-sphviewer", + "title": "github/alejandrobll/py-sphviewer", + "url": " https://rseng.github.io/software/repository/github/alejandrobll/py-sphviewer", + "content": "Py-SPHViewer is a framework for rendering cosmological simulations in Python using the Smoothed Particle Hydrodynamics scheme." }, "github/bioexcel/biobb_wf_flexdyn": { "id": "github/bioexcel/biobb_wf_flexdyn", @@ -16647,1067 +16377,1121 @@ "url": " https://rseng.github.io/software/repository/github/bioexcel/biobb_wf_flexdyn", "content": "None" }, - "github/mraveri/tensiometer": { - "id": "github/mraveri/tensiometer", - "title": "github/mraveri/tensiometer", - "url": " https://rseng.github.io/software/repository/github/mraveri/tensiometer", - "content": "None" + "github/anderslogg/geco": { + "id": "github/anderslogg/geco", + "title": "github/anderslogg/geco", + "url": " https://rseng.github.io/software/repository/github/anderslogg/geco", + "content": "A collection of solvers for the Einstein-Vlasov equations" }, - "github/AgentM-GEG/residual_feature_extraction": { - "id": "github/AgentM-GEG/residual_feature_extraction", - "title": "github/AgentM-GEG/residual_feature_extraction", - "url": " https://rseng.github.io/software/repository/github/AgentM-GEG/residual_feature_extraction", - "content": "A pipeline that carries out feature extraction of residual substructure within the residual images produced by popular galaxy structural-fitting routines such as GALFIT, GIM2D, etc. This pipeline works on model-subtracted residual images by popular structural fitting routines (e.g., GALFIT, GIM2D, etc) to extract faint low surface brightness features by isolating flux-wise and area-wise significant contiguous pixels regions by rigourous masking routine. This routine accepts the image cubes (original image, model image, residual image) and generates several data products" + "github/baiwenjia/ukbb_cardiac": { + "id": "github/baiwenjia/ukbb_cardiac", + "title": "github/baiwenjia/ukbb_cardiac", + "url": " https://rseng.github.io/software/repository/github/baiwenjia/ukbb_cardiac", + "content": "Some code for processing and analysing UK Biobank cardiac MR images." }, - "github/RichardObi/medigan": { - "id": "github/RichardObi/medigan", - "title": "github/RichardObi/medigan", - "url": " https://rseng.github.io/software/repository/github/RichardObi/medigan", - "content": "medigan - A Python Library of Pretrained Generative Models for Medical Image Synthesis" + "github/ouyang-lab/PRAS": { + "id": "github/ouyang-lab/PRAS", + "title": "github/ouyang-lab/PRAS", + "url": " https://rseng.github.io/software/repository/github/ouyang-lab/PRAS", + "content": "PRAS: predicting functional targets of RNA binding proteins based on CLIP-seq peaks" }, - "github/ester-project/ester": { - "id": "github/ester-project/ester", - "title": "github/ester-project/ester", - "url": " https://rseng.github.io/software/repository/github/ester-project/ester", - "content": "Evolution STEllaire en Rotation." + "github/BonsonW/slow5curl": { + "id": "github/BonsonW/slow5curl", + "title": "github/BonsonW/slow5curl", + "url": " https://rseng.github.io/software/repository/github/BonsonW/slow5curl", + "content": "A library and tool for accessing remote BLOW5 files." }, - "github/conchoecia/pauvre": { - "id": "github/conchoecia/pauvre", - "title": "github/conchoecia/pauvre", - "url": " https://rseng.github.io/software/repository/github/conchoecia/pauvre", - "content": "Pauvre: QC and genome browser plotting Oxford Nanopore and PacBio long reads." + "github/pepkit/geofetch": { + "id": "github/pepkit/geofetch", + "title": "github/pepkit/geofetch", + "url": " https://rseng.github.io/software/repository/github/pepkit/geofetch", + "content": "Builds a PEP from SRA or GEO accessions" }, - "github/dieghernan/tidyterra": { - "id": "github/dieghernan/tidyterra", - "title": "github/dieghernan/tidyterra", - "url": " https://rseng.github.io/software/repository/github/dieghernan/tidyterra", - "content": "tidyverse and ggplot2 methods for terra spatial objects" + "github/genotoul-bioinfo/dgenies": { + "id": "github/genotoul-bioinfo/dgenies", + "title": "github/genotoul-bioinfo/dgenies", + "url": " https://rseng.github.io/software/repository/github/genotoul-bioinfo/dgenies", + "content": "Dotplot large Genomes in an Interactive, Efficient and Simple way" }, - "github/tseemann/prokka": { - "id": "github/tseemann/prokka", - "title": "github/tseemann/prokka", - "url": " https://rseng.github.io/software/repository/github/tseemann/prokka", - "content": ":zap: :aquarius: Rapid prokaryotic genome annotation" + "github/casaluca/bolometric-corrections": { + "id": "github/casaluca/bolometric-corrections", + "title": "github/casaluca/bolometric-corrections", + "url": " https://rseng.github.io/software/repository/github/casaluca/bolometric-corrections", + "content": "compute bolometric corrections and synthetic colours for input values of stellar parameters" }, - "github/tseemann/abricate": { - "id": "github/tseemann/abricate", - "title": "github/tseemann/abricate", - "url": " https://rseng.github.io/software/repository/github/tseemann/abricate", - "content": ":mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes" + "github/mathworks/Simscape-Medical-Ventilator": { + "id": "github/mathworks/Simscape-Medical-Ventilator", + "title": "github/mathworks/Simscape-Medical-Ventilator", + "url": " https://rseng.github.io/software/repository/github/mathworks/Simscape-Medical-Ventilator", + "content": "Positive-pressure medical ventilator system using Simscape™" }, - "github/tseemann/mlst": { - "id": "github/tseemann/mlst", - "title": "github/tseemann/mlst", - "url": " https://rseng.github.io/software/repository/github/tseemann/mlst", - "content": ":id: Scan contig files against PubMLST typing schemes" + "github/FofanovLab/mtsv_tools": { + "id": "github/FofanovLab/mtsv_tools", + "title": "github/FofanovLab/mtsv_tools", + "url": " https://rseng.github.io/software/repository/github/FofanovLab/mtsv_tools", + "content": "Core metagenomic binning tools for mtsv" }, - "github/tseemann/barrnap": { - "id": "github/tseemann/barrnap", - "title": "github/tseemann/barrnap", - "url": " https://rseng.github.io/software/repository/github/tseemann/barrnap", - "content": ":microscope: :leo: Bacterial ribosomal RNA predictor" + "github/spglib/spgrep": { + "id": "github/spglib/spgrep", + "title": "github/spglib/spgrep", + "url": " https://rseng.github.io/software/repository/github/spglib/spgrep", + "content": "On-the-fly generator of space-group irreducible representations" }, - "github/tseemann/shovill": { - "id": "github/tseemann/shovill", - "title": "github/tseemann/shovill", - "url": " https://rseng.github.io/software/repository/github/tseemann/shovill", - "content": "⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads" + "github/hungyipu/Odyssey": { + "id": "github/hungyipu/Odyssey", + "title": "github/hungyipu/Odyssey", + "url": " https://rseng.github.io/software/repository/github/hungyipu/Odyssey", + "content": "Odyssey: a public, GPU-based GRRT (general relativistic radiative transfer) code" }, - "github/tseemann/samclip": { - "id": "github/tseemann/samclip", - "title": "github/tseemann/samclip", - "url": " https://rseng.github.io/software/repository/github/tseemann/samclip", - "content": "Filter SAM file for soft and hard clipped alignments" + "github/changhoonhahn/pySpectrum": { + "id": "github/changhoonhahn/pySpectrum", + "title": "github/changhoonhahn/pySpectrum", + "url": " https://rseng.github.io/software/repository/github/changhoonhahn/pySpectrum", + "content": "python package to measure power spectrum and bispectrum" }, - "github/tseemann/VelvetOptimiser": { - "id": "github/tseemann/VelvetOptimiser", - "title": "github/tseemann/VelvetOptimiser", - "url": " https://rseng.github.io/software/repository/github/tseemann/VelvetOptimiser", - "content": ":chart_with_upwards_trend: Automatically optimise three of Velvet's assembly parameters." + "github/tinglabs/scAIDE": { + "id": "github/tinglabs/scAIDE", + "title": "github/tinglabs/scAIDE", + "url": " https://rseng.github.io/software/repository/github/tinglabs/scAIDE", + "content": "None" }, - "github/tseemann/snp-dists": { - "id": "github/tseemann/snp-dists", - "title": "github/tseemann/snp-dists", - "url": " https://rseng.github.io/software/repository/github/tseemann/snp-dists", - "content": "Pairwise SNP distance matrix from a FASTA sequence alignment" + "github/JulioHC00/PEPITA": { + "id": "github/JulioHC00/PEPITA", + "title": "github/JulioHC00/PEPITA", + "url": " https://rseng.github.io/software/repository/github/JulioHC00/PEPITA", + "content": "Prediction of Exoplanet Precisions using Information in Transit Analysis" }, - "github/tseemann/snippy": { - "id": "github/tseemann/snippy", - "title": "github/tseemann/snippy", - "url": " https://rseng.github.io/software/repository/github/tseemann/snippy", - "content": ":scissors: :zap: Rapid haploid variant calling and core genome alignment" + "github/PrincetonUniversity/athena": { + "id": "github/PrincetonUniversity/athena", + "title": "github/PrincetonUniversity/athena", + "url": " https://rseng.github.io/software/repository/github/PrincetonUniversity/athena", + "content": "Athena++ GRMHD code and adaptive mesh refinement (AMR) framework" }, - "github/sachsmc/cosinor": { - "id": "github/sachsmc/cosinor", - "title": "github/sachsmc/cosinor", - "url": " https://rseng.github.io/software/repository/github/sachsmc/cosinor", - "content": "R package for estimation and prediction of the cosinor model for periodic data" + "github/PrincetonUniversity/FastTemplatePeriodogram": { + "id": "github/PrincetonUniversity/FastTemplatePeriodogram", + "title": "github/PrincetonUniversity/FastTemplatePeriodogram", + "url": " https://rseng.github.io/software/repository/github/PrincetonUniversity/FastTemplatePeriodogram", + "content": "NlogN algorithm for least-squares fitting of periodic templates to noisy, non-equispaced time-series data." }, - "github/ryanvarley/exodata": { - "id": "github/ryanvarley/exodata", - "title": "github/ryanvarley/exodata", - "url": " https://rseng.github.io/software/repository/github/ryanvarley/exodata", - "content": "Exoplanet catalogue interface and exploratory analysis tool" + "github/PrincetonUniversity/Athena-Cversion": { + "id": "github/PrincetonUniversity/Athena-Cversion", + "title": "github/PrincetonUniversity/Athena-Cversion", + "url": " https://rseng.github.io/software/repository/github/PrincetonUniversity/Athena-Cversion", + "content": "None" }, - "github/mdruett/COCOPLOT": { - "id": "github/mdruett/COCOPLOT", - "title": "github/mdruett/COCOPLOT", - "url": " https://rseng.github.io/software/repository/github/mdruett/COCOPLOT", - "content": "COlor COllapsed PLOTting quick-look and context image software is designed to convey spectral profile information from all of the spatial pixels in a 3D datacube as a single image, using color." + "github/felixbosco/KeplerFit": { + "id": "github/felixbosco/KeplerFit", + "title": "github/felixbosco/KeplerFit", + "url": " https://rseng.github.io/software/repository/github/felixbosco/KeplerFit", + "content": "A small piece of code to fit a Keplerian velocity distribution model to position-velocity data" }, - "github/SCM-NV/qmflows-namd": { - "id": "github/SCM-NV/qmflows-namd", - "title": "github/SCM-NV/qmflows-namd", - "url": " https://rseng.github.io/software/repository/github/SCM-NV/qmflows-namd", - "content": "Package containing several workflows to compute molecular properties for nanomaterials" + "github/actris-cloudnet/cloudnetpy": { + "id": "github/actris-cloudnet/cloudnetpy", + "title": "github/actris-cloudnet/cloudnetpy", + "url": " https://rseng.github.io/software/repository/github/actris-cloudnet/cloudnetpy", + "content": "Python package for Cloudnet data processing " }, - "github/SCM-NV/qmflows": { - "id": "github/SCM-NV/qmflows", - "title": "github/SCM-NV/qmflows", - "url": " https://rseng.github.io/software/repository/github/SCM-NV/qmflows", - "content": "This library tackles the construction and efficient execution of computational chemistry workflows" + "github/arangrhie/merfin": { + "id": "github/arangrhie/merfin", + "title": "github/arangrhie/merfin", + "url": " https://rseng.github.io/software/repository/github/arangrhie/merfin", + "content": "Evaluate variant calls and its combination with k-mer multiplicity" }, - "github/SCM-NV/pyZacros": { - "id": "github/SCM-NV/pyZacros", - "title": "github/SCM-NV/pyZacros", - "url": " https://rseng.github.io/software/repository/github/SCM-NV/pyZacros", - "content": "Python library to handle KMC codes." + "github/kircherlab/ReMM": { + "id": "github/kircherlab/ReMM", + "title": "github/kircherlab/ReMM", + "url": " https://rseng.github.io/software/repository/github/kircherlab/ReMM", + "content": "ReMM score snakemake workflow " }, - "github/mengyao/Complete-Striped-Smith-Waterman-Library": { - "id": "github/mengyao/Complete-Striped-Smith-Waterman-Library", - "title": "github/mengyao/Complete-Striped-Smith-Waterman-Library", - "url": " https://rseng.github.io/software/repository/github/mengyao/Complete-Striped-Smith-Waterman-Library", - "content": "Smith-Waterman aligner based on libssw" + "github/ICESat2-SlideRule/paper": { + "id": "github/ICESat2-SlideRule/paper", + "title": "github/ICESat2-SlideRule/paper", + "url": " https://rseng.github.io/software/repository/github/ICESat2-SlideRule/paper", + "content": "JOSS paper materials" + }, + "github/pfaucon/PBSIM-PacBio-Simulator": { + "id": "github/pfaucon/PBSIM-PacBio-Simulator", + "title": "github/pfaucon/PBSIM-PacBio-Simulator", + "url": " https://rseng.github.io/software/repository/github/pfaucon/PBSIM-PacBio-Simulator", + "content": "This is an updated mirror of the original PacBio Read Simulator" + }, + "github/mlaparie/sigh": { + "id": "github/mlaparie/sigh", + "title": "github/mlaparie/sigh", + "url": " https://rseng.github.io/software/repository/github/mlaparie/sigh", + "content": "sigh, a program to cure optimism and automatically scrape worldwide data about reported disaster and perturbation events." + }, + "github/mlaparie/phidget-tools": { + "id": "github/mlaparie/phidget-tools", + "title": "github/mlaparie/phidget-tools", + "url": " https://rseng.github.io/software/repository/github/mlaparie/phidget-tools", + "content": "Terminal tools to record/monitor from Phidget 1048_1B USB-thermocouple devices" + }, + "github/fredstro/hilbertmodgroup": { + "id": "github/fredstro/hilbertmodgroup", + "title": "github/fredstro/hilbertmodgroup", + "url": " https://rseng.github.io/software/repository/github/fredstro/hilbertmodgroup", + "content": "Implementation of Hilbert modular groups using SageMath" + }, + "github/aschafu/PSSH2": { + "id": "github/aschafu/PSSH2", + "title": "github/aschafu/PSSH2", + "url": " https://rseng.github.io/software/repository/github/aschafu/PSSH2", + "content": "Scripts for generating pssh2" }, - "github/hippke/PyOSE": { - "id": "github/hippke/PyOSE", - "title": "github/hippke/PyOSE", - "url": " https://rseng.github.io/software/repository/github/hippke/PyOSE", - "content": "Stacked exomoons with the Orbital Sampling Effect" + "github/obreschkow/dftools": { + "id": "github/obreschkow/dftools", + "title": "github/obreschkow/dftools", + "url": " https://rseng.github.io/software/repository/github/obreschkow/dftools", + "content": "None" }, - "github/hippke/pandora": { - "id": "github/hippke/pandora", - "title": "github/hippke/pandora", - "url": " https://rseng.github.io/software/repository/github/hippke/pandora", - "content": "A fast transit-fitting algorithm to search for transits of exomoons" + "github/ChristopherWilks/megadepth": { + "id": "github/ChristopherWilks/megadepth", + "title": "github/ChristopherWilks/megadepth", + "url": " https://rseng.github.io/software/repository/github/ChristopherWilks/megadepth", + "content": "BigWig and BAM utilities" }, - "github/hippke/communication": { - 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The software is being developed based on the study of other software, standards of accessibility like the ISO 9241-171:2008 (Guidance on software accessibility) and theoretical framework based on literature review and end user tests." + "github/arvados/arvados": { + "id": "github/arvados/arvados", + "title": "github/arvados/arvados", + "url": " https://rseng.github.io/software/repository/github/arvados/arvados", + "content": "An open source platform for managing and analyzing biomedical big data" }, - "github/torluca/morphofit": { - "id": "github/torluca/morphofit", - "title": "github/torluca/morphofit", - "url": " https://rseng.github.io/software/repository/github/torluca/morphofit", - "content": "A Python package for the morphological analysis of galaxies (Tortorelli & Mercurio 2023)." + "github/pontoppi/radlite": { + "id": "github/pontoppi/radlite", + "title": "github/pontoppi/radlite", + "url": " https://rseng.github.io/software/repository/github/pontoppi/radlite", + "content": "RADLite is the fast 2D/3D raytracer for infrared lines" }, - "github/berenslab/MorphoPy": { - "id": "github/berenslab/MorphoPy", - "title": "github/berenslab/MorphoPy", - "url": " https://rseng.github.io/software/repository/github/berenslab/MorphoPy", - "content": "None" + "github/matthias-mayr/Cartesian-Impedance-Controller": { + "id": "github/matthias-mayr/Cartesian-Impedance-Controller", + "title": "github/matthias-mayr/Cartesian-Impedance-Controller", + "url": " https://rseng.github.io/software/repository/github/matthias-mayr/Cartesian-Impedance-Controller", + "content": "A C++ implementation of Cartesian impedance control for torque-controlled manipulators with ROS bindings." }, - "github/voutcn/megahit": { - "id": "github/voutcn/megahit", - "title": "github/voutcn/megahit", - "url": " https://rseng.github.io/software/repository/github/voutcn/megahit", - "content": "Ultra-fast and memory-efficient (meta-)genome assembler" + "github/AllenInstitute/bmtk": { + "id": "github/AllenInstitute/bmtk", + "title": "github/AllenInstitute/bmtk", + "url": " https://rseng.github.io/software/repository/github/AllenInstitute/bmtk", + "content": "Brain Modeling Toolkit" }, - "github/dtamayo/reboundx": { - "id": "github/dtamayo/reboundx", - "title": "github/dtamayo/reboundx", - "url": " https://rseng.github.io/software/repository/github/dtamayo/reboundx", - "content": "A library for adding additional forces to the REBOUND N-body integration package" + "github/ACCarnall/SpectRes": { + "id": "github/ACCarnall/SpectRes", + "title": "github/ACCarnall/SpectRes", + "url": " https://rseng.github.io/software/repository/github/ACCarnall/SpectRes", + "content": "SpectRes is a Python module which efficiently resamples spectra and their associated uncertainties onto an arbitrary wavelength grid. 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JavaScript module built with Svelte and Snowpack." }, - "github/LucIJspeert/star_shadow": { - "id": "github/LucIJspeert/star_shadow", - "title": "github/LucIJspeert/star_shadow", - "url": " https://rseng.github.io/software/repository/github/LucIJspeert/star_shadow", - "content": "Recipe to fully automatically analyse eclipsing binary light curves and find eccentricity and more" + "github/samirmartins/pydaq": { + "id": "github/samirmartins/pydaq", + "title": "github/samirmartins/pydaq", + "url": " https://rseng.github.io/software/repository/github/samirmartins/pydaq", + "content": "Data Acquisition and Experimental Analysis with Python and Graphical User Interface" }, - "github/weecology/retriever": { - "id": "github/weecology/retriever", - "title": "github/weecology/retriever", - "url": " https://rseng.github.io/software/repository/github/weecology/retriever", - "content": "Quickly download, clean up, and install public datasets into a database management system" + "github/bblodfon/emba": { + "id": "github/bblodfon/emba", + "title": "github/bblodfon/emba", + "url": " https://rseng.github.io/software/repository/github/bblodfon/emba", + "content": "Ensemble Model Biomarker Analysis R package" }, - 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It can compute matter power-spectra (CDM and total), redshift-space multipole power-spectra P0,P2,P4 and do halofinding on the fly. 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Generate, analyze and export complex 2D space partitions like metallic grain structures" + "github/KBNLresearch/ochre": { + "id": "github/KBNLresearch/ochre", + "title": "github/KBNLresearch/ochre", + "url": " https://rseng.github.io/software/repository/github/KBNLresearch/ochre", + "content": "Toolbox for OCR post-correction" }, - "github/Theano/Theano": { - "id": "github/Theano/Theano", - "title": "github/Theano/Theano", - "url": " https://rseng.github.io/software/repository/github/Theano/Theano", - "content": "Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently. 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"url": " https://rseng.github.io/software/repository/github/RuthAngus/gprotation", - "content": "Measuring stellar rotation periods with Gaussian processes" + "github/astro-informatics/DarkMappy": { + "id": "github/astro-informatics/DarkMappy", + "title": "github/astro-informatics/DarkMappy", + "url": " https://rseng.github.io/software/repository/github/astro-informatics/DarkMappy", + "content": "Scalable mapping of the dark universe" }, - "github/RuthAngus/stardate": { - "id": "github/RuthAngus/stardate", - "title": "github/RuthAngus/stardate", - "url": " https://rseng.github.io/software/repository/github/RuthAngus/stardate", - "content": "Combining dating methods for better stellar ages" + "github/astro-informatics/comb": { + "id": "github/astro-informatics/comb", + "title": "github/astro-informatics/comb", + "url": " https://rseng.github.io/software/repository/github/astro-informatics/comb", + "content": "Compact object simulations on the sphere" }, - "github/DeltaRCM/pyDeltaRCM": { - "id": "github/DeltaRCM/pyDeltaRCM", - "title": "github/DeltaRCM/pyDeltaRCM", - "url": " https://rseng.github.io/software/repository/github/DeltaRCM/pyDeltaRCM", - "content": "Delta model with a reduced-complexity approach" + "github/astro-informatics/ssht": { + "id": "github/astro-informatics/ssht", + "title": "github/astro-informatics/ssht", + "url": " https://rseng.github.io/software/repository/github/astro-informatics/ssht", + "content": "Fast and exact spin spherical harmonic transforms" }, - "github/sfschen/velocileptors": { - "id": "github/sfschen/velocileptors", - "title": "github/sfschen/velocileptors", - "url": " https://rseng.github.io/software/repository/github/sfschen/velocileptors", - "content": "A code for velocity-based Lagrangian and Eulerian PT expansions of redshift-space distortions." + "github/astro-informatics/massmappy": { + "id": "github/astro-informatics/massmappy", + "title": "github/astro-informatics/massmappy", + "url": " https://rseng.github.io/software/repository/github/astro-informatics/massmappy", + "content": "Mapping dark matter on the celestial sphere" }, - "github/LMBooth/pybci": { - "id": "github/LMBooth/pybci", - "title": "github/LMBooth/pybci", - "url": " https://rseng.github.io/software/repository/github/LMBooth/pybci", - "content": "Create real-time BCI's with the LSL, PyTorch, SKLearn and TensorFlow packages." + "github/astro-informatics/flag-archive": { + "id": "github/astro-informatics/flag-archive", + "title": "github/astro-informatics/flag-archive", + "url": " https://rseng.github.io/software/repository/github/astro-informatics/flag-archive", + "content": "Fast Fourier-Laguerre transform on the ball and exact spherical Bessel and Fourier-Bessel transforms" }, - "github/biaslab/RxInfer.jl": { - "id": "github/biaslab/RxInfer.jl", - "title": "github/biaslab/RxInfer.jl", - "url": " https://rseng.github.io/software/repository/github/biaslab/RxInfer.jl", - "content": "Julia package for automated Bayesian inference on a factor graph with reactive message passing" + "github/astro-informatics/RequiSim": { + "id": "github/astro-informatics/RequiSim", + "title": "github/astro-informatics/RequiSim", + "url": " https://rseng.github.io/software/repository/github/astro-informatics/RequiSim", + "content": "None" + }, + "github/astro-informatics/QuantifAI": { + "id": "github/astro-informatics/QuantifAI", + "title": "github/astro-informatics/QuantifAI", + "url": " https://rseng.github.io/software/repository/github/astro-informatics/QuantifAI", + "content": "PyTorch-based RI imaging reconstruction package with scalable Bayesian uncertainty quantification relying on data-driven (learned) priors" }, - 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"github/tolkit/telomeric-identifier": { - "id": "github/tolkit/telomeric-identifier", - "title": "github/tolkit/telomeric-identifier", - "url": " https://rseng.github.io/software/repository/github/tolkit/telomeric-identifier", - "content": "Identify and find telomeres, or telomeric repeats in a genome." + "github/ComplexGroupInteractions/xgi": { + "id": "github/ComplexGroupInteractions/xgi", + "title": "github/ComplexGroupInteractions/xgi", + "url": " https://rseng.github.io/software/repository/github/ComplexGroupInteractions/xgi", + "content": "CompleX Group Interactions (XGI) provides an ecosystem for the analysis and representation of complex systems with group interactions." }, - "github/ExaScience/elprep": { - "id": "github/ExaScience/elprep", - "title": "github/ExaScience/elprep", - "url": " https://rseng.github.io/software/repository/github/ExaScience/elprep", - "content": "a high-performance tool for analyzing .sam/.bam files (up to and including variant calling) in sequencing pipelines." + "github/a-griffiths/AutoSpec": { + "id": "github/a-griffiths/AutoSpec", + "title": "github/a-griffiths/AutoSpec", + "url": " https://rseng.github.io/software/repository/github/a-griffiths/AutoSpec", + "content": "Fast Automated Spectral Extraction Software for IFU Datacubes" }, - "github/eleniadam/npgreat": { - "id": "github/eleniadam/npgreat", - "title": "github/eleniadam/npgreat", - "url": " https://rseng.github.io/software/repository/github/eleniadam/npgreat", - "content": "A hybrid assembly method that utilizes Nanopore and Linked-Reads datasets for the assembly of the human subtelomere regions." + "github/SchlossLab/mikropml": { + "id": "github/SchlossLab/mikropml", + "title": "github/SchlossLab/mikropml", + "url": " https://rseng.github.io/software/repository/github/SchlossLab/mikropml", + "content": "User-Friendly R Package for Supervised Machine Learning Pipelines" }, - "github/timothydmorton/isochrones": { - "id": "github/timothydmorton/isochrones", - "title": "github/timothydmorton/isochrones", - "url": " https://rseng.github.io/software/repository/github/timothydmorton/isochrones", - "content": "Pythonic stellar model grid access; easy MCMC fitting of stellar properties" + "github/YosefLab/scvi-tools": { + "id": "github/YosefLab/scvi-tools", + "title": "github/YosefLab/scvi-tools", + "url": " https://rseng.github.io/software/repository/github/YosefLab/scvi-tools", + "content": "Deep probabilistic analysis of single-cell omics data" }, - "github/timothydmorton/vespa": { - "id": "github/timothydmorton/vespa", - "title": "github/timothydmorton/vespa", - "url": " https://rseng.github.io/software/repository/github/timothydmorton/vespa", - "content": "Validation of Exoplanet Signals using a Probabilistic Algorithm--- calculating false positive probabilities for transit signals" + "github/JacksonBurns/astartes": { + "id": "github/JacksonBurns/astartes", + "title": "github/JacksonBurns/astartes", + "url": " https://rseng.github.io/software/repository/github/JacksonBurns/astartes", + "content": "Better Data Splits for Machine Learning" }, - "github/jdswinbank/Comet": { - "id": "github/jdswinbank/Comet", - "title": "github/jdswinbank/Comet", - "url": " https://rseng.github.io/software/repository/github/jdswinbank/Comet", - "content": "A complete VOEvent transport system" + "github/jackmwolf/tehtuner": { + "id": "github/jackmwolf/tehtuner", + "title": "github/jackmwolf/tehtuner", + "url": " https://rseng.github.io/software/repository/github/jackmwolf/tehtuner", + "content": "An R Package to Fit and Tune to Models to Detect Treatment Effect Heterogeneity " }, - "github/erling6232/imagedata": { - "id": "github/erling6232/imagedata", - "title": "github/erling6232/imagedata", - "url": " https://rseng.github.io/software/repository/github/erling6232/imagedata", - "content": "Read/write medical image data" + "github/joshjchayes/TransitFit": { + "id": "github/joshjchayes/TransitFit", + "title": "github/joshjchayes/TransitFit", + "url": " https://rseng.github.io/software/repository/github/joshjchayes/TransitFit", + "content": "Transit light curve fitting using nested sampling" }, - "github/Beuth-Erdelt/DBMS-Benchmarker": { - "id": "github/Beuth-Erdelt/DBMS-Benchmarker", - "title": "github/Beuth-Erdelt/DBMS-Benchmarker", - "url": " https://rseng.github.io/software/repository/github/Beuth-Erdelt/DBMS-Benchmarker", - "content": "DBMS-Benchmarker is a Python-based application-level blackbox benchmark tool for Database Management Systems (DBMS). It connects to a given list of DBMS (via JDBC) and runs a given list of parametrized and randomized (SQL) benchmark queries. Evaluations are available via a Python interface and on an interactive multi-dimensional dashboard." + "github/JohannesBuchner/BXA": { + "id": "github/JohannesBuchner/BXA", + "title": "github/JohannesBuchner/BXA", + "url": " https://rseng.github.io/software/repository/github/JohannesBuchner/BXA", + "content": "Bayesian X-ray analysis (nested sampling for Xspec and Sherpa)" }, - "github/MJTemple/qsogen": { - "id": "github/MJTemple/qsogen", - "title": "github/MJTemple/qsogen", - "url": " https://rseng.github.io/software/repository/github/MJTemple/qsogen", - "content": "Model quasar SEDs" + "github/JohannesBuchner/UltraNest": { + "id": "github/JohannesBuchner/UltraNest", + "title": "github/JohannesBuchner/UltraNest", + "url": " https://rseng.github.io/software/repository/github/JohannesBuchner/UltraNest", + "content": "Fit and compare complex models reliably and rapidly. Advanced nested sampling." }, - "github/jpierel14/snsed": { - "id": "github/jpierel14/snsed", - "title": "github/jpierel14/snsed", - "url": " https://rseng.github.io/software/repository/github/jpierel14/snsed", - "content": "None" + "github/JohannesBuchner/nway": { + "id": "github/JohannesBuchner/nway", + "title": "github/JohannesBuchner/nway", + "url": " https://rseng.github.io/software/repository/github/JohannesBuchner/nway", + "content": "nway -- Bayesian cross-matching of astronomical catalogues" }, - "github/jpierel14/sntd": { - "id": "github/jpierel14/sntd", - "title": "github/jpierel14/sntd", - "url": " https://rseng.github.io/software/repository/github/jpierel14/sntd", - "content": "SNTD is a Python package dedicated to measuring time delays for strongly lensed and multiply-imaged SN. The package can simulate lensed SN, fit for each SN time delay, and propagate the results all the way through to cosmological constraints." + "github/JohannesBuchner/PyMultiNest": { + "id": "github/JohannesBuchner/PyMultiNest", + "title": "github/JohannesBuchner/PyMultiNest", + "url": " https://rseng.github.io/software/repository/github/JohannesBuchner/PyMultiNest", + "content": "Pythonic Bayesian inference and visualization for the MultiNest Nested Sampling Algorithm and PyCuba's cubature algorithms." }, - "github/mc-imperial/jfs": { - "id": "github/mc-imperial/jfs", - "title": "github/mc-imperial/jfs", - "url": " https://rseng.github.io/software/repository/github/mc-imperial/jfs", - "content": "Constraint solver based on coverage-guided fuzzing" + "github/sheryl-ai/MetaPred": { + "id": "github/sheryl-ai/MetaPred", + "title": "github/sheryl-ai/MetaPred", + "url": " https://rseng.github.io/software/repository/github/sheryl-ai/MetaPred", + "content": "MetaPred: Meta-Learning for Clinical Risk Prediction with Limited Patient Electronic Health Records (KDD 2019)" }, - "github/mc-imperial/gpuverify": { - "id": "github/mc-imperial/gpuverify", - "title": "github/mc-imperial/gpuverify", - "url": " https://rseng.github.io/software/repository/github/mc-imperial/gpuverify", - "content": "GPUVerify: a Verifier for GPU Kernels" + "github/akcochrane/TEfits": { + "id": "github/akcochrane/TEfits", + "title": "github/akcochrane/TEfits", + "url": " https://rseng.github.io/software/repository/github/akcochrane/TEfits", + "content": "R package for streamlined nonlinear regression" }, - "github/mc-imperial/multicore-test-harness": { - "id": "github/mc-imperial/multicore-test-harness", - "title": "github/mc-imperial/multicore-test-harness", - "url": " https://rseng.github.io/software/repository/github/mc-imperial/multicore-test-harness", - "content": "A multicore microprocessor test harness for measuring interference" + "github/liulei/volks2": { + "id": "github/liulei/volks2", + "title": "github/liulei/volks2", + "url": " https://rseng.github.io/software/repository/github/liulei/volks2", + "content": "VLBI Observation for single pulse Localization Keen Searcher, 2nd release" }, - "github/zhongqiu1245/CCS-Net": { - "id": "github/zhongqiu1245/CCS-Net", - "title": "github/zhongqiu1245/CCS-Net", - "url": " https://rseng.github.io/software/repository/github/zhongqiu1245/CCS-Net", + "github/transientskp/lpf": { + "id": "github/transientskp/lpf", + "title": "github/transientskp/lpf", + "url": " https://rseng.github.io/software/repository/github/transientskp/lpf", "content": "None" }, - "github/SESMG/SESMG": { - "id": "github/SESMG/SESMG", - "title": "github/SESMG/SESMG", - "url": " https://rseng.github.io/software/repository/github/SESMG/SESMG", - "content": "Model generator for the optimization of energy systems, based on the modeling framework oemof. No programming skills are required to use it, as the parameters are entered using spreadsheets (e.g. Excel, LibreOffice)." + "github/transientskp/pyse": { + "id": "github/transientskp/pyse", + "title": "github/transientskp/pyse", + "url": " https://rseng.github.io/software/repository/github/transientskp/pyse", + "content": "Python Source Extractor" }, - "github/ledatelescope/bifrost": { - "id": "github/ledatelescope/bifrost", - "title": "github/ledatelescope/bifrost", - "url": " https://rseng.github.io/software/repository/github/ledatelescope/bifrost", - "content": "A stream processing framework for high-throughput applications." + "github/transientskp/tkp": { + "id": "github/transientskp/tkp", + "title": "github/transientskp/tkp", + "url": " https://rseng.github.io/software/repository/github/transientskp/tkp", + "content": "A transients-discovery pipeline for astronomical image-based surveys" }, - "github/trevisanj/PFANT": { - "id": "github/trevisanj/PFANT", - "title": "github/trevisanj/PFANT", - "url": " https://rseng.github.io/software/repository/github/trevisanj/PFANT", - "content": "Stellar Spectral Synthesis code for Astronomy" + "github/wpb-astro/MCSED": { + "id": "github/wpb-astro/MCSED", + "title": "github/wpb-astro/MCSED", + "url": " https://rseng.github.io/software/repository/github/wpb-astro/MCSED", + "content": "None" }, - "github/sundarjhu/2-DUST": { - "id": "github/sundarjhu/2-DUST", - "title": "github/sundarjhu/2-DUST", - "url": " https://rseng.github.io/software/repository/github/sundarjhu/2-DUST", - "content": "2-DUST is a general-purpose dust radiative transfer code for an axisymmetric system that reveals the global energetics of dust grains in the shell and the 2-D projected morphologies of the shell that are strongly dependent on the mixed effects of the axisymmetric dust distribution and inclination angle. It can be used to model a variety of axisymmetric astronomical dust systems." + "github/circuitgraph/circuitgraph": { + "id": "github/circuitgraph/circuitgraph", + "title": "github/circuitgraph/circuitgraph", + "url": " https://rseng.github.io/software/repository/github/circuitgraph/circuitgraph", + "content": "Tools for working with circuits as graphs in python" }, - "github/bokulich-lab/q2-fondue": { - "id": "github/bokulich-lab/q2-fondue", - "title": "github/bokulich-lab/q2-fondue", - "url": " https://rseng.github.io/software/repository/github/bokulich-lab/q2-fondue", - "content": "Functions for reproducibly Obtaining and Normalizing Data re-Used from Elsewhere" + "github/flyaflya/causact": { + "id": "github/flyaflya/causact", + "title": "github/flyaflya/causact", + "url": " https://rseng.github.io/software/repository/github/flyaflya/causact", + "content": "causact: R package to accelerate Bayesian analytics workflows." }, - "github/clwainwright/CosmoTransitions": { - "id": "github/clwainwright/CosmoTransitions", - "title": "github/clwainwright/CosmoTransitions", - "url": " https://rseng.github.io/software/repository/github/clwainwright/CosmoTransitions", - "content": "A package for analyzing finite or zero-temperature cosmological phase transitions driven by single or multiple scalar fields." + "github/Martinsos/edlib": { + "id": "github/Martinsos/edlib", + "title": "github/Martinsos/edlib", + "url": " https://rseng.github.io/software/repository/github/Martinsos/edlib", + "content": "Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance." + }, + "github/DICP1810/SpotLink": { + "id": "github/DICP1810/SpotLink", + "title": "github/DICP1810/SpotLink", + "url": " https://rseng.github.io/software/repository/github/DICP1810/SpotLink", + "content": "SpotLinkTest" + }, + "github/DICP1810/ComMap": { + "id": "github/DICP1810/ComMap", + "title": "github/DICP1810/ComMap", + "url": " https://rseng.github.io/software/repository/github/DICP1810/ComMap", + "content": "CXMS generated cross-linking pairs mapping to structures" + }, + "github/RasmussenLab/vamb": { + "id": "github/RasmussenLab/vamb", + "title": "github/RasmussenLab/vamb", + "url": " https://rseng.github.io/software/repository/github/RasmussenLab/vamb", + "content": "Variational autoencoder for metagenomic binning" + }, + "github/psi4/psi4": { + "id": "github/psi4/psi4", + "title": "github/psi4/psi4", + "url": " https://rseng.github.io/software/repository/github/psi4/psi4", + "content": "Open-Source Quantum Chemistry – an electronic structure package in C++ driven by Python" }, - "github/discsim/frank": { - "id": "github/discsim/frank", - "title": "github/discsim/frank", - "url": " https://rseng.github.io/software/repository/github/discsim/frank", - "content": "1D radial brightness profile reconstruction for interferometric sources" + "github/mneeleman/qubefit": { + "id": "github/mneeleman/qubefit", + "title": "github/mneeleman/qubefit", + "url": " https://rseng.github.io/software/repository/github/mneeleman/qubefit", + "content": "None" }, - "github/theosanderson/chronumental": { - "id": "github/theosanderson/chronumental", - "title": "github/theosanderson/chronumental", - "url": " https://rseng.github.io/software/repository/github/theosanderson/chronumental", - "content": "Estimating time trees from very large phylogenies" + "github/churchmanlab/genewalk": { + "id": "github/churchmanlab/genewalk", + "title": "github/churchmanlab/genewalk", + "url": " https://rseng.github.io/software/repository/github/churchmanlab/genewalk", + "content": "GeneWalk identifies relevant gene functions for a biological context using network representation learning" }, - 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" + "github/sanger-pathogens/Roary": { + "id": "github/sanger-pathogens/Roary", + "title": "github/sanger-pathogens/Roary", + "url": " https://rseng.github.io/software/repository/github/sanger-pathogens/Roary", + "content": "Rapid large-scale prokaryote pan genome analysis" }, - "github/algo-cancer/CAMMiQ": { - "id": "github/algo-cancer/CAMMiQ", - "title": "github/algo-cancer/CAMMiQ", - "url": " https://rseng.github.io/software/repository/github/algo-cancer/CAMMiQ", - "content": "Metagenomics microbial abundance quantification" + "github/sanger-pathogens/iva": { + "id": "github/sanger-pathogens/iva", + "title": "github/sanger-pathogens/iva", + "url": " https://rseng.github.io/software/repository/github/sanger-pathogens/iva", + "content": "de novo virus assembler of Illumina paired reads" }, - "github/dmey/synthia": { - "id": "github/dmey/synthia", - "title": "github/dmey/synthia", - "url": " https://rseng.github.io/software/repository/github/dmey/synthia", - "content": "📈 🐍 Multidimensional synthetic data generation in Python" + "github/sanger-pathogens/gubbins": { + "id": "github/sanger-pathogens/gubbins", + "title": "github/sanger-pathogens/gubbins", + "url": " https://rseng.github.io/software/repository/github/sanger-pathogens/gubbins", + "content": "Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins" }, - "github/seqan/lara": { - "id": "github/seqan/lara", - "title": "github/seqan/lara", - "url": " https://rseng.github.io/software/repository/github/seqan/lara", - "content": "LaRA 2: Lagrangian Relaxed structural Alignment" + "github/sanger-pathogens/Bio-Tradis": { + "id": "github/sanger-pathogens/Bio-Tradis", + "title": "github/sanger-pathogens/Bio-Tradis", + "url": " https://rseng.github.io/software/repository/github/sanger-pathogens/Bio-Tradis", + "content": "A set of tools to analyse the output from TraDIS analyses" }, - "github/seqan/flexbar": { - "id": "github/seqan/flexbar", - "title": "github/seqan/flexbar", - "url": " https://rseng.github.io/software/repository/github/seqan/flexbar", - "content": "flexible barcode and adapter removal" + "github/sanger-pathogens/assembly-stats": { + "id": "github/sanger-pathogens/assembly-stats", + "title": "github/sanger-pathogens/assembly-stats", + "url": " https://rseng.github.io/software/repository/github/sanger-pathogens/assembly-stats", + "content": "Get assembly statistics from FASTA and FASTQ files" }, - "github/seqan/lambda": { - "id": "github/seqan/lambda", - "title": "github/seqan/lambda", - "url": " https://rseng.github.io/software/repository/github/seqan/lambda", - "content": "LAMBDA – the Local Aligner for Massive Biological DatA " + "github/sanger-pathogens/ariba": { + "id": "github/sanger-pathogens/ariba", + "title": "github/sanger-pathogens/ariba", + "url": " https://rseng.github.io/software/repository/github/sanger-pathogens/ariba", + "content": "Antimicrobial Resistance Identification By Assembly" }, - "github/henrycousins/gspa": { - "id": "github/henrycousins/gspa", - "title": "github/henrycousins/gspa", - "url": " https://rseng.github.io/software/repository/github/henrycousins/gspa", - "content": "Python implementation of gene set proximity analysis" + "github/sanger-pathogens/pymummer": { + "id": "github/sanger-pathogens/pymummer", + "title": "github/sanger-pathogens/pymummer", + "url": " https://rseng.github.io/software/repository/github/sanger-pathogens/pymummer", + "content": "Python3 module for running MUMmer and reading the output" }, - "github/EnsembleGovServices/kamodo-core": { - "id": "github/EnsembleGovServices/kamodo-core", - "title": "github/EnsembleGovServices/kamodo-core", - "url": " https://rseng.github.io/software/repository/github/EnsembleGovServices/kamodo-core", - "content": "A functional API for space weather models and data" + "github/sanger-pathogens/snp-sites": { + "id": "github/sanger-pathogens/snp-sites", + "title": "github/sanger-pathogens/snp-sites", + "url": " https://rseng.github.io/software/repository/github/sanger-pathogens/snp-sites", + "content": "Finds SNP sites from a multi-FASTA alignment file" }, - "github/vals/umis": { - "id": "github/vals/umis", - "title": "github/vals/umis", - "url": " https://rseng.github.io/software/repository/github/vals/umis", - "content": "Tools for processing UMI RNA-tag data" + "github/sanger-pathogens/circlator": { + "id": "github/sanger-pathogens/circlator", + "title": "github/sanger-pathogens/circlator", + "url": " https://rseng.github.io/software/repository/github/sanger-pathogens/circlator", + "content": "Circlator is a tool to circularize genome assemblies. The input is a genome assembly in FASTA format and corrected PacBio or nanopore reads in FASTA or FASTQ format. Circlator will attempt to identify each circular sequence and output a linearised version of it. It does this by assembling all reads that map to contig ends and comparing the resulting contigs with the input assembly." }, - "github/epruesse/SINA": { - "id": "github/epruesse/SINA", - "title": "github/epruesse/SINA", - "url": " https://rseng.github.io/software/repository/github/epruesse/SINA", - "content": "SINA - Reference based multiple sequence alignment" + "github/ArgoCanada/argodata": { + "id": "github/ArgoCanada/argodata", + "title": "github/ArgoCanada/argodata", + "url": " https://rseng.github.io/software/repository/github/ArgoCanada/argodata", + "content": "Download Argo Ocean Float Data" }, - "github/institut-de-genomique/HAPO-G": { - "id": "github/institut-de-genomique/HAPO-G", - "title": "github/institut-de-genomique/HAPO-G", - "url": " https://rseng.github.io/software/repository/github/institut-de-genomique/HAPO-G", - "content": "Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads." + "github/ndaniyar/aphot": { + "id": "github/ndaniyar/aphot", + "title": "github/ndaniyar/aphot", + "url": " https://rseng.github.io/software/repository/github/ndaniyar/aphot", + "content": "Photon Asymmetry" }, - "github/multiscale/muscle3": { - "id": "github/multiscale/muscle3", - "title": "github/multiscale/muscle3", - "url": " https://rseng.github.io/software/repository/github/multiscale/muscle3", - "content": "The third major version of the MUltiScale Coupling Library and Environment" + "github/suneeshjacob/ACRoD": { + "id": "github/suneeshjacob/ACRoD", + "title": "github/suneeshjacob/ACRoD", + "url": " https://rseng.github.io/software/repository/github/suneeshjacob/ACRoD", + "content": "Automatic Computation for Robot Design" }, - "github/morisUtokyo/uTR": { - "id": "github/morisUtokyo/uTR", - "title": "github/morisUtokyo/uTR", - "url": " https://rseng.github.io/software/repository/github/morisUtokyo/uTR", - "content": "Detect key Units in mosaic Tandem Repeats from representative reads from the same locus " + "github/phipsonlab/propeller-paper-analysis": { + "id": "github/phipsonlab/propeller-paper-analysis", + "title": "github/phipsonlab/propeller-paper-analysis", + "url": " https://rseng.github.io/software/repository/github/phipsonlab/propeller-paper-analysis", + "content": "The website hosts the analysis and evaluation of different statistical methods for determining differences in cell type proportions in single cell RNA-seq data." }, - "github/pangenome/smoothxg": { - "id": "github/pangenome/smoothxg", - "title": "github/pangenome/smoothxg", - "url": " https://rseng.github.io/software/repository/github/pangenome/smoothxg", - "content": "linearize and simplify variation graphs using blocked partial order alignment" + "github/bradkav/WIMpy_NREFT": { + "id": "github/bradkav/WIMpy_NREFT", + "title": "github/bradkav/WIMpy_NREFT", + "url": " https://rseng.github.io/software/repository/github/bradkav/WIMpy_NREFT", + "content": "WIMpy_NREFT is a code for calculating Dark Matter direct detection rates in the framework of non-relativistic effective field theory (NREFT)." }, - "github/esplint/IRACpm": { - "id": "github/esplint/IRACpm", - "title": "github/esplint/IRACpm", - "url": " https://rseng.github.io/software/repository/github/esplint/IRACpm", - "content": "IRACpm R Package: Applies a 7-8 order distortion correction to IRAC astrometric data from the Spitzer Space Telescope" + "github/bradkav/AntiparticleDM": { + "id": "github/bradkav/AntiparticleDM", + "title": "github/bradkav/AntiparticleDM", + "url": " https://rseng.github.io/software/repository/github/bradkav/AntiparticleDM", + "content": "Prospects for discriminating between Majorana and Dirac Dark Matter using future direct detection data. " }, - "github/yongsukyee/uncertain_blackholemass": { - "id": "github/yongsukyee/uncertain_blackholemass", - "title": "github/yongsukyee/uncertain_blackholemass", - "url": " https://rseng.github.io/software/repository/github/yongsukyee/uncertain_blackholemass", - "content": "Uncertainty quantification of black hole mass estimation" + "github/bradkav/EarthScatterLikelihood": { + "id": "github/bradkav/EarthScatterLikelihood", + "title": "github/bradkav/EarthScatterLikelihood", + "url": " https://rseng.github.io/software/repository/github/bradkav/EarthScatterLikelihood", + "content": "Code for calculating event rates and likelihoods for Dark Matter direct detection experiments in the presence of Earth-Scattering" }, - "github/phillippro/pexo": { - "id": "github/phillippro/pexo", - "title": "github/phillippro/pexo", - "url": " https://rseng.github.io/software/repository/github/phillippro/pexo", - "content": "a global modeling framework for ns timing, μas astrometry, and μm/s radial velocities" + "github/bradkav/BlackHolesDarkDress": { + "id": "github/bradkav/BlackHolesDarkDress", + "title": "github/bradkav/BlackHolesDarkDress", + "url": " https://rseng.github.io/software/repository/github/bradkav/BlackHolesDarkDress", + "content": "Code for studying primordial black hole (PBH) binaries, clothed in dark matter (DM) halos, associated with the paper "Black Holes' Dark Dress: On the merger rate of a subdominant population of primordial black holes"." }, - "github/phillippro/agatha": { - "id": "github/phillippro/agatha", - "title": "github/phillippro/agatha", - "url": " https://rseng.github.io/software/repository/github/phillippro/agatha", - "content": "Disentangling period signals from correlated noise in a periodogram framework" + "github/bradkav/runDM": { + "id": "github/bradkav/runDM", + "title": "github/bradkav/runDM", + "url": " https://rseng.github.io/software/repository/github/bradkav/runDM", + "content": "A tool (in Mathematica and Python) for calculating the running of the couplings of Dark Matter (DM) to the Standard Model (SM) in simplified models with vector mediators." }, - "github/occupationMeasurement/occupationMeasurement": { - "id": "github/occupationMeasurement/occupationMeasurement", - "title": "github/occupationMeasurement/occupationMeasurement", - "url": " https://rseng.github.io/software/repository/github/occupationMeasurement/occupationMeasurement", - "content": "A package to help with the (interactive) coding and measurement of occupations" + "github/bradkav/EarthShadow": { + "id": "github/bradkav/EarthShadow", + "title": "github/bradkav/EarthShadow", + "url": " https://rseng.github.io/software/repository/github/bradkav/EarthShadow", + "content": "A tool for calculating the impact of Earth-scattering on the distribution of Dark Matter (DM) particles. Includes (Mathematica) code, numerical results, plots and animations." }, - "github/quinlanW/dbMisLoc": { - "id": "github/quinlanW/dbMisLoc", - "title": "github/quinlanW/dbMisLoc", - "url": " https://rseng.github.io/software/repository/github/quinlanW/dbMisLoc", - "content": "None" + "github/bradkav/verne": { + "id": "github/bradkav/verne", + "title": "github/bradkav/verne", + "url": " https://rseng.github.io/software/repository/github/bradkav/verne", + "content": "Python code for calculating the Earth-stopping effect for super-heavy Dark Matter (DM)." }, - "github/RafaelSdeSouza/qrpca": { - "id": "github/RafaelSdeSouza/qrpca", - "title": "github/RafaelSdeSouza/qrpca", - "url": " https://rseng.github.io/software/repository/github/RafaelSdeSouza/qrpca", - "content": "QR based Principal Components Analysis" + "github/bradkav/CEvNS": { + "id": "github/bradkav/CEvNS", + "title": "github/bradkav/CEvNS", + "url": " https://rseng.github.io/software/repository/github/bradkav/CEvNS", + "content": "Code for calculating Coherent Elastic Neutrino-Nucleus Scattering (CEvNS) cross sections and recoil spectra. Also includes code for obtaining New Physics constraints from the COHERENT-2017 results." + }, + "github/bradkav/DMRadon": { + "id": "github/bradkav/DMRadon", + "title": "github/bradkav/DMRadon", + "url": " https://rseng.github.io/software/repository/github/bradkav/DMRadon", + "content": "Tools for calculating the Radon Transform, for use in the analysis of Directional Dark Matter Direct Detection" }, - "github/vdemichev/DiaNN": { - "id": "github/vdemichev/DiaNN", - "title": "github/vdemichev/DiaNN", - "url": " https://rseng.github.io/software/repository/github/vdemichev/DiaNN", - "content": "DIA-NN - a universal automated software suite for DIA proteomics data analysis. 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Professional geographical SIR model with a flexible plugin architecture to support complex scenario modelling" }, - "github/seawander/DebrisDiskFM": { - "id": "github/seawander/DebrisDiskFM", - "title": "github/seawander/DebrisDiskFM", - "url": " https://rseng.github.io/software/repository/github/seawander/DebrisDiskFM", - "content": "Debris Disk Forward Modeling" + "github/MMV-Lab/mmv_im2im": { + "id": "github/MMV-Lab/mmv_im2im", + "title": "github/MMV-Lab/mmv_im2im", + "url": " https://rseng.github.io/software/repository/github/MMV-Lab/mmv_im2im", + "content": "Python package for deep learning based image to image transformation" }, - "github/seawander/centerRadon": { - "id": "github/seawander/centerRadon", - "title": "github/seawander/centerRadon", - "url": " https://rseng.github.io/software/repository/github/seawander/centerRadon", - "content": "Center determination code based on Radon Transform" + "github/NickMilsonPhysics/BinaryStarSolver": { + "id": "github/NickMilsonPhysics/BinaryStarSolver", + "title": "github/NickMilsonPhysics/BinaryStarSolver", + "url": " https://rseng.github.io/software/repository/github/NickMilsonPhysics/BinaryStarSolver", + "content": "BinaryStarSolver is a Python 3 program which solves for the orbital elements of binary stars, given radial velocity time series" }, - "github/chhylp123/hifiasm": { - "id": "github/chhylp123/hifiasm", - "title": "github/chhylp123/hifiasm", - "url": " https://rseng.github.io/software/repository/github/chhylp123/hifiasm", - "content": "Hifiasm: a haplotype-resolved assembler for accurate Hifi reads " + "github/bionlplab/GlaucomaNet": { + "id": "github/bionlplab/GlaucomaNet", + "title": "github/bionlplab/GlaucomaNet", + "url": " https://rseng.github.io/software/repository/github/bionlplab/GlaucomaNet", + "content": "A deep-learning algorithm for the diagnosis of primary open-angle glaucoma from fundus photographs" }, - "github/reality/klarigi": { - "id": "github/reality/klarigi", - "title": "github/reality/klarigi", - "url": " https://rseng.github.io/software/repository/github/reality/klarigi", - "content": "None" + "github/sstadick/perbase": { + "id": "github/sstadick/perbase", + "title": "github/sstadick/perbase", + "url": " https://rseng.github.io/software/repository/github/sstadick/perbase", + "content": "Per-base per-nucleotide depth analysis" }, - "github/ECP-copa/Cabana": { - "id": "github/ECP-copa/Cabana", - "title": "github/ECP-copa/Cabana", - "url": " https://rseng.github.io/software/repository/github/ECP-copa/Cabana", - "content": "Performance-portable library for particle-based simulations" + "github/jellis18/PTMCMCSampler": { + "id": "github/jellis18/PTMCMCSampler", + "title": "github/jellis18/PTMCMCSampler", + "url": " https://rseng.github.io/software/repository/github/jellis18/PTMCMCSampler", + "content": "Parallel tempering MCMC sampler package written in Python" }, - "github/keatonb/Pyriod": { - "id": "github/keatonb/Pyriod", - "title": "github/keatonb/Pyriod", - "url": " https://rseng.github.io/software/repository/github/keatonb/Pyriod", - "content": "Python implementation of basic period detection and fitting routines for astronomical time series." + "github/NathanSkene/EWCE": { + "id": "github/NathanSkene/EWCE", + "title": "github/NathanSkene/EWCE", + "url": " https://rseng.github.io/software/repository/github/NathanSkene/EWCE", + "content": "Expression Weighted Celltype Enrichment. See the package website for up-to-date instructions on usage." }, - "github/keatonb/TESS_PRF": { - "id": "github/keatonb/TESS_PRF", - "title": "github/keatonb/TESS_PRF", - "url": " https://rseng.github.io/software/repository/github/keatonb/TESS_PRF", - "content": "Tools to display the TESS pixel response function (PRF) at any location on the detector" + "github/NathanSkene/MAGMA_Celltyping": { + "id": "github/NathanSkene/MAGMA_Celltyping", + "title": "github/NathanSkene/MAGMA_Celltyping", + "url": " https://rseng.github.io/software/repository/github/NathanSkene/MAGMA_Celltyping", + "content": "Find causal cell-types underlying complex trait genetics" }, - "github/xraypy/xraylarch": { - "id": "github/xraypy/xraylarch", - "title": "github/xraypy/xraylarch", - "url": " https://rseng.github.io/software/repository/github/xraypy/xraylarch", - "content": "Larch: Applications and Python Library for Data Analysis of X-ray Absorption Spectroscopy (XAS, XANES, XAFS, EXAFS), X-ray Fluorescence (XRF) Spectroscopy and Imaging, and more." + "github/Zilong-Li/PCAone": { + "id": "github/Zilong-Li/PCAone", + "title": "github/Zilong-Li/PCAone", + "url": " https://rseng.github.io/software/repository/github/Zilong-Li/PCAone", + "content": "Principal Component Analysis All in One" }, - "github/yhoogstrate/fastafs": { - "id": "github/yhoogstrate/fastafs", - "title": "github/yhoogstrate/fastafs", - "url": " https://rseng.github.io/software/repository/github/yhoogstrate/fastafs", - "content": "toolkit for file system virtualisation of random access compressed FASTA, FAI, DICT & TWOBIT files" + "github/tseemann/abricate": { + "id": "github/tseemann/abricate", + "title": "github/tseemann/abricate", + "url": " https://rseng.github.io/software/repository/github/tseemann/abricate", + "content": ":mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes" }, - "github/arviz-devs/preliz": { - "id": "github/arviz-devs/preliz", - "title": "github/arviz-devs/preliz", - "url": " https://rseng.github.io/software/repository/github/arviz-devs/preliz", - "content": "Tools to help you pick a prior" + "github/tseemann/mlst": { + "id": "github/tseemann/mlst", + "title": "github/tseemann/mlst", + "url": " https://rseng.github.io/software/repository/github/tseemann/mlst", + "content": ":id: Scan contig files against PubMLST typing schemes" }, - "github/arviz-devs/arviz": { - "id": "github/arviz-devs/arviz", - "title": "github/arviz-devs/arviz", - "url": " https://rseng.github.io/software/repository/github/arviz-devs/arviz", - "content": "Exploratory analysis of Bayesian models with Python" + "github/tseemann/snippy": { + "id": "github/tseemann/snippy", + "title": "github/tseemann/snippy", + "url": " https://rseng.github.io/software/repository/github/tseemann/snippy", + "content": ":scissors: :zap: Rapid haploid variant calling and core genome alignment" }, - "github/wasserman-group/pyCADMium": { - "id": "github/wasserman-group/pyCADMium", - "title": "github/wasserman-group/pyCADMium", - "url": " https://rseng.github.io/software/repository/github/wasserman-group/pyCADMium", - "content": "Solve the Kohn-Sham equations on a prolate spheroidal grid. 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It aims to be a better 'top'." + "github/tseemann/VelvetOptimiser": { + "id": "github/tseemann/VelvetOptimiser", + "title": "github/tseemann/VelvetOptimiser", + "url": " https://rseng.github.io/software/repository/github/tseemann/VelvetOptimiser", + "content": ":chart_with_upwards_trend: Automatically optimise three of Velvet's assembly parameters." }, - "github/python-streamz/streamz": { - "id": "github/python-streamz/streamz", - "title": "github/python-streamz/streamz", - "url": " https://rseng.github.io/software/repository/github/python-streamz/streamz", - "content": "Real-time stream processing for python" + "github/tseemann/snp-dists": { + "id": "github/tseemann/snp-dists", + "title": "github/tseemann/snp-dists", + "url": " https://rseng.github.io/software/repository/github/tseemann/snp-dists", + "content": "Pairwise SNP distance matrix from a FASTA sequence alignment" }, - "github/julie-forman-kay-lab/SPyCi-PDB": { - "id": "github/julie-forman-kay-lab/SPyCi-PDB", - "title": "github/julie-forman-kay-lab/SPyCi-PDB", - 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"title": "github/hyperopt/hyperopt", - "url": " https://rseng.github.io/software/repository/github/hyperopt/hyperopt", - "content": "Distributed Asynchronous Hyperparameter Optimization in Python" + "github/medema-group/bigslice": { + "id": "github/medema-group/bigslice", + "title": "github/medema-group/bigslice", + "url": " https://rseng.github.io/software/repository/github/medema-group/bigslice", + "content": "A highly scalable, user-interactive tool for the large scale analysis of Biosynthetic Gene Clusters data" + }, + "github/TearsWaiting/MIMML": { + "id": "github/TearsWaiting/MIMML", + "title": "github/TearsWaiting/MIMML", + "url": " https://rseng.github.io/software/repository/github/TearsWaiting/MIMML", + "content": "The implement of MIMML in paper: Accelerating Bioactive Peptides Discovery via Mutual Information based Meta-learning" }, - "github/nickelnine37/pykronecker": { - "id": "github/nickelnine37/pykronecker", - "title": "github/nickelnine37/pykronecker", - "url": " https://rseng.github.io/software/repository/github/nickelnine37/pykronecker", - "content": "A python library for creating Kronecker Product operators with efficient lazy computation" + "github/vallis/libstempo": { + "id": "github/vallis/libstempo", + "title": "github/vallis/libstempo", + "url": " https://rseng.github.io/software/repository/github/vallis/libstempo", + "content": "libstempo — a Python wrapper for tempo2" }, - "github/shaelebrown/TDApplied": { - "id": "github/shaelebrown/TDApplied", - "title": "github/shaelebrown/TDApplied", - "url": " https://rseng.github.io/software/repository/github/shaelebrown/TDApplied", - "content": "An R package for statistics and machine learning with persistence diagrams" + "github/vallis/mc3pta": { + "id": "github/vallis/mc3pta", + "title": "github/vallis/mc3pta", + "url": " https://rseng.github.io/software/repository/github/vallis/mc3pta", + "content": "Bayesian-inference tools for pulsar-timing-array data" }, - "github/MikkelSchubert/adapterremoval": { - "id": "github/MikkelSchubert/adapterremoval", - "title": "github/MikkelSchubert/adapterremoval", - "url": " https://rseng.github.io/software/repository/github/MikkelSchubert/adapterremoval", - "content": "AdapterRemoval v2 - rapid adapter trimming, identification, and read merging" + "github/abschneider/StrainHub": { + "id": "github/abschneider/StrainHub", + "title": "github/abschneider/StrainHub", + "url": " https://rseng.github.io/software/repository/github/abschneider/StrainHub", + "content": "Welcome to the StrainHub Repo - Files and Data - StrainHub Online:" }, - "github/gtayana/CVRMS": { - "id": "github/gtayana/CVRMS", - "title": "github/gtayana/CVRMS", - "url": " https://rseng.github.io/software/repository/github/gtayana/CVRMS", - "content": "Marker selection for genome-wide prediction" + "github/rasg-affiliates/healvis": { + "id": "github/rasg-affiliates/healvis", + "title": "github/rasg-affiliates/healvis", + "url": " https://rseng.github.io/software/repository/github/rasg-affiliates/healvis", + "content": "Visibility simulation off of HEALPix shells." }, - "github/fermisurfaces/IFermi": { - "id": "github/fermisurfaces/IFermi", - "title": "github/fermisurfaces/IFermi", - "url": " https://rseng.github.io/software/repository/github/fermisurfaces/IFermi", - "content": "Fermi surface generation, analysis and visualisation." + "github/landlab/landlab": { + "id": "github/landlab/landlab", + "title": "github/landlab/landlab", + "url": " https://rseng.github.io/software/repository/github/landlab/landlab", + "content": "Landlab codebase, wiki, and tests" }, - "github/aidenlab/juicer": { - "id": "github/aidenlab/juicer", - "title": "github/aidenlab/juicer", - "url": " https://rseng.github.io/software/repository/github/aidenlab/juicer", - "content": "A One-Click System for Analyzing Loop-Resolution Hi-C Experiments" + "github/tschad/pycelp": { + "id": "github/tschad/pycelp", + "title": "github/tschad/pycelp", + "url": " https://rseng.github.io/software/repository/github/tschad/pycelp", + "content": "a Python package for Coronal Emission Line Polarization " }, - "github/RongquanWang/ELF-DPC": { - "id": "github/RongquanWang/ELF-DPC", - "title": "github/RongquanWang/ELF-DPC", - "url": " https://rseng.github.io/software/repository/github/RongquanWang/ELF-DPC", - "content": "An ensemble learning framework for detecting protein complexes from PPI networks" + "github/shilpagarg/WHdenovo": { + "id": "github/shilpagarg/WHdenovo", + "title": "github/shilpagarg/WHdenovo", + "url": " https://rseng.github.io/software/repository/github/shilpagarg/WHdenovo", + "content": "None" }, - "github/hsergi/Roman_Coronagraph_ETC": { - "id": "github/hsergi/Roman_Coronagraph_ETC", - "title": "github/hsergi/Roman_Coronagraph_ETC", - "url": " https://rseng.github.io/software/repository/github/hsergi/Roman_Coronagraph_ETC", - "content": "Exposure Time Calculator for the Roman Coronagraph Instrument" + "github/gorpipe/gor": { + "id": "github/gorpipe/gor", + "title": "github/gorpipe/gor", + "url": " https://rseng.github.io/software/repository/github/gorpipe/gor", + "content": "GORpipe is a tool based on a genomic ordered relational architecture and allows analysis of large sets of genomic and phenotypic tabular data using declarative query language, in a parallel execution engine." }, - 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JOAN facilitates communication between human input devices and CARLA, the implementation of haptic feedback, systematically storing experiment data, and the automatic execution of experiments with multiple experimental conditions." }, - "github/r-spatial/rgee": { - "id": "github/r-spatial/rgee", - "title": "github/r-spatial/rgee", - "url": " https://rseng.github.io/software/repository/github/r-spatial/rgee", - "content": "Google Earth Engine for R" + "github/QEF/q-e": { + "id": "github/QEF/q-e", + "title": "github/QEF/q-e", + "url": " https://rseng.github.io/software/repository/github/QEF/q-e", + "content": "Mirror of the Quantum ESPRESSO repository. Please do not post Issues or pull requests here. Use gitlab.com/QEF/q-e instead." }, - "github/hsinnan75/GSAlign": { - "id": "github/hsinnan75/GSAlign", - "title": "github/hsinnan75/GSAlign", - "url": " https://rseng.github.io/software/repository/github/hsinnan75/GSAlign", - "content": "GSAlign: an ultra-fast sequence alignment algorithm for intra-species genome comparison" + "github/ruggiero/galstep": { + "id": "github/ruggiero/galstep", + "title": "github/ruggiero/galstep", + "url": " https://rseng.github.io/software/repository/github/ruggiero/galstep", + "content": "Generates initial conditions for a spiral galaxy simulation in a format that can be read in GADGET2 or RAMSES, or alternatively in the HDF5 format." }, - "github/hsinnan75/MapCaller": { - "id": "github/hsinnan75/MapCaller", - "title": "github/hsinnan75/MapCaller", - "url": " https://rseng.github.io/software/repository/github/hsinnan75/MapCaller", - "content": "MapCaller – An efficient and versatile approach for short-read alignment and variant detection in high-throughput sequenced genomes" + "github/ruggiero/clustep": { + "id": "github/ruggiero/clustep", + "title": "github/ruggiero/clustep", + "url": " https://rseng.github.io/software/repository/github/ruggiero/clustep", + "content": "Generates initial conditions for a galaxy cluster halo simulation in a format that can be read in GADGET2 or RAMSES." }, - "github/AlexMikes/AutoFunc": { - "id": "github/AlexMikes/AutoFunc", - "title": "github/AlexMikes/AutoFunc", - "url": " https://rseng.github.io/software/repository/github/AlexMikes/AutoFunc", - "content": "Data Mining for Automated Functional Representations" + "github/dirac-institute/asterogap": { + "id": "github/dirac-institute/asterogap", + "title": "github/dirac-institute/asterogap", + "url": " https://rseng.github.io/software/repository/github/dirac-institute/asterogap", + "content": "A Bayesian-based Gaussian Process model set to fit sparsely-sampled asteroid light curves." }, - "github/NASA-PDS/naif-pds4-bundler": { - "id": "github/NASA-PDS/naif-pds4-bundler", - "title": "github/NASA-PDS/naif-pds4-bundler", - "url": " https://rseng.github.io/software/repository/github/NASA-PDS/naif-pds4-bundler", - "content": "Package to generate PDS4 SPICE Kernels Archives" + "github/doriancazeneuve/ODNet": { + "id": "github/doriancazeneuve/ODNet", + "title": "github/doriancazeneuve/ODNet", + "url": " https://rseng.github.io/software/repository/github/doriancazeneuve/ODNet", + "content": "ODNet : Asteroid Occultation Detection Convolutional Neural Network" }, - "github/eliotayache/GAMMA": { - "id": "github/eliotayache/GAMMA", - "title": "github/eliotayache/GAMMA", - "url": " https://rseng.github.io/software/repository/github/eliotayache/GAMMA", - "content": "Relativistic hydro and local cooling on a moving mesh" + "github/Ge-Lab/USAT": { + "id": "github/Ge-Lab/USAT", + "title": "github/Ge-Lab/USAT", + "url": " https://rseng.github.io/software/repository/github/Ge-Lab/USAT", + "content": "USAT is a software for analyzing and visualizing the Tandem Repeat (TR) alleles" }, - "github/aothmane-control/Algebraic-differentiators": { - "id": "github/aothmane-control/Algebraic-differentiators", - "title": "github/aothmane-control/Algebraic-differentiators", - "url": " https://rseng.github.io/software/repository/github/aothmane-control/Algebraic-differentiators", - "content": "A Python class implementing all necessary tools for the design, analysis, and discretization of algebraic differentiators. An interface to Matlab is also provided." + "github/OpenBioLink/Explorer": { + "id": "github/OpenBioLink/Explorer", + "title": "github/OpenBioLink/Explorer", + "url": " https://rseng.github.io/software/repository/github/OpenBioLink/Explorer", + "content": "None" }, - "github/drcandacemakedamoore/cleanX": { - "id": "github/drcandacemakedamoore/cleanX", - "title": "github/drcandacemakedamoore/cleanX", - "url": " https://rseng.github.io/software/repository/github/drcandacemakedamoore/cleanX", - "content": "Python library for exploring, cleaning, normalizing, and augmenting large datasets of radiological data." + "github/byuflowlab/GXBeam.jl": { + "id": "github/byuflowlab/GXBeam.jl", + "title": "github/byuflowlab/GXBeam.jl", + "url": " https://rseng.github.io/software/repository/github/byuflowlab/GXBeam.jl", + "content": "Pure Julia Implementation of Geometrically Exact Beam Theory" }, - "github/pmkruyen/dearscholar": { - "id": "github/pmkruyen/dearscholar", - "title": "github/pmkruyen/dearscholar", - "url": " https://rseng.github.io/software/repository/github/pmkruyen/dearscholar", - "content": "DearScholar: An open-source smartphone app for longitudinal scientific qualitative and quantitative (self-report) diary, log and survey research" + "github/phillippro/agatha": { + "id": "github/phillippro/agatha", + "title": "github/phillippro/agatha", + "url": " https://rseng.github.io/software/repository/github/phillippro/agatha", + "content": "Disentangling period signals from correlated noise in a periodogram framework" }, - "github/ACTCollaboration/zCluster": { - "id": "github/ACTCollaboration/zCluster", - "title": "github/ACTCollaboration/zCluster", - "url": " https://rseng.github.io/software/repository/github/ACTCollaboration/zCluster", - "content": "A package for measuring galaxy cluster photometric redshifts using data from large public surveys." + "github/phillippro/pexo": { + "id": "github/phillippro/pexo", + "title": "github/phillippro/pexo", + "url": " https://rseng.github.io/software/repository/github/phillippro/pexo", + "content": "a global modeling framework for ns timing, μas astrometry, and μm/s radial velocities" }, - "github/saezlab/PHONEMeS": { - "id": "github/saezlab/PHONEMeS", - "title": "github/saezlab/PHONEMeS", - "url": " https://rseng.github.io/software/repository/github/saezlab/PHONEMeS", - "content": " PHONEMeS (PHOsphorylation NEtworks for Mass Spectrometry) is an R package to model signalling networks based on untargeted phosphoproteomics" + "github/CRPropa/CRPropa3": { + "id": "github/CRPropa/CRPropa3", + "title": "github/CRPropa/CRPropa3", + "url": " https://rseng.github.io/software/repository/github/CRPropa/CRPropa3", + "content": " CRPropa is a public astrophysical simulation framework for propagating extraterrestrial ultra-high energy particles. https://crpropa.github.io/CRPropa3/" }, - "github/optimusmoose/jsms": { - "id": "github/optimusmoose/jsms", - "title": "github/optimusmoose/jsms", - "url": " https://rseng.github.io/software/repository/github/optimusmoose/jsms", - "content": "A modular JavaScript viewer for mass spectrometry data" + "github/CRPropa/CRPropa2": { + "id": "github/CRPropa/CRPropa2", + "title": "github/CRPropa/CRPropa2", + "url": " https://rseng.github.io/software/repository/github/CRPropa/CRPropa2", + "content": "Previous version of CRPropa" }, - "github/remi-adam/minot": { - "id": "github/remi-adam/minot", - "title": "github/remi-adam/minot", - "url": " https://rseng.github.io/software/repository/github/remi-adam/minot", - "content": "minot: Modeling of the ICM (Non-)thermal content and Observables prediction Tools" + "github/sonjageorgievska/CClusTera": { + "id": "github/sonjageorgievska/CClusTera", + "title": "github/sonjageorgievska/CClusTera", + "url": " https://rseng.github.io/software/repository/github/sonjageorgievska/CClusTera", + "content": "A javascript library for interactive hierarchical visualization of 3D points (suitable for large hierarchical datasets) . Based on graphosaurus.js (https://github.com/frewsxcv/graphosaurus), which runs on Three.js. 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"url": " https://rseng.github.io/software/repository/github/duffell/RT1D", - "content": "A 1D Model for Rayleigh-Taylor Instability" + "github/cconroy20/fsps": { + "id": "github/cconroy20/fsps", + "title": "github/cconroy20/fsps", + "url": " https://rseng.github.io/software/repository/github/cconroy20/fsps", + "content": "Flexible Stellar Population Synthesis" }, - "github/duffell/Disco": { - "id": "github/duffell/Disco", - "title": "github/duffell/Disco", - "url": " https://rseng.github.io/software/repository/github/duffell/Disco", - "content": "A moving-mesh magnetohydrodynamics code designed for the study of astrophysical disks." + "github/eisascience/HISTA": { + "id": "github/eisascience/HISTA", + "title": "github/eisascience/HISTA", + "url": " https://rseng.github.io/software/repository/github/eisascience/HISTA", + "content": "Human Infertility Single-cell Testis Atlas" }, - "github/dnarayanan/powderday": { - "id": "github/dnarayanan/powderday", - "title": "github/dnarayanan/powderday", - 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Described by Firtina et al. (published in NARGAB https://doi.org/10.1093/nargab/lqad004)" }, - "github/GenomePathogenAnalysisService/read-it-and-keep": { - "id": "github/GenomePathogenAnalysisService/read-it-and-keep", - "title": "github/GenomePathogenAnalysisService/read-it-and-keep", - "url": " https://rseng.github.io/software/repository/github/GenomePathogenAnalysisService/read-it-and-keep", - "content": "Read contamination removal" + "github/slzarate/parliament2": { + "id": "github/slzarate/parliament2", + "title": "github/slzarate/parliament2", + "url": " https://rseng.github.io/software/repository/github/slzarate/parliament2", + "content": "Runs a combination of tools to generate structural variant calls on short-read whole-genome sequencing data" }, - "github/Mat-dp/mat-dp-core": { - "id": "github/Mat-dp/mat-dp-core", - "title": "github/Mat-dp/mat-dp-core", - "url": " https://rseng.github.io/software/repository/github/Mat-dp/mat-dp-core", - "content": "Mat-dp core cotains the key methods used in the broader Mat-dp model. Mat-dp aims to deliver user-friendly and open-access software to study the environmental implications of materials used for building low-carbon systems." + "github/dingshandeng/diskmint": { + "id": "github/dingshandeng/diskmint", + "title": "github/dingshandeng/diskmint", + "url": " https://rseng.github.io/software/repository/github/dingshandeng/diskmint", + "content": "DiskMINT (Disk Model For INdividual Targets): a tool to estimate disk masses with CO isotopologues" }, - "github/timoast/signac": { - "id": "github/timoast/signac", - "title": "github/timoast/signac", - "url": " https://rseng.github.io/software/repository/github/timoast/signac", - "content": "R toolkit for the analysis of single-cell chromatin data" + "github/SietzeN/glottospace": { + "id": "github/SietzeN/glottospace", + "title": "github/SietzeN/glottospace", + "url": " https://rseng.github.io/software/repository/github/SietzeN/glottospace", + "content": "Geospatial analysis of linguistic data" }, - "github/UBC-Astrophysics/kd-match": { - "id": "github/UBC-Astrophysics/kd-match", - "title": "github/UBC-Astrophysics/kd-match", - "url": " https://rseng.github.io/software/repository/github/UBC-Astrophysics/kd-match", - "content": "Rapidly matches stellar catalogues" + "github/jczarnowski/DeepFactors": { + "id": "github/jczarnowski/DeepFactors", + "title": "github/jczarnowski/DeepFactors", + "url": " https://rseng.github.io/software/repository/github/jczarnowski/DeepFactors", + "content": "Real-Time Probabilistic Dense Monocular SLAM Using Compact Code Representation" }, - "github/cwentland0/perform": { - "id": "github/cwentland0/perform", - "title": "github/cwentland0/perform", - "url": " https://rseng.github.io/software/repository/github/cwentland0/perform", - "content": "One-dimensional unsteady compressible reacting flow simulation framework, designed for simple prototyping and testing of novel reduced-order model methods." + "github/hknd23/idcempy": { + "id": "github/hknd23/idcempy", + "title": "github/hknd23/idcempy", + "url": " https://rseng.github.io/software/repository/github/hknd23/idcempy", + "content": "Inflated Discrete Choice Models" }, - "github/pelahi/TreeFrog": { - "id": "github/pelahi/TreeFrog", - "title": "github/pelahi/TreeFrog", - "url": " https://rseng.github.io/software/repository/github/pelahi/TreeFrog", - "content": "Software to build Halo Merger Trees/compare halo catalogs" + "github/dunhamlab/PacRAT": { + "id": "github/dunhamlab/PacRAT", + "title": "github/dunhamlab/PacRAT", + "url": " https://rseng.github.io/software/repository/github/dunhamlab/PacRAT", + "content": "Improving long-read barcode-variant mapping using multiple sequence alignment. " }, - "github/pelahi/VELOCIraptor-STF": { - "id": "github/pelahi/VELOCIraptor-STF", - "title": "github/pelahi/VELOCIraptor-STF", - "url": " https://rseng.github.io/software/repository/github/pelahi/VELOCIraptor-STF", - "content": "Galaxy/(sub)Halo finder for N-body simulations" + "github/bjmorgan/py-sc-fermi": { + "id": "github/bjmorgan/py-sc-fermi", + "title": "github/bjmorgan/py-sc-fermi", + "url": " https://rseng.github.io/software/repository/github/bjmorgan/py-sc-fermi", + "content": "py-sc-fermi is a materials modelling code for calculating self-consistent Fermi energies and defect concentrations under thermodynamic equilibrium (or quasi-equilibrium) given defect formation energies." }, - "github/frescigno/magpy_rv": { - "id": "github/frescigno/magpy_rv", - "title": "github/frescigno/magpy_rv", - "url": " https://rseng.github.io/software/repository/github/frescigno/magpy_rv", - "content": "Modelling Activity with Gaussian process regression in Python" + "github/epi2me-labs/mapula": { + "id": "github/epi2me-labs/mapula", + "title": "github/epi2me-labs/mapula", + "url": " https://rseng.github.io/software/repository/github/epi2me-labs/mapula", + "content": "Generate mapping stats at your chosen level of aggregation" }, - 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It is written in Java, runs an all major platforms and it is easy to use. FDT is based on an asynchronous, flexible multithreaded system and is using the capabilities of the Java NIO libraries." + }, + "github/svi-opensource/libics": { + "id": "github/svi-opensource/libics", + "title": "github/svi-opensource/libics", + "url": " https://rseng.github.io/software/repository/github/svi-opensource/libics", + "content": "Image Cytometry Standard file reading and writing." + }, + "github/thejasvibr/bat_beamshapes": { + "id": "github/thejasvibr/bat_beamshapes", + "title": "github/thejasvibr/bat_beamshapes", + "url": " https://rseng.github.io/software/repository/github/thejasvibr/bat_beamshapes", + "content": "Directivity functions for various sound sources" + }, + "github/EGaraldi/corecon": { + "id": "github/EGaraldi/corecon", + "title": "github/EGaraldi/corecon", + "url": " https://rseng.github.io/software/repository/github/EGaraldi/corecon", + "content": "User-friendly collection of Reionization-related constraints" }, - "github/ylab-hi/ScanITD": { - "id": "github/ylab-hi/ScanITD", - 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A python tool for the calculation and tabulation of atomic response functions for ionization via dark matter-electron scatterings." }, - "github/anmolter/XLUR": { - "id": "github/anmolter/XLUR", - "title": "github/anmolter/XLUR", - "url": " https://rseng.github.io/software/repository/github/anmolter/XLUR", - "content": "A Python toolbox for ArcGIS Pro that enables the development and application of land use regression models." + "github/temken/DaMaSCUS": { + "id": "github/temken/DaMaSCUS", + "title": "github/temken/DaMaSCUS", + "url": " https://rseng.github.io/software/repository/github/temken/DaMaSCUS", + "content": "Dark Matter Simulation Code for Underground Scatterings" }, - "github/linneas/condetri": { - "id": "github/linneas/condetri", - "title": "github/linneas/condetri", - "url": " https://rseng.github.io/software/repository/github/linneas/condetri", - "content": "Automatically exported from code.google.com/p/condetri" + "github/theLongLab/CATE": { + "id": "github/theLongLab/CATE", + "title": "github/theLongLab/CATE", + "url": " https://rseng.github.io/software/repository/github/theLongLab/CATE", + "content": "A fast and scalable CUDA implementation to conduct highly parallelized evolutionary tests on large scale genomic data." }, - 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"title": "github/astrostat/Automark", - "url": " https://rseng.github.io/software/repository/github/astrostat/Automark", - "content": "Automatic marking of marked Poisson process in astronomical high-dimensional datasets" + "github/Parsl/parsl": { + "id": "github/Parsl/parsl", + "title": "github/Parsl/parsl", + "url": " https://rseng.github.io/software/repository/github/Parsl/parsl", + "content": "Parsl - Parallel Scripting Library" }, - "github/astrostat/BASCS": { - "id": "github/astrostat/BASCS", - "title": "github/astrostat/BASCS", - "url": " https://rseng.github.io/software/repository/github/astrostat/BASCS", - "content": "Bayesian Separation of Close Sources" + "github/gogetdata/ggd-utils": { + "id": "github/gogetdata/ggd-utils", + "title": "github/gogetdata/ggd-utils", + "url": " https://rseng.github.io/software/repository/github/gogetdata/ggd-utils", + "content": "programs for use in ggd" }, - "github/astrostat/LIRA": { - "id": "github/astrostat/LIRA", - "title": "github/astrostat/LIRA", - "url": " https://rseng.github.io/software/repository/github/astrostat/LIRA", - "content": "Low-counts Image Reconstruction and Analysis" + "github/4pisky/fourpisky-core": { + "id": "github/4pisky/fourpisky-core", + "title": "github/4pisky/fourpisky-core", + "url": " https://rseng.github.io/software/repository/github/4pisky/fourpisky-core", + "content": "Core code defining alert handling, etc for the 4PiSky voevent hub." }, - "github/INCEPTdk/adaptr": { - "id": "github/INCEPTdk/adaptr", - "title": "github/INCEPTdk/adaptr", - "url": " https://rseng.github.io/software/repository/github/INCEPTdk/adaptr", - "content": "Adaptive Trial Simulator" + "github/tesselle/aion": { + "id": "github/tesselle/aion", + "title": "github/tesselle/aion", + "url": " https://rseng.github.io/software/repository/github/tesselle/aion", + "content": ":stopwatch: Archaeological Time Series" }, - "github/brainets/frites": { - "id": "github/brainets/frites", - "title": "github/brainets/frites", - "url": " https://rseng.github.io/software/repository/github/brainets/frites", - "content": "Framework for Information Theoretical analysis of Electrophysiological data and Statistics" + "github/refresh-bio/whisper": { + "id": "github/refresh-bio/whisper", + "title": "github/refresh-bio/whisper", + "url": " https://rseng.github.io/software/repository/github/refresh-bio/whisper", + "content": "None" }, - "github/nwchemgit/nwchem": { - "id": "github/nwchemgit/nwchem", - "title": "github/nwchemgit/nwchem", - "url": " https://rseng.github.io/software/repository/github/nwchemgit/nwchem", - "content": "NWChem: Open Source High-Performance Computational Chemistry" + "github/refresh-bio/agc": { + "id": "github/refresh-bio/agc", + "title": "github/refresh-bio/agc", + "url": " https://rseng.github.io/software/repository/github/refresh-bio/agc", + "content": "Assembled Genomes Compressor" }, - "github/ttgump/scDHMap": { - "id": "github/ttgump/scDHMap", - "title": "github/ttgump/scDHMap", - "url": " https://rseng.github.io/software/repository/github/ttgump/scDHMap", - "content": "Model-based deep hyperbolic manifold learning for visualizing complex hierarchical structures in single-cell genomics data" + "github/eEcoLiDAR/laserchicken": { + "id": "github/eEcoLiDAR/laserchicken", + "title": "github/eEcoLiDAR/laserchicken", + "url": " https://rseng.github.io/software/repository/github/eEcoLiDAR/laserchicken", + "content": "None" }, - 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A software package for massively parallel forward simulation of Pulsed Gradient Spin Echo diffusion weighted MRI experiments on biophysically accurate tissue systems. " }, - "github/kateharborne/SimSpin": { - "id": "github/kateharborne/SimSpin", - "title": "github/kateharborne/SimSpin", - "url": " https://rseng.github.io/software/repository/github/kateharborne/SimSpin", - "content": "SimSpin - A package for the kinematic analysis of galaxy simulations" + "github/KULL-Centre/DEERpredict": { + "id": "github/KULL-Centre/DEERpredict", + "title": "github/KULL-Centre/DEERpredict", + "url": " https://rseng.github.io/software/repository/github/KULL-Centre/DEERpredict", + "content": "Software for the prediction of DEER and PRE data from conformational ensembles." }, - "github/steineggerlab/foldseek": { - "id": "github/steineggerlab/foldseek", - "title": "github/steineggerlab/foldseek", - "url": " https://rseng.github.io/software/repository/github/steineggerlab/foldseek", - "content": "Foldseek enables fast and sensitive comparisons of large structure sets." + "github/bcbio/bcbio.variation.recall": { + "id": "github/bcbio/bcbio.variation.recall", + "title": "github/bcbio/bcbio.variation.recall", + "url": " https://rseng.github.io/software/repository/github/bcbio/bcbio.variation.recall", + "content": "Parallel merging, squaring off and ensemble calling for genomic variants" }, - "github/migueldvb/cine": { - "id": "github/migueldvb/cine", - "title": "github/migueldvb/cine", - "url": " https://rseng.github.io/software/repository/github/migueldvb/cine", - "content": "Calculate infrared pumping rates by solar radiation" + "github/bcbio/bcbio-nextgen": { + "id": "github/bcbio/bcbio-nextgen", + "title": "github/bcbio/bcbio-nextgen", + "url": " https://rseng.github.io/software/repository/github/bcbio/bcbio-nextgen", + "content": "Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis" }, - "github/bblodfon/emba": { - "id": "github/bblodfon/emba", - "title": "github/bblodfon/emba", - "url": " https://rseng.github.io/software/repository/github/bblodfon/emba", - "content": "Ensemble Model Biomarker Analysis R package" + "github/google/jax": { + "id": "github/google/jax", + "title": "github/google/jax", + "url": " https://rseng.github.io/software/repository/github/google/jax", + "content": "Composable transformations of Python+NumPy programs: differentiate, vectorize, JIT to GPU/TPU, and more" }, - "github/orbisgis/lczexplore": { - "id": "github/orbisgis/lczexplore", - "title": "github/orbisgis/lczexplore", - "url": " https://rseng.github.io/software/repository/github/orbisgis/lczexplore", - "content": "None" + "github/google/caliban": { + "id": "github/google/caliban", + "title": "github/google/caliban", + "url": " https://rseng.github.io/software/repository/github/google/caliban", + "content": "Research workflows made easy, locally and in the Cloud." }, - "github/fkoehlin/montepython_2cosmos_public": { - "id": "github/fkoehlin/montepython_2cosmos_public", - "title": "github/fkoehlin/montepython_2cosmos_public", - "url": " https://rseng.github.io/software/repository/github/fkoehlin/montepython_2cosmos_public", - "content": "Public repository for the Monte Python Code modified to work with two independent cosmological parameter sets and independent cosmological calculations per likelihood." + "github/google/best": { + "id": "github/google/best", + "title": "github/google/best", + "url": " https://rseng.github.io/software/repository/github/google/best", + "content": "Bam Error Stats Tool (best): analysis of error types in aligned reads." }, - "github/sfarrens/sfof": { - "id": "github/sfarrens/sfof", - "title": "github/sfarrens/sfof", - "url": " https://rseng.github.io/software/repository/github/sfarrens/sfof", - "content": "SFoF is a friends-of-friends galaxy cluster detection algorithm that operates in either spectroscopic or photometric redshift space. The linking parameters, both transverse and along the line-of-sight, change as a function of redshift to account for selection effects. The code is written in C++ and implements OMP to loop through the photometric redshift bins." + "github/BioMeCIS-Lab/OpenOmics": { + "id": "github/BioMeCIS-Lab/OpenOmics", + "title": "github/BioMeCIS-Lab/OpenOmics", + "url": " https://rseng.github.io/software/repository/github/BioMeCIS-Lab/OpenOmics", + "content": "A bioinformatics API and web-app to integrate multi-omics datasets & interface with public databases." }, - "github/sfarrens/sf_deconvolve": { - "id": "github/sfarrens/sf_deconvolve", - "title": "github/sfarrens/sf_deconvolve", - "url": " https://rseng.github.io/software/repository/github/sfarrens/sf_deconvolve", - "content": "A Python code designed for PSF deconvolution using a low-rank approximation and sparsity. The code can handle a fixed PSF for the entire field or a stack of PSFs for each galaxy position." + "github/PynPoint/PynPoint": { + "id": "github/PynPoint/PynPoint", + "title": "github/PynPoint/PynPoint", + "url": " https://rseng.github.io/software/repository/github/PynPoint/PynPoint", + "content": "Pipeline for processing and analysis of high-contrast imaging data" }, - "github/Trovemaster/Duo": { - "id": "github/Trovemaster/Duo", - "title": "github/Trovemaster/Duo", - "url": " https://rseng.github.io/software/repository/github/Trovemaster/Duo", - "content": "Duo is a diatomic code for solving a fully coupled rovibronic Schroedinger equation" + "github/siminegroup/E2EDNA2": { + "id": "github/siminegroup/E2EDNA2", + "title": "github/siminegroup/E2EDNA2", + "url": " https://rseng.github.io/software/repository/github/siminegroup/E2EDNA2", + "content": "None" }, - "github/Trovemaster/exocross": { - "id": "github/Trovemaster/exocross", - "title": "github/Trovemaster/exocross", - "url": " https://rseng.github.io/software/repository/github/Trovemaster/exocross", - "content": "Fortran 2003 code to generate molecular spectra, partition functions, lifetimes, cooling functions etc using ExoMol line lists" + "github/spinicist/riesling": { + "id": "github/spinicist/riesling", + "title": "github/spinicist/riesling", + "url": " https://rseng.github.io/software/repository/github/spinicist/riesling", + "content": "Radial Interstices Enable Speedy Low-Volume Imaging" }, - "github/Trovemaster/TROVE": { - "id": "github/Trovemaster/TROVE", - "title": "github/Trovemaster/TROVE", - "url": " https://rseng.github.io/software/repository/github/Trovemaster/TROVE", - "content": "Theoretical ROVibrational Energies: A variational program for accurate nuclear motion calculations" + "github/zavolanlab/PAQR2": { + "id": "github/zavolanlab/PAQR2", + "title": "github/zavolanlab/PAQR2", + "url": " https://rseng.github.io/software/repository/github/zavolanlab/PAQR2", + "content": "Updated version of PAQR, which was previously available in the PAQR_KAPAC joint repository." }, - 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"id": "github/tripathi/Atmospheric-Athena", - "title": "github/tripathi/Atmospheric-Athena", - "url": " https://rseng.github.io/software/repository/github/tripathi/Atmospheric-Athena", - "content": "3D Atmospheric escape model with ionizing radiative transfer" + "github/UTEL-UIUC/gtfs_segments": { + "id": "github/UTEL-UIUC/gtfs_segments", + "title": "github/UTEL-UIUC/gtfs_segments", + "url": " https://rseng.github.io/software/repository/github/UTEL-UIUC/gtfs_segments", + "content": "GTFS Segments: A fast and efficient library to generate bus stop spacings" }, - "github/dirmeier/surjectors": { - "id": "github/dirmeier/surjectors", - "title": "github/dirmeier/surjectors", - "url": " https://rseng.github.io/software/repository/github/dirmeier/surjectors", - "content": "Surjection layers for density estimation with normalizing flows" + "github/PanKonstantinos/MEvA-X": { + "id": "github/PanKonstantinos/MEvA-X", + "title": "github/PanKonstantinos/MEvA-X", + "url": " https://rseng.github.io/software/repository/github/PanKonstantinos/MEvA-X", + "content": "Open source Biomarker discovery tool based on multi-objective Evolutionary algorithm and the XGBoost Classifier" }, - 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Please contact asa.stahl@rice.edu or sytang@lowell.edu for more detail." }, - "github/biocore/sortmerna": { - "id": "github/biocore/sortmerna", - "title": "github/biocore/sortmerna", - "url": " https://rseng.github.io/software/repository/github/biocore/sortmerna", - "content": "SortMeRNA: next-generation sequence filtering and alignment tool" + "github/chadagreene/Tide-Model-Driver": { + "id": "github/chadagreene/Tide-Model-Driver", + "title": "github/chadagreene/Tide-Model-Driver", + "url": " https://rseng.github.io/software/repository/github/chadagreene/Tide-Model-Driver", + "content": "Tide Model Driver for MATLAB, version 3.0" }, - "github/biocore/emperor": { - "id": "github/biocore/emperor", - "title": "github/biocore/emperor", - "url": " https://rseng.github.io/software/repository/github/biocore/emperor", - "content": "Emperor a tool for the analysis and visualization of large microbial ecology datasets" + "github/AdrianA-T/cytomorph": { + "id": "github/AdrianA-T/cytomorph", + "title": "github/AdrianA-T/cytomorph", + "url": " https://rseng.github.io/software/repository/github/AdrianA-T/cytomorph", + "content": "Cytomorph is a open software based on the main general features of cytoneme-meditated gradient formation. This sfotware allows to upload different experimental data to study in silico the role of different biological parameters of this type of signaling. Cytomorph can also work as an in silico tester for other biological hypotheses that are difficult to validate experimentally. In addition, the software architecture is designed in different modules that make Cytomorph an adaptive computational tool in which new advances can be integrated." }, - "github/raghuastro/GRIZZLY": { - "id": "github/raghuastro/GRIZZLY", - "title": "github/raghuastro/GRIZZLY", - "url": " https://rseng.github.io/software/repository/github/raghuastro/GRIZZLY", - "content": "None" + "github/philres/ngmlr": { + "id": "github/philres/ngmlr", + "title": "github/philres/ngmlr", + "url": " https://rseng.github.io/software/repository/github/philres/ngmlr", + "content": "NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations" }, - "github/sebastien-plutniak/archeoviz": { - "id": "github/sebastien-plutniak/archeoviz", - "title": "github/sebastien-plutniak/archeoviz", - "url": " https://rseng.github.io/software/repository/github/sebastien-plutniak/archeoviz", - "content": "Visualisation, Exploration, and Web Communication of Archaeological Spatial Data" + "github/philres/catfishq": { + "id": "github/philres/catfishq", + "title": "github/philres/catfishq", + "url": " https://rseng.github.io/software/repository/github/philres/catfishq", + "content": "Cat FASTQ files" }, - "github/sebastien-plutniak/archeofrag": { - "id": "github/sebastien-plutniak/archeofrag", - "title": "github/sebastien-plutniak/archeofrag", - "url": " https://rseng.github.io/software/repository/github/sebastien-plutniak/archeofrag", - "content": "R package for Refitting and Spatial Analysis in Archaeology" + "github/galaxy001/pirs": { + "id": "github/galaxy001/pirs", + "title": "github/galaxy001/pirs", + "url": " https://rseng.github.io/software/repository/github/galaxy001/pirs", + "content": "profile basd Illumina pair-end Reads Simulator" }, - "github/PeterBartram/TES": { - "id": "github/PeterBartram/TES", - "title": "github/PeterBartram/TES", - "url": " https://rseng.github.io/software/repository/github/PeterBartram/TES", - "content": "Terrestrial Exoplanet Simulator public repository" + "github/AstroVPK/kali": { + "id": "github/AstroVPK/kali", + "title": "github/AstroVPK/kali", + "url": " https://rseng.github.io/software/repository/github/AstroVPK/kali", + "content": "A library to model a time series as a Continuous-time ARMA process" }, - "github/SAIL-Labs/AMICAL": { - "id": "github/SAIL-Labs/AMICAL", - "title": "github/SAIL-Labs/AMICAL", - "url": " https://rseng.github.io/software/repository/github/SAIL-Labs/AMICAL", - "content": "Extraction pipeline and analysis tools for Aperture Masking Interferometry mode of the last generation of instruments (ground-based and space)." + "github/lkmklsmn/DrivAER": { + "id": "github/lkmklsmn/DrivAER", + "title": "github/lkmklsmn/DrivAER", + "url": " https://rseng.github.io/software/repository/github/lkmklsmn/DrivAER", + "content": "DrivAER: Identification of Driving transcriptional programs using AutoEncoder based Relevance scores" }, - "github/ouyang-lab/PRAS": { - "id": "github/ouyang-lab/PRAS", - "title": "github/ouyang-lab/PRAS", - "url": " https://rseng.github.io/software/repository/github/ouyang-lab/PRAS", - "content": "PRAS: predicting functional targets of RNA binding proteins based on CLIP-seq peaks" + "github/giswqs/lidar": { + "id": "github/giswqs/lidar", + "title": "github/giswqs/lidar", + "url": " https://rseng.github.io/software/repository/github/giswqs/lidar", + "content": "A Python package for delineating nested surface depressions from digital elevation data." }, - "github/davemlz/eemont": { - "id": "github/davemlz/eemont", - "title": "github/davemlz/eemont", - "url": " https://rseng.github.io/software/repository/github/davemlz/eemont", - "content": "A python package that extends Google Earth Engine." + "github/giswqs/leafmap": { + "id": "github/giswqs/leafmap", + "title": "github/giswqs/leafmap", + "url": " https://rseng.github.io/software/repository/github/giswqs/leafmap", + "content": "A Python package for interactive mapping and geospatial analysis with minimal coding in a Jupyter environment" }, - "github/tbronzwaer/raptor": { - "id": "github/tbronzwaer/raptor", - "title": "github/tbronzwaer/raptor", - "url": " https://rseng.github.io/software/repository/github/tbronzwaer/raptor", - "content": "Public version of the RAPTOR code for radiative transfer in arbitrary spacetimes. See README file for instructions and contact details." + "github/giswqs/geemap": { + "id": "github/giswqs/geemap", + "title": "github/giswqs/geemap", + "url": " https://rseng.github.io/software/repository/github/giswqs/geemap", + "content": "A Python package for interactive mapping with Google Earth Engine, ipyleaflet, and ipywidgets" }, - "github/Libsharp/libsharp": { - "id": "github/Libsharp/libsharp", - "title": "github/Libsharp/libsharp", - "url": " https://rseng.github.io/software/repository/github/Libsharp/libsharp", - "content": "Library for fast spherical harmonic transforms, see http://arxiv.org/abs/1303.4945" + "github/rickhelmus/patRoon": { + "id": "github/rickhelmus/patRoon", + "title": "github/rickhelmus/patRoon", + "url": " https://rseng.github.io/software/repository/github/rickhelmus/patRoon", + "content": "Workflow solutions for mass-spectrometry based non-target analysis." }, - "github/tcherninceline/PPInteractions": { - "id": "github/tcherninceline/PPInteractions", - "title": "github/tcherninceline/PPInteractions", - "url": " https://rseng.github.io/software/repository/github/tcherninceline/PPInteractions", - "content": "None" + "github/montilab/nf-gwas-pipeline": { + "id": "github/montilab/nf-gwas-pipeline", + "title": "github/montilab/nf-gwas-pipeline", + "url": " https://rseng.github.io/software/repository/github/montilab/nf-gwas-pipeline", + "content": "A Nextflow Genome-Wide Association Study (GWAS) Pipeline" }, - "github/mikesmitka/truvot": { - "id": "github/mikesmitka/truvot", - "title": "github/mikesmitka/truvot", - "url": " https://rseng.github.io/software/repository/github/mikesmitka/truvot", - "content": "None" + "github/esa/NIDN": { + "id": "github/esa/NIDN", + "title": "github/esa/NIDN", + "url": " https://rseng.github.io/software/repository/github/esa/NIDN", + "content": "Neural Inverse Design of Nanostructures" }, - "github/OttoStruve/muler": { - "id": "github/OttoStruve/muler", - "title": "github/OttoStruve/muler", - "url": " https://rseng.github.io/software/repository/github/OttoStruve/muler", - "content": "A Python package for working with pipeline-produced spectra from IGRINS, HPF, and Keck NIRSPEC" + "github/esa/pagmo2-paper": { + "id": "github/esa/pagmo2-paper", + "title": "github/esa/pagmo2-paper", + "url": " https://rseng.github.io/software/repository/github/esa/pagmo2-paper", + "content": "paper for JOSS on pagmo and pygmo" }, - "github/idptools/metapredict": { - "id": "github/idptools/metapredict", - "title": "github/idptools/metapredict", - "url": " https://rseng.github.io/software/repository/github/idptools/metapredict", - "content": "A machine learning based protein disorder predictor." + "github/benvanwerkhoven/kernel_tuner": { + "id": "github/benvanwerkhoven/kernel_tuner", + "title": "github/benvanwerkhoven/kernel_tuner", + "url": " https://rseng.github.io/software/repository/github/benvanwerkhoven/kernel_tuner", + "content": "Kernel Tuner" + }, + "github/hsocasnavarro/NICOLE": { + "id": "github/hsocasnavarro/NICOLE", + "title": "github/hsocasnavarro/NICOLE", + "url": " https://rseng.github.io/software/repository/github/hsocasnavarro/NICOLE", + "content": "NLTE Stokes Synthesis/Inversion Code" }, - "github/ngbusca/QuasarNET": { - "id": "github/ngbusca/QuasarNET", - "title": "github/ngbusca/QuasarNET", - "url": " https://rseng.github.io/software/repository/github/ngbusca/QuasarNET", + "github/pydemull/activAnalyzer": { + "id": "github/pydemull/activAnalyzer", + "title": "github/pydemull/activAnalyzer", + "url": " https://rseng.github.io/software/repository/github/pydemull/activAnalyzer", "content": "None" }, - "github/FelixKrueger/TrimGalore": { - "id": "github/FelixKrueger/TrimGalore", - "title": "github/FelixKrueger/TrimGalore", - "url": " https://rseng.github.io/software/repository/github/FelixKrueger/TrimGalore", - "content": "A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data" + "github/neuroneural/brainchop": { + "id": "github/neuroneural/brainchop", + "title": "github/neuroneural/brainchop", + "url": " https://rseng.github.io/software/repository/github/neuroneural/brainchop", + "content": "Brainchop: In-browser 3D MRI rendering and segmentation" }, - "github/pavanvidem/chira": { - "id": "github/pavanvidem/chira", - "title": "github/pavanvidem/chira", - "url": " https://rseng.github.io/software/repository/github/pavanvidem/chira", - "content": "Chimeric Read Annotator" + "github/Taywee/args": { + "id": "github/Taywee/args", + "title": "github/Taywee/args", + "url": " https://rseng.github.io/software/repository/github/Taywee/args", + "content": " A simple header-only C++ argument parser library. Supposed to be flexible and powerful, and attempts to be compatible with the functionality of the Python standard argparse library (though not necessarily the API)." }, - "github/DidierMurilloF/FielDHub": { - "id": "github/DidierMurilloF/FielDHub", - "title": "github/DidierMurilloF/FielDHub", - "url": " https://rseng.github.io/software/repository/github/DidierMurilloF/FielDHub", - "content": "FielDHub is an R Shiny design of experiments (DOE) app that aids in the creation of traditional, unreplicated, augmented and partially-replicated designs applied to agriculture, plant breeding, forestry, animal and biological sciences." + "github/BenNordick/HiLoop": { + "id": "github/BenNordick/HiLoop", + "title": "github/BenNordick/HiLoop", + "url": " https://rseng.github.io/software/repository/github/BenNordick/HiLoop", + "content": "None" }, - "github/chenjj2/forecaster": { - "id": "github/chenjj2/forecaster", - "title": "github/chenjj2/forecaster", - "url": " https://rseng.github.io/software/repository/github/chenjj2/forecaster", + "github/francescoa97outlook/pyExoRaMa": { + "id": "github/francescoa97outlook/pyExoRaMa", + "title": "github/francescoa97outlook/pyExoRaMa", + "url": " https://rseng.github.io/software/repository/github/francescoa97outlook/pyExoRaMa", "content": "None" }, - "github/jonzink/EDI_Vetter_unplugged": { - "id": "github/jonzink/EDI_Vetter_unplugged", - "title": "github/jonzink/EDI_Vetter_unplugged", - "url": " https://rseng.github.io/software/repository/github/jonzink/EDI_Vetter_unplugged", - "content": "A compact version of EDI-Vetter, which uses the TLS output to quickly vet transit signals. All your favorite hits in a simplified format." + "github/barklem/hlinop": { + "id": "github/barklem/hlinop", + "title": "github/barklem/hlinop", + "url": " https://rseng.github.io/software/repository/github/barklem/hlinop", + "content": "Codes for modelling hydrogen line opacity in stellar atmospheres. See Barklem & Piskunov (2003)" }, - "github/jonzink/EDI-Vetter": { - "id": "github/jonzink/EDI-Vetter", - "title": "github/jonzink/EDI-Vetter", - "url": " https://rseng.github.io/software/repository/github/jonzink/EDI-Vetter", - "content": "The (Exoplanet Detection Identifier) EDI-Vetter is the rock'n roll love child of Terra and RoboVetter, optimized to vet K2 transit signals." + "github/barklem/abo-cross": { + "id": "github/barklem/abo-cross", + "title": "github/barklem/abo-cross", + "url": " https://rseng.github.io/software/repository/github/barklem/abo-cross", + "content": "Interpolate in Anstee-Barklem-O'Mara cross sections for collisional broadening due to hydrogen" }, - "github/tommyau/bamclipper": { - "id": "github/tommyau/bamclipper", - "title": "github/tommyau/bamclipper", - "url": " https://rseng.github.io/software/repository/github/tommyau/bamclipper", - "content": "Remove primer sequence from BAM alignments by soft-clipping" + "github/barklem/kaulakys": { + "id": "github/barklem/kaulakys", + "title": "github/barklem/kaulakys", + "url": " https://rseng.github.io/software/repository/github/barklem/kaulakys", + "content": "Code to calculate cross sections and rate coefficients for inelastic collisions between Rydberg atoms and hydrogen atoms according to the free electron model of Kaulakys (1986, 1991)." }, - "github/steven-murray/pydftools": { - "id": "github/steven-murray/pydftools", - "title": "github/steven-murray/pydftools", - "url": " https://rseng.github.io/software/repository/github/steven-murray/pydftools", - "content": "A pure-python port of the R dftools package" + "github/barklem/mswavef": { + "id": "github/barklem/mswavef", + "title": "github/barklem/mswavef", + "url": " https://rseng.github.io/software/repository/github/barklem/mswavef", + "content": "Code to calculate hydrogenic and non-hydrogenic momentum-space electronic wavefunctions" }, - "github/steven-murray/powerbox": { - "id": "github/steven-murray/powerbox", - "title": "github/steven-murray/powerbox", - "url": " https://rseng.github.io/software/repository/github/steven-murray/powerbox", - "content": "A python package for making arbitrarily structured, arbitrary-dimension boxes" + "github/matplotlib/matplotlib": { + "id": "github/matplotlib/matplotlib", + "title": "github/matplotlib/matplotlib", + "url": " https://rseng.github.io/software/repository/github/matplotlib/matplotlib", + "content": "matplotlib: plotting with Python" }, - "github/steven-murray/mrpy": { - "id": "github/steven-murray/mrpy", - "title": "github/steven-murray/mrpy", - "url": " https://rseng.github.io/software/repository/github/steven-murray/mrpy", - "content": "A Python package for calculations with the MRP parameterisation of the Halo Mass Function." + "github/FAU-LAP/NOMAD-CAMELS": { + "id": "github/FAU-LAP/NOMAD-CAMELS", + "title": "github/FAU-LAP/NOMAD-CAMELS", + "url": " https://rseng.github.io/software/repository/github/FAU-LAP/NOMAD-CAMELS", + "content": "We are developing a configurable measurement software (CAMELS), targeted towards the requirements of experimental solid-state physics. Here many experiments utilize a multitude of measurement devices used in dynamically changing setups." }, - "github/VMBoehm/MADLens": { - "id": "github/VMBoehm/MADLens", - "title": "github/VMBoehm/MADLens", - "url": " https://rseng.github.io/software/repository/github/VMBoehm/MADLens", - "content": "a differentiable lensing simulator" + "github/cosmodesi/pycorr": { + "id": "github/cosmodesi/pycorr", + "title": "github/cosmodesi/pycorr", + "url": " https://rseng.github.io/software/repository/github/cosmodesi/pycorr", + "content": "2-pt correlation function estimation" }, - "github/radifar/PyPLIF-HIPPOS": { - "id": "github/radifar/PyPLIF-HIPPOS", - "title": "github/radifar/PyPLIF-HIPPOS", - "url": " https://rseng.github.io/software/repository/github/radifar/PyPLIF-HIPPOS", - "content": "HIPPOS Is PyPLIF On Steroids. A Molecular Interaction Fingerprinting Tool for Docking Results of Autodock Vina and PLANTS" + "github/gbrammer/grizli": { + "id": "github/gbrammer/grizli", + "title": "github/gbrammer/grizli", + "url": " https://rseng.github.io/software/repository/github/gbrammer/grizli", + "content": "Grizli: The "Grism redshift and line" analysis software" }, - "github/jalombar/starsmasher": { - "id": "github/jalombar/starsmasher", - "title": "github/jalombar/starsmasher", - "url": " https://rseng.github.io/software/repository/github/jalombar/starsmasher", - "content": "A Smoothed Particle Hydrodynamics code for smashing stars (and planets)" + "github/danxhuber/evolstate": { + "id": "github/danxhuber/evolstate", + "title": "github/danxhuber/evolstate", + "url": " https://rseng.github.io/software/repository/github/danxhuber/evolstate", + "content": "Assign simple evolutionary states to stars" }, - "github/cullanhowlett/l-picola": { - "id": "github/cullanhowlett/l-picola", - "title": "github/cullanhowlett/l-picola", - "url": " https://rseng.github.io/software/repository/github/cullanhowlett/l-picola", - "content": "A public repository for the code L-PICOLA" + "github/danxhuber/galclassify": { + "id": "github/danxhuber/galclassify", + "title": "github/danxhuber/galclassify", + "url": " https://rseng.github.io/software/repository/github/danxhuber/galclassify", + "content": "Perform stellar classifications using a galactic population synthesis model" }, - "github/cgre-aachen/gemgis": { - "id": "github/cgre-aachen/gemgis", - "title": "github/cgre-aachen/gemgis", - "url": " https://rseng.github.io/software/repository/github/cgre-aachen/gemgis", - "content": "Spatial data processing for geomodeling" + "github/FraunhoferIWES/foxes": { + "id": "github/FraunhoferIWES/foxes", + "title": "github/FraunhoferIWES/foxes", + "url": " https://rseng.github.io/software/repository/github/FraunhoferIWES/foxes", + "content": "Farm Optimization and eXtended yield Evaluation Software" }, - "github/jiahecui/SenAOReFoc": { - "id": "github/jiahecui/SenAOReFoc", - "title": "github/jiahecui/SenAOReFoc", - "url": " https://rseng.github.io/software/repository/github/jiahecui/SenAOReFoc", - "content": "A closed-loop sensorbased adaptive optics and remote focusing control software that works with a deformable mirror and a Shack-Hartmann wavefront sensor." + "github/rezeebe/orbitN": { + "id": "github/rezeebe/orbitN", + "title": "github/rezeebe/orbitN", + "url": " https://rseng.github.io/software/repository/github/rezeebe/orbitN", + "content": "Symplectic integrator for near-Keplerian planetary systems" }, - "github/pachterlab/kallisto": { - "id": "github/pachterlab/kallisto", - "title": "github/pachterlab/kallisto", - "url": " https://rseng.github.io/software/repository/github/pachterlab/kallisto", - "content": "Near-optimal RNA-Seq quantification" + "github/uclchem/Chemulator": { + "id": "github/uclchem/Chemulator", + "title": "github/uclchem/Chemulator", + "url": " https://rseng.github.io/software/repository/github/uclchem/Chemulator", + "content": "The thermochemical emulator for hydrodynamical modelling" }, - 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" + "github/rambaut/jebl2": { + "id": "github/rambaut/jebl2", + "title": "github/rambaut/jebl2", + "url": " https://rseng.github.io/software/repository/github/rambaut/jebl2", + "content": "Automatically exported from code.google.com/p/jebl2" }, - "github/OncoRNALab/CiLiQuant": { - "id": "github/OncoRNALab/CiLiQuant", - "title": "github/OncoRNALab/CiLiQuant", - "url": " https://rseng.github.io/software/repository/github/OncoRNALab/CiLiQuant", - "content": "None" + "github/Adamtaranto/Yanagiba": { + "id": "github/Adamtaranto/Yanagiba", + "title": "github/Adamtaranto/Yanagiba", + "url": " https://rseng.github.io/software/repository/github/Adamtaranto/Yanagiba", + "content": "Filter and slice Nanopore reads which have been basecalled with Albacore." }, - "github/HCGB-IGTP/spaTyper": { - "id": "github/HCGB-IGTP/spaTyper", - "title": "github/HCGB-IGTP/spaTyper", - "url": " https://rseng.github.io/software/repository/github/HCGB-IGTP/spaTyper", - "content": "Computational method for finding spa types." + "github/AbbasAlameer/geoCancerPrognosticDatasetsRetriever": { + "id": "github/AbbasAlameer/geoCancerPrognosticDatasetsRetriever", + "title": "github/AbbasAlameer/geoCancerPrognosticDatasetsRetriever", + "url": " https://rseng.github.io/software/repository/github/AbbasAlameer/geoCancerPrognosticDatasetsRetriever", + "content": "GEO Cancer Prognostic Datasets Retriever is a bioinformatics tool for cancer prognostic dataset retrieval from the GEO website." }, - 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"id": "github/BioHPC/MegaD", - "title": "github/BioHPC/MegaD", - "url": " https://rseng.github.io/software/repository/github/BioHPC/MegaD", - "content": "Deep learning for metagenomic sample classification" + "github/dcjones/quip": { + "id": "github/dcjones/quip", + "title": "github/dcjones/quip", + "url": " https://rseng.github.io/software/repository/github/dcjones/quip", + "content": "Compressing next-generation sequencing data with extreme prejudice." }, - "github/JakobBD/pounce": { - "id": "github/JakobBD/pounce", - "title": "github/JakobBD/pounce", - "url": " https://rseng.github.io/software/repository/github/JakobBD/pounce", - "content": "None" + "github/tloredo/CUDAHM": { + "id": "github/tloredo/CUDAHM", + "title": "github/tloredo/CUDAHM", + "url": " https://rseng.github.io/software/repository/github/tloredo/CUDAHM", + "content": "Routines for using CUDA to perform MCMC Sampling of Hierarchical Models with GPUs." + }, + "github/moldyn/msmhelper": { + "id": "github/moldyn/msmhelper", + "title": "github/moldyn/msmhelper", + "url": " https://rseng.github.io/software/repository/github/moldyn/msmhelper", + "content": "Helper function for Markov State Models" }, - 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A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:" }, - "github/jmd-dk/concept": { - "id": "github/jmd-dk/concept", - "title": "github/jmd-dk/concept", - "url": " https://rseng.github.io/software/repository/github/jmd-dk/concept", - "content": "COsmological N-body CodE in PyThon" + "github/saberyoung/haffet": { + "id": "github/saberyoung/haffet", + "title": "github/saberyoung/haffet", + "url": " https://rseng.github.io/software/repository/github/saberyoung/haffet", + "content": "Repository to analyze SN photometric and spectroscopic data" }, - "github/tatekawa-astron/3LPT-init": { - "id": "github/tatekawa-astron/3LPT-init", - "title": "github/tatekawa-astron/3LPT-init", - "url": " https://rseng.github.io/software/repository/github/tatekawa-astron/3LPT-init", + "github/astronomical-data-processing/RAPP": { + "id": "github/astronomical-data-processing/RAPP", + "title": "github/astronomical-data-processing/RAPP", + "url": " https://rseng.github.io/software/repository/github/astronomical-data-processing/RAPP", "content": "None" }, - "github/tatekawa-astron/PN": { - "id": "github/tatekawa-astron/PN", - "title": "github/tatekawa-astron/PN", - "url": " https://rseng.github.io/software/repository/github/tatekawa-astron/PN", - "content": "None" + "github/OxES/k2sc": { + "id": "github/OxES/k2sc", + "title": "github/OxES/k2sc", + "url": " https://rseng.github.io/software/repository/github/OxES/k2sc", + "content": "K2 systematics correction using Gaussian processes" }, - "github/rhysf/HaplotypeTools": { - "id": "github/rhysf/HaplotypeTools", - "title": "github/rhysf/HaplotypeTools", - "url": " https://rseng.github.io/software/repository/github/rhysf/HaplotypeTools", - "content": "A toolkit for identifying recombination and recombinant genotypes" + "github/oscaribv/exotrending": { + "id": "github/oscaribv/exotrending", + "title": "github/oscaribv/exotrending", + "url": " https://rseng.github.io/software/repository/github/oscaribv/exotrending", + "content": "A fast and easy-to-use light curve detrending software for exoplanets" }, - "github/stamatak/AxPcoords.dist": { - "id": "github/stamatak/AxPcoords.dist", - "title": "github/stamatak/AxPcoords.dist", - "url": " https://rseng.github.io/software/repository/github/stamatak/AxPcoords.dist", - "content": "AxPcoords implementation " + "github/oscaribv/pyaneti": { + "id": "github/oscaribv/pyaneti", + "title": "github/oscaribv/pyaneti", + "url": " https://rseng.github.io/software/repository/github/oscaribv/pyaneti", + "content": "A multi-planet Radial Velocity and Transit modelling software" }, - "github/stamatak/ExaML": { - "id": "github/stamatak/ExaML", - "title": "github/stamatak/ExaML", - "url": " https://rseng.github.io/software/repository/github/stamatak/ExaML", - "content": "Exascale Maximum Likelihood (ExaML) code for phylogenetic inference using MPI" + "github/oscaribv/citlalicue": { + "id": "github/oscaribv/citlalicue", + "title": "github/oscaribv/citlalicue", + "url": " https://rseng.github.io/software/repository/github/oscaribv/citlalicue", + "content": "Create and manipulate stellar light curves!" }, - "github/podondra/bayesian-sznet": { - "id": "github/podondra/bayesian-sznet", - "title": "github/podondra/bayesian-sznet", - "url": " https://rseng.github.io/software/repository/github/podondra/bayesian-sznet", - "content": "Bayesian deep learning to predict redshift with uncertainty" + "github/twinl/website": { + "id": "github/twinl/website", + "title": "github/twinl/website", + "url": " https://rseng.github.io/software/repository/github/twinl/website", + "content": "TwiNL: website code" }, - "github/podondra/eidein": { - "id": "github/podondra/eidein", - "title": "github/podondra/eidein", - "url": " https://rseng.github.io/software/repository/github/podondra/eidein", - "content": "Interactive tool for dimensionality reduction of spectra and their visualisation" + "github/mzytnicki/srnaMapper": { + "id": "github/mzytnicki/srnaMapper", + "title": "github/mzytnicki/srnaMapper", + "url": " https://rseng.github.io/software/repository/github/mzytnicki/srnaMapper", + "content": "Mapping small RNA data to a genome." }, - "github/loosolab/TOBIAS": { - "id": "github/loosolab/TOBIAS", - "title": "github/loosolab/TOBIAS", - "url": " https://rseng.github.io/software/repository/github/loosolab/TOBIAS", - "content": "Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal " + "github/watts-dev/watts": { + "id": "github/watts-dev/watts", + "title": "github/watts-dev/watts", + "url": " https://rseng.github.io/software/repository/github/watts-dev/watts", + "content": "Workflow and Template Toolkit for Simulation (WATTS)" }, - "github/Single-Cell-Graph-Learning/scSGL": { - "id": "github/Single-Cell-Graph-Learning/scSGL", - "title": "github/Single-Cell-Graph-Learning/scSGL", - "url": " https://rseng.github.io/software/repository/github/Single-Cell-Graph-Learning/scSGL", - "content": "Signed Graph Learning for single cell RNA-seq data" + "github/VIB-PSB/MINI-EX": { + "id": "github/VIB-PSB/MINI-EX", + "title": "github/VIB-PSB/MINI-EX", + "url": " https://rseng.github.io/software/repository/github/VIB-PSB/MINI-EX", + "content": "Motif-Informed Network Inference of cell type-specific gene regulatory networks in plants" }, - 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PyRice design is modular and implements a smart query system which fits the computing resources to optimize the query speed." }, - "github/maize-genetics/rTASSEL": { - "id": "github/maize-genetics/rTASSEL", - "title": "github/maize-genetics/rTASSEL", - "url": " https://rseng.github.io/software/repository/github/maize-genetics/rTASSEL", - "content": "R front-end for TASSEL" + "github/GabrielaCR/AGNfitter": { + "id": "github/GabrielaCR/AGNfitter", + "title": "github/GabrielaCR/AGNfitter", + "url": " https://rseng.github.io/software/repository/github/GabrielaCR/AGNfitter", + "content": "SED-fitting code for AGN and galaxies from a MCMC approach" }, - "github/ipython/ipython": { - "id": "github/ipython/ipython", - "title": "github/ipython/ipython", - "url": " https://rseng.github.io/software/repository/github/ipython/ipython", - "content": "Official repository for IPython itself. Other repos in the IPython organization contain things like the website, documentation builds, etc." + "github/genostats/LowKi": { + "id": "github/genostats/LowKi", + "title": "github/genostats/LowKi", + "url": " https://rseng.github.io/software/repository/github/genostats/LowKi", + "content": "None" }, - "github/PNNL-m-q/mza": { - "id": "github/PNNL-m-q/mza", - "title": "github/PNNL-m-q/mza", - "url": " https://rseng.github.io/software/repository/github/PNNL-m-q/mza", - "content": "Software to convert multidimensional MS data from files in proprietary vendor formats to HDF5 format in the simple MZA data structure." + "github/cheerfuluser/tessreduce": { + "id": "github/cheerfuluser/tessreduce", + "title": "github/cheerfuluser/tessreduce", + "url": " https://rseng.github.io/software/repository/github/cheerfuluser/tessreduce", + "content": "Transient focused reduction for TESS data" }, - "github/SchmollerLab/Cell_ACDC": { - "id": "github/SchmollerLab/Cell_ACDC", - "title": "github/SchmollerLab/Cell_ACDC", - "url": " https://rseng.github.io/software/repository/github/SchmollerLab/Cell_ACDC", - "content": "A Python GUI-based framework for segmentation, tracking and cell cycle annotations of micrscopy data" + "github/delve-team/delve": { + "id": "github/delve-team/delve", + "title": "github/delve-team/delve", + "url": " https://rseng.github.io/software/repository/github/delve-team/delve", + "content": "PyTorch model training and layer saturation monitor" }, - "github/astromer-science/main-code": { - "id": "github/astromer-science/main-code", - "title": "github/astromer-science/main-code", - "url": " https://rseng.github.io/software/repository/github/astromer-science/main-code", - "content": "Latest stable implemention of ASTROMER " + "github/drcandacemakedamoore/cleanX": { + "id": "github/drcandacemakedamoore/cleanX", + "title": "github/drcandacemakedamoore/cleanX", + "url": " https://rseng.github.io/software/repository/github/drcandacemakedamoore/cleanX", + "content": "Python library for exploring, cleaning, normalizing, and augmenting large datasets of radiological data." }, - "github/RozanskiT/suppnet": { - "id": "github/RozanskiT/suppnet", - "title": "github/RozanskiT/suppnet", - "url": " https://rseng.github.io/software/repository/github/RozanskiT/suppnet", - "content": "SUPPNet: Neural network for stellar spectrum normalisation" + "github/SchedMD/slurm": { + "id": "github/SchedMD/slurm", + "title": "github/SchedMD/slurm", + "url": " https://rseng.github.io/software/repository/github/SchedMD/slurm", + "content": "Slurm: A Highly Scalable Workload Manager" }, - "github/ZhaiLab-SUSTech/FLEPSeq": { - "id": "github/ZhaiLab-SUSTech/FLEPSeq", - "title": "github/ZhaiLab-SUSTech/FLEPSeq", - "url": " https://rseng.github.io/software/repository/github/ZhaiLab-SUSTech/FLEPSeq", - "content": "The analysis pipeline for FLEP-seq" + "github/kiyo-masui/bitshuffle": { + "id": "github/kiyo-masui/bitshuffle", + "title": "github/kiyo-masui/bitshuffle", + "url": " https://rseng.github.io/software/repository/github/kiyo-masui/bitshuffle", + "content": "Filter for improving compression of typed binary data." }, - "github/tgrimes/SeqNet": { - "id": "github/tgrimes/SeqNet", - "title": "github/tgrimes/SeqNet", - "url": " https://rseng.github.io/software/repository/github/tgrimes/SeqNet", - "content": "An R package for simulating RNA-sequence datasets from regulatory networks" + "github/JiangFangzhou/SIDM": { + "id": "github/JiangFangzhou/SIDM", + "title": "github/JiangFangzhou/SIDM", + "url": " https://rseng.github.io/software/repository/github/JiangFangzhou/SIDM", + "content": "analytical model for the density profiles of self-interacting dark-matter halos with inhabitant galaxies" }, - "github/raphael-group/hatchet": { - "id": "github/raphael-group/hatchet", - "title": "github/raphael-group/hatchet", - "url": " https://rseng.github.io/software/repository/github/raphael-group/hatchet", - "content": "HATCHet (Holistic Allele-specific Tumor Copy-number Heterogeneity) is an algorithm that infers allele and clone-specific CNAs and WGDs jointly across multiple tumor samples from the same patient, and that leverages the relationships between clones in these samples." + "github/chenjj2/forecaster": { + "id": "github/chenjj2/forecaster", + "title": "github/chenjj2/forecaster", + "url": " https://rseng.github.io/software/repository/github/chenjj2/forecaster", + "content": "None" }, - "github/dib-lab/dammit": { - "id": "github/dib-lab/dammit", - "title": "github/dib-lab/dammit", - "url": " https://rseng.github.io/software/repository/github/dib-lab/dammit", - "content": "just annotate it, dammit!" + "github/StingraySoftware/stingray": { + "id": "github/StingraySoftware/stingray", + "title": "github/StingraySoftware/stingray", + "url": " https://rseng.github.io/software/repository/github/StingraySoftware/stingray", + "content": "Anything can happen in the next half hour (including spectral timing made easy)!" }, - "github/dib-lab/sourmash": { - "id": "github/dib-lab/sourmash", - "title": "github/dib-lab/sourmash", - "url": " https://rseng.github.io/software/repository/github/dib-lab/sourmash", - "content": "Quickly search, compare, and analyze genomic and metagenomic data sets." + "github/StingraySoftware/HENDRICS": { + "id": "github/StingraySoftware/HENDRICS", + "title": "github/StingraySoftware/HENDRICS", + "url": " https://rseng.github.io/software/repository/github/StingraySoftware/HENDRICS", + "content": "Shell scripts for spectral-timing analysis of X-ray astronomical data." }, - 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"github/rcarragh/c212": { - "id": "github/rcarragh/c212", - "title": "github/rcarragh/c212", - "url": " https://rseng.github.io/software/repository/github/rcarragh/c212", - "content": "Methods for detecting safety signals in clinical trials using groupings of adverse events by body-system or system organ class." + "github/NeuralEnsemble/elephant": { + "id": "github/NeuralEnsemble/elephant", + "title": "github/NeuralEnsemble/elephant", + "url": " https://rseng.github.io/software/repository/github/NeuralEnsemble/elephant", + "content": "Elephant is the Electrophysiology Analysis Toolkit" }, - "github/HEML/HEML": { - "id": "github/HEML/HEML", - "title": "github/HEML/HEML", - "url": " https://rseng.github.io/software/repository/github/HEML/HEML", - "content": "Open Source v1 for the Hyper-Elastic Mass Links (HEML) software" + "github/NeuralEnsemble/PyNN": { + "id": "github/NeuralEnsemble/PyNN", + "title": "github/NeuralEnsemble/PyNN", + "url": " https://rseng.github.io/software/repository/github/NeuralEnsemble/PyNN", + "content": "A Python package for simulator-independent specification of neuronal network models." }, - "github/votca/xtp": { - "id": "github/votca/xtp", - "title": "github/votca/xtp", - "url": " https://rseng.github.io/software/repository/github/votca/xtp", - "content": "GW-BSE for excited state Quantum Chemistry in a Gaussian Orbital basis, electronic spectroscopy with QM/MM, charge and energy dynamics in complex molecular systems" + "github/statdivlab/rigr": { + "id": "github/statdivlab/rigr", + "title": "github/statdivlab/rigr", + "url": " https://rseng.github.io/software/repository/github/statdivlab/rigr", + "content": "Regression, Inference, and General Data Analysis Tools for R " }, - "github/kokron/skyLine": { - "id": "github/kokron/skyLine", - "title": "github/kokron/skyLine", - "url": " https://rseng.github.io/software/repository/github/kokron/skyLine", + "github/klho/FLAM": { + "id": "github/klho/FLAM", + "title": "github/klho/FLAM", + "url": " https://rseng.github.io/software/repository/github/klho/FLAM", + "content": "Fast linear algebra in MATLAB" + }, + "github/lu-yizhou/ClusterSeg": { + "id": "github/lu-yizhou/ClusterSeg", + "title": "github/lu-yizhou/ClusterSeg", + "url": " https://rseng.github.io/software/repository/github/lu-yizhou/ClusterSeg", "content": "None" }, - "github/spyder-ide/spyder": { - "id": "github/spyder-ide/spyder", - "title": "github/spyder-ide/spyder", - "url": " https://rseng.github.io/software/repository/github/spyder-ide/spyder", - "content": "Official repository for Spyder - The Scientific Python Development Environment" + "github/tlancian/bio_cs": { + "id": "github/tlancian/bio_cs", + "title": "github/tlancian/bio_cs", + "url": " https://rseng.github.io/software/repository/github/tlancian/bio_cs", + "content": ""Contrast Subgraphs Allow Comparing Homogeneous and Heterogeneous Networks Derived from Omics Data" - T. 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"github/sapearson/HSS": { - "id": "github/sapearson/HSS", - "title": "github/sapearson/HSS", - "url": " https://rseng.github.io/software/repository/github/sapearson/HSS", - "content": "The Hough Stream Spotter (HSS)" + "github/pypeit/PypeIt": { + "id": "github/pypeit/PypeIt", + "title": "github/pypeit/PypeIt", + "url": " https://rseng.github.io/software/repository/github/pypeit/PypeIt", + "content": "The Python Spectroscopic Data Reduction Pipeline" }, - "github/mithun218/GiNaCDE": { - "id": "github/mithun218/GiNaCDE", - "title": "github/mithun218/GiNaCDE", - "url": " https://rseng.github.io/software/repository/github/mithun218/GiNaCDE", - "content": "GiNaC Differential Equation Solver" + "github/DMGW-Goethe/imripy": { + "id": "github/DMGW-Goethe/imripy", + "title": "github/DMGW-Goethe/imripy", + "url": " https://rseng.github.io/software/repository/github/DMGW-Goethe/imripy", + "content": "A python code able to simulate Intermediate Mass Ratio Inspirals (IMRI)" }, - "github/genostats/LowKi": { - 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Please fork the repository before making any changes and read the Coding Practices page in the wiki. 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All your favorite hits in a simplified format." }, - "github/nlesc-nano/flamingo": { - "id": "github/nlesc-nano/flamingo", - "title": "github/nlesc-nano/flamingo", - "url": " https://rseng.github.io/software/repository/github/nlesc-nano/flamingo", - "content": "Computation and filtering of molecular properties" + "github/apertif/apercal": { + "id": "github/apertif/apercal", + "title": "github/apertif/apercal", + "url": " https://rseng.github.io/software/repository/github/apertif/apercal", + "content": "None" }, - "github/nlesc-nano/Moka": { - "id": "github/nlesc-nano/Moka", - "title": "github/nlesc-nano/Moka", - "url": " https://rseng.github.io/software/repository/github/nlesc-nano/Moka", - "content": "command line interface to compute and molecular properties from a database" + "github/spicy-oil/hfs_fit": { + "id": "github/spicy-oil/hfs_fit", + "title": "github/spicy-oil/hfs_fit", + "url": " https://rseng.github.io/software/repository/github/spicy-oil/hfs_fit", + "content": "None" }, - "github/nlesc-nano/ceiba-cli": { - "id": "github/nlesc-nano/ceiba-cli", - "title": "github/nlesc-nano/ceiba-cli", - "url": " https://rseng.github.io/software/repository/github/nlesc-nano/ceiba-cli", - "content": "command-line interface to compute and molecular properties from a database" + "github/HaowenZhang/TRINITY": { + "id": "github/HaowenZhang/TRINITY", + "title": "github/HaowenZhang/TRINITY", + "url": " https://rseng.github.io/software/repository/github/HaowenZhang/TRINITY", + "content": "An empirical model that statistically connects dark matter halos, galaxies and supermassive black holes from z=0-10." }, - "github/nlesc-nano/insilico-server": { - "id": "github/nlesc-nano/insilico-server", - "title": "github/nlesc-nano/insilico-server", - "url": " https://rseng.github.io/software/repository/github/nlesc-nano/insilico-server", - "content": "web server to handle the properties" + "github/LTLA/basilisk": { + "id": "github/LTLA/basilisk", + "title": "github/LTLA/basilisk", + "url": " https://rseng.github.io/software/repository/github/LTLA/basilisk", + "content": "Clone of the Bioconductor repository for the basilisk package." }, - "github/nlesc-nano/ceiba": { - "id": "github/nlesc-nano/ceiba", - "title": "github/nlesc-nano/ceiba", - "url": " https://rseng.github.io/software/repository/github/nlesc-nano/ceiba", - "content": "Web service to manage scientific simulation data" + "github/LTLA/gesel.js": { + "id": "github/LTLA/gesel.js", + "title": "github/LTLA/gesel.js", + "url": " https://rseng.github.io/software/repository/github/LTLA/gesel.js", + "content": "Client-side gene set queries." }, - "github/nlesc-nano/CAT": { - "id": "github/nlesc-nano/CAT", - "title": "github/nlesc-nano/CAT", - "url": " https://rseng.github.io/software/repository/github/nlesc-nano/CAT", - "content": "A collection of tools designed for the automatic construction, and subsequent analysis, of chemical compounds." + "github/HIPS/autograd": { + "id": "github/HIPS/autograd", + "title": "github/HIPS/autograd", + "url": " https://rseng.github.io/software/repository/github/HIPS/autograd", + "content": "Efficiently computes derivatives of numpy code." }, - "github/backyardworlds/wiseview": { - "id": "github/backyardworlds/wiseview", - "title": "github/backyardworlds/wiseview", - "url": " https://rseng.github.io/software/repository/github/backyardworlds/wiseview", - "content": "WiseView: Visualizing Motion and Variability of Faint WISE Sources" + "github/IanevskiAleksandr/sc-type": { + "id": "github/IanevskiAleksandr/sc-type", + "title": "github/IanevskiAleksandr/sc-type", + "url": " https://rseng.github.io/software/repository/github/IanevskiAleksandr/sc-type", + "content": "None" }, - "github/astropy/halotools": { - "id": "github/astropy/halotools", - "title": "github/astropy/halotools", - "url": " https://rseng.github.io/software/repository/github/astropy/halotools", - "content": "Python package for studying large scale structure, cosmology, and galaxy evolution using N-body simulations and halo models" + "github/vals/umis": { + "id": "github/vals/umis", + "title": "github/vals/umis", + "url": " https://rseng.github.io/software/repository/github/vals/umis", + "content": "Tools for processing UMI RNA-tag data" }, - "github/astropy/astroquery": { - "id": "github/astropy/astroquery", - "title": "github/astropy/astroquery", - "url": " https://rseng.github.io/software/repository/github/astropy/astroquery", - "content": "Functions and classes to access online data resources. Maintainers: @keflavich and @bsipocz and @ceb8" + "github/davtsang/slimplectic": { + "id": "github/davtsang/slimplectic", + "title": "github/davtsang/slimplectic", + "url": " https://rseng.github.io/software/repository/github/davtsang/slimplectic", + "content": "Python code for generating and running "slimplectic" integrators (nonconservative variational integrators)" }, - "github/astropy/astroplan": { - "id": "github/astropy/astroplan", - "title": "github/astropy/astroplan", - "url": " https://rseng.github.io/software/repository/github/astropy/astroplan", - "content": "Observation planning package for astronomers" + "github/dgrun/FateID": { + "id": "github/dgrun/FateID", + "title": "github/dgrun/FateID", + "url": " https://rseng.github.io/software/repository/github/dgrun/FateID", + "content": "R package for the inference of cell fate bias from single-cell RNA-seq data." }, - "github/astropy/astroscrappy": { - "id": "github/astropy/astroscrappy", - "title": "github/astropy/astroscrappy", - "url": " https://rseng.github.io/software/repository/github/astropy/astroscrappy", - "content": "Speedy Cosmic Ray Annihilation Package in Python" + "github/pencil-code/pencil-code": { + "id": "github/pencil-code/pencil-code", + "title": "github/pencil-code/pencil-code", + "url": " https://rseng.github.io/software/repository/github/pencil-code/pencil-code", + "content": "A high-order finite-difference code for compressible hydrodynamic flows with magnetic fields and particles" }, - "github/astropy/specutils": { - "id": "github/astropy/specutils", - "title": "github/astropy/specutils", - "url": " https://rseng.github.io/software/repository/github/astropy/specutils", - "content": "An Astropy coordinated package for astronomical spectroscopy. Maintainers: @nmearl @rosteen @keflavich @eteq" + "github/kritiyer/AngioNet": { + "id": "github/kritiyer/AngioNet", + "title": "github/kritiyer/AngioNet", + "url": " https://rseng.github.io/software/repository/github/kritiyer/AngioNet", + "content": "Semantic segmentation network for X-ray angiography images, based on Deeplabv3+" }, - "github/astropy/SPISEA": { - "id": "github/astropy/SPISEA", - "title": "github/astropy/SPISEA", - "url": " https://rseng.github.io/software/repository/github/astropy/SPISEA", - "content": "Stellar Population Synthesis Modeling" + "github/zhoux85/scAdapt": { + "id": "github/zhoux85/scAdapt", + "title": "github/zhoux85/scAdapt", + "url": " https://rseng.github.io/software/repository/github/zhoux85/scAdapt", + "content": "None" }, - "github/astropy/astropy": { - "id": "github/astropy/astropy", - "title": "github/astropy/astropy", - "url": " https://rseng.github.io/software/repository/github/astropy/astropy", - "content": "Repository for the Astropy core package" + "github/wouterpeere/GHEtool": { + "id": "github/wouterpeere/GHEtool", + "title": "github/wouterpeere/GHEtool", + "url": " https://rseng.github.io/software/repository/github/wouterpeere/GHEtool", + "content": "GHEtool is an open-source tool for borefield sizing and ground temperature evolution plotting." }, - "github/astropy/ccdproc": { - "id": "github/astropy/ccdproc", - "title": "github/astropy/ccdproc", - "url": " https://rseng.github.io/software/repository/github/astropy/ccdproc", - "content": "Astropy affiliated package for reducing optical/IR CCD data" + "github/sciris/sciris": { + "id": "github/sciris/sciris", + "title": "github/sciris/sciris", + "url": " https://rseng.github.io/software/repository/github/sciris/sciris", + "content": "Fast, flexible tools to simplify scientific Python" }, - "github/OnroerendErfgoed/atramhasis": { - "id": "github/OnroerendErfgoed/atramhasis", - "title": "github/OnroerendErfgoed/atramhasis", - "url": " https://rseng.github.io/software/repository/github/OnroerendErfgoed/atramhasis", - "content": "An online SKOS editor" + "github/esteinig/nanoq": { + "id": "github/esteinig/nanoq", + "title": "github/esteinig/nanoq", + "url": " https://rseng.github.io/software/repository/github/esteinig/nanoq", + "content": "Minimal but speedy quality control for nanopore reads in Rust :bear:" }, - "github/megbedell/wobble": { - "id": "github/megbedell/wobble", - "title": "github/megbedell/wobble", - "url": " https://rseng.github.io/software/repository/github/megbedell/wobble", - "content": "precise data-driven RV fitting, now with tellurics!" + "github/sanjibs/bmcmc": { + "id": "github/sanjibs/bmcmc", + "title": "github/sanjibs/bmcmc", + "url": " https://rseng.github.io/software/repository/github/sanjibs/bmcmc", + "content": "MCMC package for Bayesian data analysis" }, - "github/liamedeiros/ehtplot": { - "id": "github/liamedeiros/ehtplot", - "title": "github/liamedeiros/ehtplot", - "url": " https://rseng.github.io/software/repository/github/liamedeiros/ehtplot", - "content": "Plotting functions for the Event Horizon Telescope" + "github/naonori/hitomi": { + "id": "github/naonori/hitomi", + "title": "github/naonori/hitomi", + "url": " https://rseng.github.io/software/repository/github/naonori/hitomi", + "content": "Public repository for the Hitomi Code" }, - "github/ulelab/ultraplex": { - "id": "github/ulelab/ultraplex", - "title": "github/ulelab/ultraplex", - "url": " https://rseng.github.io/software/repository/github/ulelab/ultraplex", - "content": "Ultra-fast 5' and 3' demultiplexer" + "github/alstat/ALUES": { + "id": "github/alstat/ALUES", + "title": "github/alstat/ALUES", + "url": " https://rseng.github.io/software/repository/github/alstat/ALUES", + "content": "Agricultural Land Use Evaluation System" }, - "github/rafaeleufrasio/lightning": { - "id": "github/rafaeleufrasio/lightning", - "title": "github/rafaeleufrasio/lightning", - "url": " https://rseng.github.io/software/repository/github/rafaeleufrasio/lightning", - "content": "Lightning SED Fitting Package" + "github/chianti-atomic/ChiantiPy": { + "id": "github/chianti-atomic/ChiantiPy", + "title": "github/chianti-atomic/ChiantiPy", + "url": " https://rseng.github.io/software/repository/github/chianti-atomic/ChiantiPy", + "content": "ChiantiPy is a python package to calculate the radiative properties of astrophysical plasmas based on the CHIANTI atomic database" }, - "github/ejhigson/nestcheck": { - "id": "github/ejhigson/nestcheck", - "title": "github/ejhigson/nestcheck", - "url": " https://rseng.github.io/software/repository/github/ejhigson/nestcheck", - "content": "Error analysis, diagnostic tests and plots for nested sampling calculations." + "github/viromelab/tracespipe": { + "id": "github/viromelab/tracespipe", + "title": "github/viromelab/tracespipe", + "url": " https://rseng.github.io/software/repository/github/viromelab/tracespipe", + "content": "Reconstruction and analysis of viral and host genomes at multi-organ level" }, - "github/ejhigson/dyPolyChord": { - "id": "github/ejhigson/dyPolyChord", - "title": "github/ejhigson/dyPolyChord", - "url": " https://rseng.github.io/software/repository/github/ejhigson/dyPolyChord", - "content": "Super fast dynamic nested sampling with PolyChord (Python, C++ and Fortran likelihoods)." + "github/Xomics/ACTIONdemonstrator_workflow": { + "id": "github/Xomics/ACTIONdemonstrator_workflow", + "title": "github/Xomics/ACTIONdemonstrator_workflow", + "url": " https://rseng.github.io/software/repository/github/Xomics/ACTIONdemonstrator_workflow", + "content": "X-omics ACTION demonstrator multi-omics analysis workflow" }, - "github/ejhigson/perfectns": { - "id": "github/ejhigson/perfectns", - "title": "github/ejhigson/perfectns", - "url": " https://rseng.github.io/software/repository/github/ejhigson/perfectns", - "content": ""Perfect" dynamic and standard nested sampling for spherically symmetric likelihoods and priors." + "github/ExObsSim/ExoRad2-public": { + "id": "github/ExObsSim/ExoRad2-public", + "title": "github/ExObsSim/ExoRad2-public", + "url": " https://rseng.github.io/software/repository/github/ExObsSim/ExoRad2-public", + "content": "ExoRad, the generic point source radiometric model." }, - "github/OpenWaterAnalytics/EPyT": { - "id": "github/OpenWaterAnalytics/EPyT", - "title": "github/OpenWaterAnalytics/EPyT", - "url": " https://rseng.github.io/software/repository/github/OpenWaterAnalytics/EPyT", - "content": "EPyT: An EPANET-Python Toolkit for Smart Water Network Simulations" + "github/gperezs/StarcNet": { + "id": "github/gperezs/StarcNet", + "title": "github/gperezs/StarcNet", + "url": " https://rseng.github.io/software/repository/github/gperezs/StarcNet", + "content": "Machine learning for star cluster classification" }, - "github/OpenWaterAnalytics/pyswmm": { - "id": "github/OpenWaterAnalytics/pyswmm", - "title": "github/OpenWaterAnalytics/pyswmm", - "url": " https://rseng.github.io/software/repository/github/OpenWaterAnalytics/pyswmm", - "content": "Python Wrappers for SWMM" + "github/Someone789/galax2d": { + "id": "github/Someone789/galax2d", + "title": "github/Someone789/galax2d", + "url": " https://rseng.github.io/software/repository/github/Someone789/galax2d", + "content": "matlab or octave code to compute the 2D stationary solution of the isothermal Euler equations of gas dynamics in a rotating galaxy with a weak bar" }, - "github/fair-data/fairdatapoint-client": { - "id": "github/fair-data/fairdatapoint-client", - "title": "github/fair-data/fairdatapoint-client", - "url": " https://rseng.github.io/software/repository/github/fair-data/fairdatapoint-client", - "content": "Interact with your resources (catalogs/datasets/distributions) in a FDP using python" + "github/stevertaylor/gw_pta_emulator": { + "id": "github/stevertaylor/gw_pta_emulator", + "title": "github/stevertaylor/gw_pta_emulator", + "url": " https://rseng.github.io/software/repository/github/stevertaylor/gw_pta_emulator", + "content": "A notebook and data associated with the paper Taylor, Simon, Sampson (2017)" }, - "github/benlansdell/ethome": { - "id": "github/benlansdell/ethome", - "title": "github/benlansdell/ethome", - "url": " https://rseng.github.io/software/repository/github/benlansdell/ethome", - "content": "Tools for machine learning of animal behavior" + "github/chanzuckerberg/shasta": { + "id": "github/chanzuckerberg/shasta", + "title": "github/chanzuckerberg/shasta", + "url": " https://rseng.github.io/software/repository/github/chanzuckerberg/shasta", + "content": "De novo assembly from Oxford Nanopore reads." }, - "github/CosmoLike/CosmoCov": { - "id": "github/CosmoLike/CosmoCov", - "title": "github/CosmoLike/CosmoCov", - "url": " https://rseng.github.io/software/repository/github/CosmoLike/CosmoCov", - "content": "Configuration Space Covariances for Projected Galaxy 2-Point Statistics" + "github/chanzuckerberg/idseq-dag": { + "id": "github/chanzuckerberg/idseq-dag", + "title": "github/chanzuckerberg/idseq-dag", + "url": " https://rseng.github.io/software/repository/github/chanzuckerberg/idseq-dag", + "content": "Please see https://github.com/chanzuckerberg/czid-workflows for the latest version of CZ ID workflows." }, - "github/ruta-k/uGMRT-pipeline": { - "id": "github/ruta-k/uGMRT-pipeline", - "title": "github/ruta-k/uGMRT-pipeline", - "url": " https://rseng.github.io/software/repository/github/ruta-k/uGMRT-pipeline", - "content": "None" + "github/chanzuckerberg/cellxgene": { + "id": "github/chanzuckerberg/cellxgene", + "title": "github/chanzuckerberg/cellxgene", + "url": " https://rseng.github.io/software/repository/github/chanzuckerberg/cellxgene", + "content": "an interactive explorer for single-cell transcriptomics data" }, - "github/vbakis/mrs": { - "id": "github/vbakis/mrs", - "title": "github/vbakis/mrs", - "url": " https://rseng.github.io/software/repository/github/vbakis/mrs", - "content": "This repository is created for the MOS Reduction Software." + "github/bwoshea/ZEUS-MP_2": { + "id": "github/bwoshea/ZEUS-MP_2", + "title": "github/bwoshea/ZEUS-MP_2", + "url": " https://rseng.github.io/software/repository/github/bwoshea/ZEUS-MP_2", + "content": "This repository is the home of the ZEUS-MP 2.0 code, which was created by John Hayes and others at the Laboratory for Computational Astrophysics at UIUC and UCSD." }, - "github/junkoda/sidm-nbody": { - "id": "github/junkoda/sidm-nbody", - "title": "github/junkoda/sidm-nbody", - "url": " https://rseng.github.io/software/repository/github/junkoda/sidm-nbody", - "content": "Monte Carlo N-body Simulation for Self-Interacting Dark Matter" + "github/RavenGan/GR2D2": { + "id": "github/RavenGan/GR2D2", + "title": "github/RavenGan/GR2D2", + "url": " https://rseng.github.io/software/repository/github/RavenGan/GR2D2", + "content": "Take Monte Carlo samples from the posterior distribution based on the graphical R2D2 prior, to estimate the precision matrix for multivariate Gaussian data" }, - "github/kundajelab/phantompeakqualtools": { - "id": "github/kundajelab/phantompeakqualtools", - "title": "github/kundajelab/phantompeakqualtools", - "url": " https://rseng.github.io/software/repository/github/kundajelab/phantompeakqualtools", - "content": "This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays." + "github/onnela-lab/beiwe-backend": { + "id": "github/onnela-lab/beiwe-backend", + "title": "github/onnela-lab/beiwe-backend", + "url": " https://rseng.github.io/software/repository/github/onnela-lab/beiwe-backend", + "content": "Beiwe is a smartphone-based digital phenotyping research platform. This is the Beiwe backend code" }, - "github/dgobbi/vtk-dicom": { - "id": "github/dgobbi/vtk-dicom", - "title": "github/dgobbi/vtk-dicom", - "url": " https://rseng.github.io/software/repository/github/dgobbi/vtk-dicom", - "content": "A set of classes for using DICOM in VTK." + "github/xfcui/onn4arg": { + "id": "github/xfcui/onn4arg", + "title": "github/xfcui/onn4arg", + "url": " https://rseng.github.io/software/repository/github/xfcui/onn4arg", + "content": "None" }, - "github/dnonatar/Sequoia": { - "id": "github/dnonatar/Sequoia", - "title": "github/dnonatar/Sequoia", - "url": " https://rseng.github.io/software/repository/github/dnonatar/Sequoia", + "github/tomoyukif/MCPtaggR": { + "id": "github/tomoyukif/MCPtaggR", + "title": "github/tomoyukif/MCPtaggR", + "url": " https://rseng.github.io/software/repository/github/tomoyukif/MCPtaggR", "content": "None" }, - "github/TeamCOMPAS/COMPAS": { - "id": "github/TeamCOMPAS/COMPAS", - "title": "github/TeamCOMPAS/COMPAS", - "url": " https://rseng.github.io/software/repository/github/TeamCOMPAS/COMPAS", - "content": "COMPAS rapid binary population synthesis code" + "github/HofstadterTools/HofstadterTools": { + "id": "github/HofstadterTools/HofstadterTools", + "title": "github/HofstadterTools/HofstadterTools", + "url": " https://rseng.github.io/software/repository/github/HofstadterTools/HofstadterTools", + "content": "A Python package for analyzing the Hofstadter model." }, - "github/entangled/entangled": { - "id": "github/entangled/entangled", - "title": "github/entangled/entangled", - "url": " https://rseng.github.io/software/repository/github/entangled/entangled", - "content": "bi-directional tangle daemon for literate programming" + "github/carronj/lenspyx": { + "id": "github/carronj/lenspyx", + "title": "github/carronj/lenspyx", + "url": " https://rseng.github.io/software/repository/github/carronj/lenspyx", + "content": "Curved-sky python lensed CMB maps simulation package" }, - "github/octopus-sensing/octopus-sensing": { - "id": "github/octopus-sensing/octopus-sensing", - "title": "github/octopus-sensing/octopus-sensing", - "url": " https://rseng.github.io/software/repository/github/octopus-sensing/octopus-sensing", - "content": "None" + "github/carronj/plancklens": { + "id": "github/carronj/plancklens", + "title": "github/carronj/plancklens", + "url": " https://rseng.github.io/software/repository/github/carronj/plancklens", + "content": "Planck 2018 lensing pipeline" }, - "github/xinglunju/pyAmor": { - "id": "github/xinglunju/pyAmor", - "title": "github/xinglunju/pyAmor", - "url": " https://rseng.github.io/software/repository/github/xinglunju/pyAmor", - "content": "python code to derive temperatures using Ammonia spectral lines" + "github/ClapeyronThermo/GCIdentifier.jl": { + "id": "github/ClapeyronThermo/GCIdentifier.jl", + "title": "github/ClapeyronThermo/GCIdentifier.jl", + "url": " https://rseng.github.io/software/repository/github/ClapeyronThermo/GCIdentifier.jl", + "content": "tools to perform group contribution (GC) identification, given the SMILES of a compound" }, - "github/molgenis/graph2vr": { - "id": "github/molgenis/graph2vr", - "title": "github/molgenis/graph2vr", - "url": " https://rseng.github.io/software/repository/github/molgenis/graph2vr", - "content": "Visualising / Exploring Linked Data (SPARQL Construct queries) in Virtual Reality." + "github/lpfworld/DMPNet": { + "id": "github/lpfworld/DMPNet", + "title": "github/lpfworld/DMPNet", + "url": " https://rseng.github.io/software/repository/github/lpfworld/DMPNet", + "content": "DMPNet" }, - "github/ejeschke/ginga": { - "id": "github/ejeschke/ginga", - "title": "github/ejeschke/ginga", - "url": " https://rseng.github.io/software/repository/github/ejeschke/ginga", - "content": "The Ginga astronomical FITS file viewer" + "github/xdqso/xdqso": { + "id": "github/xdqso/xdqso", + "title": "github/xdqso/xdqso", + "url": " https://rseng.github.io/software/repository/github/xdqso/xdqso", + "content": "Quasar classification with XD" }, - "github/ihmwg/python-modelcif": { - "id": "github/ihmwg/python-modelcif", - "title": "github/ihmwg/python-modelcif", - "url": " https://rseng.github.io/software/repository/github/ihmwg/python-modelcif", - "content": " Python package for handling ModelCIF mmCIF and BinaryCIF files " + "github/zhwm/SparsePro_Paper": { + "id": "github/zhwm/SparsePro_Paper", + "title": "github/zhwm/SparsePro_Paper", + "url": " https://rseng.github.io/software/repository/github/zhwm/SparsePro_Paper", + "content": "Code repo for SparsePro Paper" }, - "github/dirostri/CREPE": { - "id": "github/dirostri/CREPE", - "title": "github/dirostri/CREPE", - "url": " https://rseng.github.io/software/repository/github/dirostri/CREPE", - "content": "GitHub Repository for CREPE: A tool for Transcription Factor Cataloguing" + "github/smithlabcode/abismal": { + "id": "github/smithlabcode/abismal", + "title": "github/smithlabcode/abismal", + "url": " https://rseng.github.io/software/repository/github/smithlabcode/abismal", + "content": "Abismal is a mapper of FASTQ bisulfite-converted short reads (between 50 and 1000 bases) to a FASTA reference genome." }, - 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"github/vhaasteren/piccard": { - "id": "github/vhaasteren/piccard", - "title": "github/vhaasteren/piccard", - "url": " https://rseng.github.io/software/repository/github/vhaasteren/piccard", - "content": "Piccard: pulsar timing data analysis package" + "github/smithlabcode/preseq": { + "id": "github/smithlabcode/preseq", + "title": "github/smithlabcode/preseq", + "url": " https://rseng.github.io/software/repository/github/smithlabcode/preseq", + "content": "Software for predicting library complexity and genome coverage in high-throughput sequencing." + }, + "github/ariedel/lacewing": { + "id": "github/ariedel/lacewing", + "title": "github/ariedel/lacewing", + "url": " https://rseng.github.io/software/repository/github/ariedel/lacewing", + "content": "Repository for the LACEwING moving group identification code (Riedel et al. 2017)" + }, + "github/adamjermyn/Skye": { + "id": "github/adamjermyn/Skye", + "title": "github/adamjermyn/Skye", + "url": " https://rseng.github.io/software/repository/github/adamjermyn/Skye", + "content": "A differentiable equation of state" }, - "github/andreasmang/claire": { - "id": "github/andreasmang/claire", - "title": "github/andreasmang/claire", - "url": " https://rseng.github.io/software/repository/github/andreasmang/claire", - "content": "Constrained Large Deformation Diffeomorphic Image Registration (CLAIRE)" + "github/tardis-sn/carsus": { + "id": "github/tardis-sn/carsus", + "title": "github/tardis-sn/carsus", + "url": " https://rseng.github.io/software/repository/github/tardis-sn/carsus", + "content": "Atomic Database for Astronomy" }, - "github/cobilab/altair": { - "id": "github/cobilab/altair", - "title": "github/cobilab/altair", - "url": " https://rseng.github.io/software/repository/github/cobilab/altair", - "content": "AltaiR: a C toolkit for alignment-free and spatial-temporal analysis of multi-FASTA data" + "github/tardis-sn/tardis": { + "id": "github/tardis-sn/tardis", + "title": "github/tardis-sn/tardis", + "url": " https://rseng.github.io/software/repository/github/tardis-sn/tardis", + "content": "TARDIS - Temperature And Radiative Diffusion In Supernovae" }, - "github/cobilab/RFSC": { - "id": "github/cobilab/RFSC", - "title": "github/cobilab/RFSC", - "url": " https://rseng.github.io/software/repository/github/cobilab/RFSC", - "content": "Reference-Free Sequence Classification Tool for DNA sequences in metagenomic samples" + "github/linneas/condetri": { + "id": "github/linneas/condetri", + "title": "github/linneas/condetri", + "url": " https://rseng.github.io/software/repository/github/linneas/condetri", + "content": "Automatically exported from code.google.com/p/condetri" }, - "github/JustinYKC/FEPOPS": { - "id": "github/JustinYKC/FEPOPS", - "title": "github/JustinYKC/FEPOPS", - "url": " https://rseng.github.io/software/repository/github/JustinYKC/FEPOPS", - "content": "Python implementation of the FEPOPS molecular descriptors" + "github/BioinfoUNIBA/REDItools2": { + "id": "github/BioinfoUNIBA/REDItools2", + "title": "github/BioinfoUNIBA/REDItools2", + "url": " https://rseng.github.io/software/repository/github/BioinfoUNIBA/REDItools2", + "content": "None" }, - "github/nrao/UniPOPS": { - "id": "github/nrao/UniPOPS", - "title": "github/nrao/UniPOPS", - "url": " https://rseng.github.io/software/repository/github/nrao/UniPOPS", - "content": "Archive of final NRAO UniPOPS source code distribution (version 3.5)" + "github/zheng-lh/UBER": { + "id": "github/zheng-lh/UBER", + "title": "github/zheng-lh/UBER", + "url": " https://rseng.github.io/software/repository/github/zheng-lh/UBER", + "content": "Universal Boltzmann Equation Solver" }, - "github/DeepRank/pdb2sql": { - "id": "github/DeepRank/pdb2sql", - "title": "github/DeepRank/pdb2sql", - "url": " https://rseng.github.io/software/repository/github/DeepRank/pdb2sql", - "content": "Fast and versatile biomolecular structure PDB file parser using SQL queries" + "github/toros-astro/corral": { + "id": "github/toros-astro/corral", + "title": "github/toros-astro/corral", + "url": " https://rseng.github.io/software/repository/github/toros-astro/corral", + "content": "The Powerful Pipeline Framework" }, - "github/DeepRank/deeprank-core": { - "id": "github/DeepRank/deeprank-core", - "title": "github/DeepRank/deeprank-core", - "url": " https://rseng.github.io/software/repository/github/DeepRank/deeprank-core", - "content": "None" + "github/toros-astro/astroalign-legacy": { + "id": "github/toros-astro/astroalign-legacy", + "title": "github/toros-astro/astroalign-legacy", + "url": " https://rseng.github.io/software/repository/github/toros-astro/astroalign-legacy", + "content": "A tool to align astronomical images based on asterism matching" }, - "github/DeepRank/DeepRank-GNN": { - "id": "github/DeepRank/DeepRank-GNN", - "title": "github/DeepRank/DeepRank-GNN", - "url": " https://rseng.github.io/software/repository/github/DeepRank/DeepRank-GNN", - "content": "Graph Network for protein-protein interface" + "github/dglaeser/gridformat": { + "id": "github/dglaeser/gridformat", + "title": "github/dglaeser/gridformat", + "url": " https://rseng.github.io/software/repository/github/dglaeser/gridformat", + "content": "Header-only C++-Library for grid file I/O" }, - "github/DeepRank/iScore": { - "id": "github/DeepRank/iScore", - "title": "github/DeepRank/iScore", - "url": " https://rseng.github.io/software/repository/github/DeepRank/iScore", - "content": "iScore: an MPI supported software for ranking protein-protein docking models based on a random walk graph kernel and support vector machines" + "github/ThomasMBury/ewstools": { + "id": "github/ThomasMBury/ewstools", + "title": "github/ThomasMBury/ewstools", + "url": " https://rseng.github.io/software/repository/github/ThomasMBury/ewstools", + "content": "Python package for early warning signals (EWS) of bifurcations in time series data." }, - "github/DeepRank/deeprank": { - "id": "github/DeepRank/deeprank", - "title": "github/DeepRank/deeprank", - "url": " https://rseng.github.io/software/repository/github/DeepRank/deeprank", - "content": "Deep learning framework for data mining protein-protein interactions using CNN" + "github/christinahedges/contaminante": { + "id": "github/christinahedges/contaminante", + "title": "github/christinahedges/contaminante", + "url": " https://rseng.github.io/software/repository/github/christinahedges/contaminante", + "content": "Find the contaminant transiting source in Kepler, K2 or TESS data." }, - "github/DeepRank/pssmgen": { - "id": "github/DeepRank/pssmgen", - "title": "github/DeepRank/pssmgen", - "url": " https://rseng.github.io/software/repository/github/DeepRank/pssmgen", - "content": "Generates consistent PSSM and/or PDB files for protein-protein complexes" + "github/NCAS-CMS/cfdm": { + "id": "github/NCAS-CMS/cfdm", + "title": "github/NCAS-CMS/cfdm", + "url": " https://rseng.github.io/software/repository/github/NCAS-CMS/cfdm", + "content": "A Python reference implementation of the CF data model" }, - "github/C-Briddon/SELCIE": { - "id": "github/C-Briddon/SELCIE", - "title": "github/C-Briddon/SELCIE", - "url": " https://rseng.github.io/software/repository/github/C-Briddon/SELCIE", - "content": "None" + "github/paulsengroup/hictk": { + "id": "github/paulsengroup/hictk", + "title": "github/paulsengroup/hictk", + "url": " https://rseng.github.io/software/repository/github/paulsengroup/hictk", + "content": "Blazing fast toolkit to work with .hic and .cool files" }, - "github/yuhuan-wu/mobilesal": { - "id": "github/yuhuan-wu/mobilesal", - "title": "github/yuhuan-wu/mobilesal", - "url": " https://rseng.github.io/software/repository/github/yuhuan-wu/mobilesal", - "content": "[IEEE TPAMI21] MobileSal: Extremely Efficient RGB-D Salient Object Detection [PyTorch & Jittor]" + "github/Singh-Lab/uKIN": { + "id": "github/Singh-Lab/uKIN", + "title": "github/Singh-Lab/uKIN", + "url": " https://rseng.github.io/software/repository/github/Singh-Lab/uKIN", + "content": "Using Knowledge In Networks" }, - "github/csuhjhjhj/GCNCMI": { - "id": "github/csuhjhjhj/GCNCMI", - "title": "github/csuhjhjhj/GCNCMI", - "url": " https://rseng.github.io/software/repository/github/csuhjhjhj/GCNCMI", - "content": "CircRNA-miRNA interaction Prediction Based on Graph Neural Network" + "github/Singh-Lab/DeMaSk": { + "id": "github/Singh-Lab/DeMaSk", + "title": "github/Singh-Lab/DeMaSk", + "url": " https://rseng.github.io/software/repository/github/Singh-Lab/DeMaSk", + "content": "Prediction of protein substitution impact using a directional substitution matrix and homolog alignments" }, - 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"github/jw-lin/cbeam": { - "id": "github/jw-lin/cbeam", - "title": "github/jw-lin/cbeam", - "url": " https://rseng.github.io/software/repository/github/jw-lin/cbeam", + "github/biobakery/halla": { + "id": "github/biobakery/halla", + "title": "github/biobakery/halla", + "url": " https://rseng.github.io/software/repository/github/biobakery/halla", "content": "None" }, - "github/jw-lin/lightbeam": { - "id": "github/jw-lin/lightbeam", - "title": "github/jw-lin/lightbeam", - "url": " https://rseng.github.io/software/repository/github/jw-lin/lightbeam", - "content": "simulate light through weakly-guiding waveguides using the finite-differences beam propagation method on an adaptive mesh" + "github/VNNikolaidis/nnlib2Rcpp": { + "id": "github/VNNikolaidis/nnlib2Rcpp", + "title": "github/VNNikolaidis/nnlib2Rcpp", + "url": " https://rseng.github.io/software/repository/github/VNNikolaidis/nnlib2Rcpp", + "content": "An R package for Neural Nets created using nnlib2" }, - "github/mihanke/athos": { - "id": "github/mihanke/athos", - "title": "github/mihanke/athos", - "url": " https://rseng.github.io/software/repository/github/mihanke/athos", - "content": "ATHOS: On-the-fly stellar parameter determination of FGK stars based on flux ratios from optical spectra" + "github/jradcliffe5/multi_self_cal": { + "id": "github/jradcliffe5/multi_self_cal", + "title": "github/jradcliffe5/multi_self_cal", + "url": " https://rseng.github.io/software/repository/github/jradcliffe5/multi_self_cal", + "content": "Multi-Source Self-Calibration is a Parseltongue (Kettenis et al. 2012) script which provides an extra calibration for VLBI data sets that image multiple target source within one observation. More information is in the README & paper Radcliffe et. al 2016. If you use this script please reference Radcliffe et al. 2016 which is the paper that accompanies this release." }, - "github/stillwater-sc/universal": { - "id": "github/stillwater-sc/universal", - "title": "github/stillwater-sc/universal", - "url": " https://rseng.github.io/software/repository/github/stillwater-sc/universal", - "content": "Large collection of number systems providing custom arithmetic and mixed-precision algorithms for AI, Machine Learning, Computer Vision, Signal Processing, CAE, EDA, control, optimization, estimation, and approximation." + "github/agurvich/FIRE_studio": { + "id": "github/agurvich/FIRE_studio", + "title": "github/agurvich/FIRE_studio", + "url": " https://rseng.github.io/software/repository/github/agurvich/FIRE_studio", + "content": "Movie Making Utilities for FIRE simulations" }, - "github/tudelft3d/3dfier": { - "id": "github/tudelft3d/3dfier", - "title": "github/tudelft3d/3dfier", - "url": " https://rseng.github.io/software/repository/github/tudelft3d/3dfier", - "content": "The open-source tool for creating of 3D models" + "github/bccp/nbodykit": { + "id": "github/bccp/nbodykit", + "title": "github/bccp/nbodykit", + "url": " https://rseng.github.io/software/repository/github/bccp/nbodykit", + "content": "Analysis kit for large-scale structure datasets, the massively parallel way" }, - "github/damonge/CRIME": { - "id": "github/damonge/CRIME", - "title": "github/damonge/CRIME", - "url": " https://rseng.github.io/software/repository/github/damonge/CRIME", - "content": "Cosmological Realizations for Intensity Mapping Experiments" + "github/fmihpc/vlasiator": { + "id": "github/fmihpc/vlasiator", + "title": "github/fmihpc/vlasiator", + "url": " https://rseng.github.io/software/repository/github/fmihpc/vlasiator", + "content": "Vlasiator - ten letters you can count on" }, - "github/damonge/schNell": { - "id": "github/damonge/schNell", - "title": "github/damonge/schNell", - "url": " https://rseng.github.io/software/repository/github/damonge/schNell", - "content": "Fast calculation of N_ell for GW anisotropies" + "github/fmihpc/analysator": { + "id": "github/fmihpc/analysator", + "title": "github/fmihpc/analysator", + "url": " https://rseng.github.io/software/repository/github/fmihpc/analysator", + "content": "Python based package for analyzing vlsv files produced by Vlasiator" }, - "github/damonge/CoLoRe": { - "id": "github/damonge/CoLoRe", - "title": "github/damonge/CoLoRe", - "url": " https://rseng.github.io/software/repository/github/damonge/CoLoRe", - "content": "CoLoRe - Cosmological Lofty Realizations" + "github/DataIntellSystLab/KARGA": { + "id": "github/DataIntellSystLab/KARGA", + "title": "github/DataIntellSystLab/KARGA", + "url": " https://rseng.github.io/software/repository/github/DataIntellSystLab/KARGA", + "content": "Multi-platform Toolkit for k-mer-based Antibiotic Resistance Gene Analysis of High-throughput Sequencing Data" }, - "github/damonge/CUTE": { - "id": "github/damonge/CUTE", - "title": "github/damonge/CUTE", - "url": " https://rseng.github.io/software/repository/github/damonge/CUTE", - "content": "Correlation Utilities and Two-point Estimation" + "github/sieunhanbom04/support-exploration-matrix-factorization": { + "id": "github/sieunhanbom04/support-exploration-matrix-factorization", + "title": "github/sieunhanbom04/support-exploration-matrix-factorization", + "url": " https://rseng.github.io/software/repository/github/sieunhanbom04/support-exploration-matrix-factorization", + "content": "Code for the paper "Structured support exploration for multi-layer sparse matrix factorization" - ICASSP 2020" + }, + "github/elizabethnewman/hessQuik": { + "id": "github/elizabethnewman/hessQuik", + "title": "github/elizabethnewman/hessQuik", + "url": " https://rseng.github.io/software/repository/github/elizabethnewman/hessQuik", + "content": "Computing gradients and Hessians of feed-forward networks with GPU acceleration" }, - "github/cweniger/swordfish": { - "id": "github/cweniger/swordfish", - "title": "github/cweniger/swordfish", - "url": " https://rseng.github.io/software/repository/github/cweniger/swordfish", - "content": "A Python tool to study the information yield of counting experiments." + "github/GENtle-persons/gentle-m": { + "id": "github/GENtle-persons/gentle-m", + "title": "github/GENtle-persons/gentle-m", + "url": " https://rseng.github.io/software/repository/github/GENtle-persons/gentle-m", + "content": "None" }, - "github/xfengnefx/hifiasm-meta": { - "id": "github/xfengnefx/hifiasm-meta", - "title": "github/xfengnefx/hifiasm-meta", - "url": " https://rseng.github.io/software/repository/github/xfengnefx/hifiasm-meta", - "content": "hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads." + "github/franciscovillaescusa/Pylians3": { + "id": "github/franciscovillaescusa/Pylians3", + "title": "github/franciscovillaescusa/Pylians3", + "url": " https://rseng.github.io/software/repository/github/franciscovillaescusa/Pylians3", + "content": "Libraries to analyze numerical simulations (python3)" }, - 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"github/FiorenSt/AutoSourceID-Light": { - "id": "github/FiorenSt/AutoSourceID-Light", - "title": "github/FiorenSt/AutoSourceID-Light", - "url": " https://rseng.github.io/software/repository/github/FiorenSt/AutoSourceID-Light", + "github/ExoSim/ExoSimPublic": { + "id": "github/ExoSim/ExoSimPublic", + "title": "github/ExoSim/ExoSimPublic", + "url": " https://rseng.github.io/software/repository/github/ExoSim/ExoSimPublic", "content": "None" }, - "github/rochoa85/NTDHealth_Forms": { - "id": "github/rochoa85/NTDHealth_Forms", - "title": "github/rochoa85/NTDHealth_Forms", - "url": " https://rseng.github.io/software/repository/github/rochoa85/NTDHealth_Forms", - "content": "Based on the OpenMRS HTML Form Entry module, you can find in this github repository a set of forms personalized for neglected tropical virus, including clinical assesment, personal history and epidemiological data. " - }, - "github/kennethcarrell/ATARRI": { - "id": "github/kennethcarrell/ATARRI", - "title": "github/kennethcarrell/ATARRI", - "url": " https://rseng.github.io/software/repository/github/kennethcarrell/ATARRI", - "content": "A TESS Archive RR Lyrae Classifier" + "github/TRASAL/AMBER": { + "id": "github/TRASAL/AMBER", + "title": "github/TRASAL/AMBER", + "url": " https://rseng.github.io/software/repository/github/TRASAL/AMBER", + "content": "A many-core transient searching pipeline, designed to search in real-time for Fast Radio Bursts." }, - "github/KenethGarcia/ClassiPyGRB": { - "id": "github/KenethGarcia/ClassiPyGRB", - "title": "github/KenethGarcia/ClassiPyGRB", - "url": " https://rseng.github.io/software/repository/github/KenethGarcia/ClassiPyGRB", - "content": "This repository contains all the updates, code, and documentation related to ClassiPyGRB." + "github/TRASAL/psrdada-python": { + "id": "github/TRASAL/psrdada-python", + "title": "github/TRASAL/psrdada-python", + "url": " https://rseng.github.io/software/repository/github/TRASAL/psrdada-python", + "content": "Python bindings to the PSRDada ringbuffer implementation" }, - "github/jnktsj/DNApi": { - "id": "github/jnktsj/DNApi", - "title": "github/jnktsj/DNApi", - "url": " https://rseng.github.io/software/repository/github/jnktsj/DNApi", - "content": "De novo adapter prediction algorithm for small RNA sequencing data" + "github/gpertea/gclib": { + "id": "github/gpertea/gclib", + "title": "github/gpertea/gclib", + "url": " https://rseng.github.io/software/repository/github/gpertea/gclib", + "content": "GCLib - Genomic C++ library of reusable code for bioinformatics projects" }, - "github/QuantEcon/QuantEcon.py": { - "id": "github/QuantEcon/QuantEcon.py", - "title": "github/QuantEcon/QuantEcon.py", - "url": " https://rseng.github.io/software/repository/github/QuantEcon/QuantEcon.py", - "content": "A community based Python library for quantitative economics" + "github/gpertea/cdbfasta": { + "id": "github/gpertea/cdbfasta", + "title": "github/gpertea/cdbfasta", + "url": " https://rseng.github.io/software/repository/github/gpertea/cdbfasta", + "content": "Constant DataBase tools for indexing and retrieving records from multi-FASTA or similarly structured files" }, - 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Trivially transition between one off use cases to massive scale production environments" + "github/insilico/cncv": { + "id": "github/insilico/cncv", + "title": "github/insilico/cncv", + "url": " https://rseng.github.io/software/repository/github/insilico/cncv", + "content": "Consensus Nested Cross-Validation" }, - "github/broadinstitute/CellBender": { - "id": "github/broadinstitute/CellBender", - "title": "github/broadinstitute/CellBender", - "url": " https://rseng.github.io/software/repository/github/broadinstitute/CellBender", - "content": "a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data." + "github/Michalychforever/AsPy": { + "id": "github/Michalychforever/AsPy", + "title": "github/Michalychforever/AsPy", + "url": " https://rseng.github.io/software/repository/github/Michalychforever/AsPy", + "content": "Code to compute the determinant of aspherical fluctuations in spherical collapse background" }, - "github/broadinstitute/picard": { - "id": "github/broadinstitute/picard", - "title": "github/broadinstitute/picard", - "url": " https://rseng.github.io/software/repository/github/broadinstitute/picard", - "content": "A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF." + "github/Hegghammer/daiR": { + "id": "github/Hegghammer/daiR", + "title": "github/Hegghammer/daiR", + "url": " https://rseng.github.io/software/repository/github/Hegghammer/daiR", + "content": "R package for Google Document AI " }, - "github/broadinstitute/wot": { - "id": "github/broadinstitute/wot", - "title": "github/broadinstitute/wot", - "url": " https://rseng.github.io/software/repository/github/broadinstitute/wot", - "content": "A software package for analyzing snapshots of developmental processes" + "github/rohinkumar/correlcalc": { + "id": "github/rohinkumar/correlcalc", + "title": "github/rohinkumar/correlcalc", + "url": " https://rseng.github.io/software/repository/github/rohinkumar/correlcalc", + "content": "A Python package to calculate 2-point correlation function from galaxy redshift surveys for any generic model of Cosmology or geometry" }, - 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"content": "Short Read Sequence Typing for Bacterial Pathogens" + "github/fastpm/fastpm": { + "id": "github/fastpm/fastpm", + "title": "github/fastpm/fastpm", + "url": " https://rseng.github.io/software/repository/github/fastpm/fastpm", + "content": "fastPM - A N-body Particle Mesh solver that scales" }, - "github/katholt/Kleborate": { - "id": "github/katholt/Kleborate", - "title": "github/katholt/Kleborate", - "url": " https://rseng.github.io/software/repository/github/katholt/Kleborate", - "content": "tool to screen Klebsiella genome assemblies" + "github/ggmichael/craterstats": { + "id": "github/ggmichael/craterstats", + "title": "github/ggmichael/craterstats", + "url": " https://rseng.github.io/software/repository/github/ggmichael/craterstats", + "content": "Craterstats - a tool to analyse and plot crater count data for planetary surface dating" }, - "github/katholt/Kaptive": { - "id": "github/katholt/Kaptive", - "title": "github/katholt/Kaptive", - "url": " https://rseng.github.io/software/repository/github/katholt/Kaptive", - "content": "obtain information about K and O types for Klebsiella genome assemblies" + "github/bodenlab/GRASP": { + "id": "github/bodenlab/GRASP", + "title": "github/bodenlab/GRASP", + "url": " https://rseng.github.io/software/repository/github/bodenlab/GRASP", + "content": "Graphical Representation of Ancestral Sequence Predictions" }, - "github/valentineap/pyprop8": { - "id": "github/valentineap/pyprop8", - "title": "github/valentineap/pyprop8", - "url": " https://rseng.github.io/software/repository/github/valentineap/pyprop8", - "content": "A lightweight Python code to calculate the seismic response of a layered half-space (including static components), and derivatives of the wavefield wrt source components." + "github/nrao/UniPOPS": { + "id": "github/nrao/UniPOPS", + "title": "github/nrao/UniPOPS", + "url": " https://rseng.github.io/software/repository/github/nrao/UniPOPS", + "content": "Archive of final NRAO UniPOPS source code distribution (version 3.5)" }, - "github/pydemull/activAnalyzer": { - "id": "github/pydemull/activAnalyzer", - "title": "github/pydemull/activAnalyzer", - "url": " https://rseng.github.io/software/repository/github/pydemull/activAnalyzer", + "github/etiennepayet/nti": { + "id": "github/etiennepayet/nti", + "title": "github/etiennepayet/nti", + "url": " https://rseng.github.io/software/repository/github/etiennepayet/nti", "content": "None" }, - "github/rqtl/qtl2": { - "id": "github/rqtl/qtl2", - "title": "github/rqtl/qtl2", - "url": " https://rseng.github.io/software/repository/github/rqtl/qtl2", - "content": "QTL analysis software for high-dimensional data and complex cross designs" + "github/jimmink/argslab": { + "id": "github/jimmink/argslab", + "title": "github/jimmink/argslab", + "url": " https://rseng.github.io/software/repository/github/jimmink/argslab", + "content": "Repository for ArGSLab, Arrested and Gelated Structures Laboratory." + }, + "github/SchmidtDSE/afscgap": { + "id": "github/SchmidtDSE/afscgap", + "title": "github/SchmidtDSE/afscgap", + "url": " https://rseng.github.io/software/repository/github/SchmidtDSE/afscgap", + "content": "Python-based tools for NOAA AFSC GAP marine species surveys data" }, - 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"github/gt1/bambamc": { - "id": "github/gt1/bambamc", - "title": "github/gt1/bambamc", - "url": " https://rseng.github.io/software/repository/github/gt1/bambamc", - "content": "lightweight C implementation of name collating BAM file input and BAM file output " + "github/orcasgit/python-fitbit": { + "id": "github/orcasgit/python-fitbit", + "title": "github/orcasgit/python-fitbit", + "url": " https://rseng.github.io/software/repository/github/orcasgit/python-fitbit", + "content": "Fitbit API Python Client Implementation" }, - "github/mrteetoe/HOI": { - "id": "github/mrteetoe/HOI", - "title": "github/mrteetoe/HOI", - "url": " https://rseng.github.io/software/repository/github/mrteetoe/HOI", - "content": "None" + "github/netsiphd/netrd": { + "id": "github/netsiphd/netrd", + "title": "github/netsiphd/netrd", + "url": " https://rseng.github.io/software/repository/github/netsiphd/netrd", + "content": "A library for network {reconstruction, distances, dynamics}" }, - "github/cosmo-ethz/CosmoHammer": { - "id": "github/cosmo-ethz/CosmoHammer", - "title": "github/cosmo-ethz/CosmoHammer", - "url": " https://rseng.github.io/software/repository/github/cosmo-ethz/CosmoHammer", - "content": "Cosmological parameter estimation with the MCMC Hammer, please use https://cosmo-gitlab.phys.ethz.ch/cosmo/CosmoHammer, this repository is outdated ! Docs at http://cosmo-docs.phys.ethz.ch/cosmoHammer/" + "github/Illumina/ExpansionHunterDenovo": { + "id": "github/Illumina/ExpansionHunterDenovo", + "title": "github/Illumina/ExpansionHunterDenovo", + "url": " https://rseng.github.io/software/repository/github/Illumina/ExpansionHunterDenovo", + "content": "(EHdn) is a suite of tools for detecting novel expansions of short tandem repeats (STRs)." }, - "github/cosmo-ethz/seek": { - "id": "github/cosmo-ethz/seek", - "title": "github/cosmo-ethz/seek", - "url": " https://rseng.github.io/software/repository/github/cosmo-ethz/seek", - "content": "A flexible and easy-to-extend data processing pipeline for single dish radio telescopes" + "github/Illumina/SpliceAI": { + "id": "github/Illumina/SpliceAI", + "title": "github/Illumina/SpliceAI", + "url": " https://rseng.github.io/software/repository/github/Illumina/SpliceAI", + "content": "A deep learning-based tool to identify splice variants" }, - "github/cosmo-ethz/hide": { - "id": "github/cosmo-ethz/hide", - "title": "github/cosmo-ethz/hide", - "url": " https://rseng.github.io/software/repository/github/cosmo-ethz/hide", - "content": "A package for simulating of a single dish radio telescope survey" + "github/Illumina/manta": { + "id": "github/Illumina/manta", + "title": "github/Illumina/manta", + "url": " https://rseng.github.io/software/repository/github/Illumina/manta", + "content": "Structural variant and indel caller for mapped sequencing data" }, - "github/refresh-bio/whisper": { - "id": "github/refresh-bio/whisper", - "title": "github/refresh-bio/whisper", - "url": " https://rseng.github.io/software/repository/github/refresh-bio/whisper", - "content": "None" + "github/Illumina/MarViN": { + "id": "github/Illumina/MarViN", + "title": "github/Illumina/MarViN", + "url": " https://rseng.github.io/software/repository/github/Illumina/MarViN", + "content": "a method for rapid genotype refinement for whole-genome sequencing data using multi-variate normal distribution. Whole-genome low-coverage sequencing has been combined with linkage-disequilibrium (LD) based genotype refinement to accurately and cost-effectively infer genotypes in large cohorts of individuals." }, - "github/refresh-bio/agc": { - "id": "github/refresh-bio/agc", - "title": "github/refresh-bio/agc", - "url": " https://rseng.github.io/software/repository/github/refresh-bio/agc", - "content": "Assembled Genomes Compressor" + "github/Illumina/strelka": { + "id": "github/Illumina/strelka", + "title": "github/Illumina/strelka", + "url": " https://rseng.github.io/software/repository/github/Illumina/strelka", + "content": "Strelka2 germline and somatic small variant caller" }, - "github/egstrom/cluster-in-a-box": { - "id": "github/egstrom/cluster-in-a-box", - "title": "github/egstrom/cluster-in-a-box", - "url": " https://rseng.github.io/software/repository/github/egstrom/cluster-in-a-box", - "content": "Statistical model of protostellar clusters" + "github/Illumina/akt": { + "id": "github/Illumina/akt", + "title": "github/Illumina/akt", + "url": " https://rseng.github.io/software/repository/github/Illumina/akt", + "content": "Ancestry and Kinship Tools" }, - 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"url": " https://rseng.github.io/software/repository/github/JulianKarlBauer/mechkit", - "content": "Continuum mechanics toolkit" + "github/Guo-Jian-Wang/colfi": { + "id": "github/Guo-Jian-Wang/colfi", + "title": "github/Guo-Jian-Wang/colfi", + "url": " https://rseng.github.io/software/repository/github/Guo-Jian-Wang/colfi", + "content": "Likelihood-free Inference with neural density estimators" }, - "github/deepmind/alphafold": { - "id": "github/deepmind/alphafold", - "title": "github/deepmind/alphafold", - "url": " https://rseng.github.io/software/repository/github/deepmind/alphafold", - "content": "Open source code for AlphaFold." + "github/ziyewang/MetaBinner": { + "id": "github/ziyewang/MetaBinner", + "title": "github/ziyewang/MetaBinner", + "url": " https://rseng.github.io/software/repository/github/ziyewang/MetaBinner", + "content": "None" }, - "github/TPI-Immunogenetics/igmat": { - "id": "github/TPI-Immunogenetics/igmat", - "title": "github/TPI-Immunogenetics/igmat", - "url": " https://rseng.github.io/software/repository/github/TPI-Immunogenetics/igmat", - "content": "Antibody Multispecies Annotation Tool" + "github/ziyewang/ARG_SHINE": { + "id": "github/ziyewang/ARG_SHINE", + "title": "github/ziyewang/ARG_SHINE", + "url": " https://rseng.github.io/software/repository/github/ziyewang/ARG_SHINE", + "content": "None" }, - "github/qMRLab/qMRLab": { - "id": "github/qMRLab/qMRLab", - "title": "github/qMRLab/qMRLab", - "url": " https://rseng.github.io/software/repository/github/qMRLab/qMRLab", - "content": "Quantitative Magnetic Resonance Imaging Made Easy with qMRLab: a Software for Data Simulation, Analysis and Visualization" + "github/aneeshnaik/spam": { + "id": "github/aneeshnaik/spam", + "title": "github/aneeshnaik/spam", + "url": " https://rseng.github.io/software/repository/github/aneeshnaik/spam", + "content": "spam is a Python 3 package, used to search for imprints of Hu-Sawicki f(R) gravity in the rotation curves of the SPARC sample." }, - "github/james-m-osborn/astrosat": { - "id": "github/james-m-osborn/astrosat", - "title": "github/james-m-osborn/astrosat", - "url": " https://rseng.github.io/software/repository/github/james-m-osborn/astrosat", - "content": "None" + "github/MD-Studio/cerise": { + "id": "github/MD-Studio/cerise", + "title": "github/MD-Studio/cerise", + "url": " https://rseng.github.io/software/repository/github/MD-Studio/cerise", + "content": "A REST service for running CWL workflows on remote clusters" }, - "github/ChenYangyao/hipp": { - "id": "github/ChenYangyao/hipp", - "title": "github/ChenYangyao/hipp", - "url": " https://rseng.github.io/software/repository/github/ChenYangyao/hipp", - "content": "HIPP: Modern C++ Toolkit for HPC" + "github/MD-Studio/cerulean": { + "id": "github/MD-Studio/cerulean", + "title": "github/MD-Studio/cerulean", + "url": " https://rseng.github.io/software/repository/github/MD-Studio/cerulean", + "content": "A Python 3 library for talking to HPC clusters and supercomputers" }, - "github/davidebolo1993/TRiCoLOR": { - "id": "github/davidebolo1993/TRiCoLOR", - "title": "github/davidebolo1993/TRiCoLOR", - "url": " https://rseng.github.io/software/repository/github/davidebolo1993/TRiCoLOR", - "content": "Tadem Repeats Caller for LOng Reads" + "github/MD-Studio/MDStudio": { + "id": "github/MD-Studio/MDStudio", + "title": "github/MD-Studio/MDStudio", + "url": " https://rseng.github.io/software/repository/github/MD-Studio/MDStudio", + "content": "A general framework for microservice based distributed applications" }, - "github/davidebolo1993/VISOR": { - "id": "github/davidebolo1993/VISOR", - "title": "github/davidebolo1993/VISOR", - "url": " https://rseng.github.io/software/repository/github/davidebolo1993/VISOR", - "content": "VarIant SimulatOR for short, long and linked reads" + "github/idaholab/moose": { + "id": "github/idaholab/moose", + "title": "github/idaholab/moose", + "url": " https://rseng.github.io/software/repository/github/idaholab/moose", + "content": "Multiphysics Object Oriented Simulation Environment" }, - "github/mrbell/fsclean": { - "id": "github/mrbell/fsclean", - "title": "github/mrbell/fsclean", - "url": " https://rseng.github.io/software/repository/github/mrbell/fsclean", - "content": "A Faraday synthesis application that performs 3D CLEAN deconvolution of multi-frequency, polarized radio interferometric data following Bell & Enßlin (2012)." + "github/TingMAC/FrMLNet": { + "id": "github/TingMAC/FrMLNet", + "title": "github/TingMAC/FrMLNet", + "url": " https://rseng.github.io/software/repository/github/TingMAC/FrMLNet", + "content": "This is a implementation of training code of this paper “FrMLNet: Framelet-based Multi-level Network for Pansharpening”" }, - "github/theLongLab/CATE": { - "id": "github/theLongLab/CATE", - "title": "github/theLongLab/CATE", - "url": " https://rseng.github.io/software/repository/github/theLongLab/CATE", - "content": "A fast and scalable CUDA implementation to conduct highly parallelized evolutionary tests on large scale genomic data." + "github/MAnalytics/akmedoids": { + "id": "github/MAnalytics/akmedoids", + "title": "github/MAnalytics/akmedoids", + "url": " https://rseng.github.io/software/repository/github/MAnalytics/akmedoids", + "content": "akmedoids for longitudinal clustering" }, - 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It features methods for automated antibody humanization (Sapiens), humanness evaluation (OASis) and an interface for computer-assisted antibody sequence design." + "github/MAnalytics/opitools": { + "id": "github/MAnalytics/opitools", + "title": "github/MAnalytics/opitools", + "url": " https://rseng.github.io/software/repository/github/MAnalytics/opitools", + "content": "An R-package for opinion analysis of social media data" }, - "github/Merck/pkglite": { - "id": "github/Merck/pkglite", - "title": "github/Merck/pkglite", - "url": " https://rseng.github.io/software/repository/github/Merck/pkglite", - "content": "Compact Package Representations" + "github/deepmodeling/DMFF": { + "id": "github/deepmodeling/DMFF", + "title": "github/deepmodeling/DMFF", + "url": " https://rseng.github.io/software/repository/github/deepmodeling/DMFF", + "content": "DMFF (Differentiable Molecular Force Field) is a Jax-based python package that provides a full differentiable implementation of molecular force field models. " }, - "github/BjoernBiltzinger/pyspi": { - "id": "github/BjoernBiltzinger/pyspi", - "title": "github/BjoernBiltzinger/pyspi", - "url": " https://rseng.github.io/software/repository/github/BjoernBiltzinger/pyspi", - "content": "Pure python tools for interfacing with INTEGRAL SPI data. It also provides a 3ML plugin for performing full forward folding spectral analysis of GRBs. The documentation with a few examples is available at https://pyspi.readthedocs.io/." + "github/n-claes/legolas": { + "id": "github/n-claes/legolas", + "title": "github/n-claes/legolas", + "url": " https://rseng.github.io/software/repository/github/n-claes/legolas", + "content": "Legolas: a modern tool for MHD spectroscopy" }, - "github/seshnadathur/Revolver": { - "id": "github/seshnadathur/Revolver", - "title": "github/seshnadathur/Revolver", - "url": " https://rseng.github.io/software/repository/github/seshnadathur/Revolver", - "content": "Real-space void locations from survey reconstruction" + "github/silburt/DeepMoon": { + "id": "github/silburt/DeepMoon", + "title": "github/silburt/DeepMoon", + "url": " https://rseng.github.io/software/repository/github/silburt/DeepMoon", + "content": "Convolutional neural network code for extracting Lunar craters from Digital Elevation Maps (DEMs)." }, - "github/elizabethnewman/hessQuik": { - "id": "github/elizabethnewman/hessQuik", - "title": "github/elizabethnewman/hessQuik", - "url": " https://rseng.github.io/software/repository/github/elizabethnewman/hessQuik", - "content": "Computing gradients and Hessians of feed-forward networks with GPU acceleration" + "github/JustinYKC/FEPOPS": { + "id": "github/JustinYKC/FEPOPS", + "title": "github/JustinYKC/FEPOPS", + "url": " https://rseng.github.io/software/repository/github/JustinYKC/FEPOPS", + "content": "Python implementation of the FEPOPS molecular descriptors" }, - "github/reggiebernardo/PTAfast": { - "id": "github/reggiebernardo/PTAfast", - "title": "github/reggiebernardo/PTAfast", - "url": " https://rseng.github.io/software/repository/github/reggiebernardo/PTAfast", - "content": "Fast code for PTA correlations from SGWB" + "github/PengyiZhang/DRR4Covid": { + "id": "github/PengyiZhang/DRR4Covid", + "title": "github/PengyiZhang/DRR4Covid", + "url": " https://rseng.github.io/software/repository/github/PengyiZhang/DRR4Covid", + "content": "DRR4Covid: Learning Automated COVID-19 Infection Segmentation from Digitally Reconstructed Radiographs" }, - 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Whole-genome low-coverage sequencing has been combined with linkage-disequilibrium (LD) based genotype refinement to accurately and cost-effectively infer genotypes in large cohorts of individuals." + "github/achaikova/frbmclust": { + "id": "github/achaikova/frbmclust", + "title": "github/achaikova/frbmclust", + "url": " https://rseng.github.io/software/repository/github/achaikova/frbmclust", + "content": "None" }, - "github/Illumina/SpliceAI": { - "id": "github/Illumina/SpliceAI", - "title": "github/Illumina/SpliceAI", - "url": " https://rseng.github.io/software/repository/github/Illumina/SpliceAI", - "content": "A deep learning-based tool to identify splice variants" + "github/kibokov/grumpy": { + "id": "github/kibokov/grumpy", + "title": "github/kibokov/grumpy", + "url": " https://rseng.github.io/software/repository/github/kibokov/grumpy", + "content": "None" }, - "github/Illumina/akt": { - "id": "github/Illumina/akt", - "title": "github/Illumina/akt", - "url": " https://rseng.github.io/software/repository/github/Illumina/akt", - "content": "Ancestry and Kinship Tools" + "github/emrecdem/emo-spectre": { + "id": "github/emrecdem/emo-spectre", + "title": "github/emrecdem/emo-spectre", + "url": " https://rseng.github.io/software/repository/github/emrecdem/emo-spectre", + "content": "None" }, - "github/Illumina/manta": { - "id": "github/Illumina/manta", - "title": "github/Illumina/manta", - "url": " https://rseng.github.io/software/repository/github/Illumina/manta", - "content": "Structural variant and indel caller for mapped sequencing data" + "github/calboo/TAWAS": { + "id": "github/calboo/TAWAS", + "title": "github/calboo/TAWAS", + "url": " https://rseng.github.io/software/repository/github/calboo/TAWAS", + "content": "TAWAS is an IDL script for solving the wave equation for torsional Alfvèn waves in a viscous plasma. The background magnetic field is axisymmetric and force-free with no azimuthal component and the plasma beta is assumed to be negligable. The solution is calculated using the analytical formula presented in https://academic.oup.com/mnras/article-abstract/510/2/1910/6449388?redirectedFrom=fulltext. " }, - "github/Illumina/ExpansionHunterDenovo": { - "id": "github/Illumina/ExpansionHunterDenovo", - "title": "github/Illumina/ExpansionHunterDenovo", - "url": " https://rseng.github.io/software/repository/github/Illumina/ExpansionHunterDenovo", - "content": "(EHdn) is a suite of tools for detecting novel expansions of short tandem repeats (STRs)." + "github/calboo/Potential_Field_Calculator": { + "id": "github/calboo/Potential_Field_Calculator", + "title": "github/calboo/Potential_Field_Calculator", + "url": " https://rseng.github.io/software/repository/github/calboo/Potential_Field_Calculator", + "content": "A collection of codes for generating and visualising potential magnetic fields. If this numerical code is used, authors kindly request an acknowledgment via citation of paper https://www.aanda.org/articles/aa/full_html/2019/05/aa34684-18/aa34684-18.html" }, - "github/chrisaberson/BetterReg": { - "id": "github/chrisaberson/BetterReg", - "title": "github/chrisaberson/BetterReg", - "url": " https://rseng.github.io/software/repository/github/chrisaberson/BetterReg", - "content": "Better statistics for regression (OLS and logistic)" + "github/calboo/wigglewave": { + "id": "github/calboo/wigglewave", + "title": "github/calboo/wigglewave", + "url": " https://rseng.github.io/software/repository/github/calboo/wigglewave", + "content": "Wigglewave is a FORTRAN code that uses an RK4 finite difference method to solve the linearised governing equations for Torsional Alfvén Waves (TAWs) propagating in a plasma with negligible plasma beta and in a force-free axisymmetric magnetic field, with no azimuthal component, embedded in a high density divergent tube structure." }, - "github/Samreay/ChainConsumer": { - "id": "github/Samreay/ChainConsumer", - "title": "github/Samreay/ChainConsumer", - "url": " https://rseng.github.io/software/repository/github/Samreay/ChainConsumer", - "content": "Corner plots, LaTeX tables and plotting walks." + "github/toddy15/medicalterms": { + "id": "github/toddy15/medicalterms", + "title": "github/toddy15/medicalterms", + "url": " https://rseng.github.io/software/repository/github/toddy15/medicalterms", + "content": "German medical dictionary words" }, - "github/Samreay/Marz": { - "id": "github/Samreay/Marz", - "title": "github/Samreay/Marz", - "url": " https://rseng.github.io/software/repository/github/Samreay/Marz", - "content": "The Marz redshifting program is intended for use in cosmology surveys, specifically for the OzDES team." + "github/jpcoles/mosaic": { + "id": "github/jpcoles/mosaic", + "title": "github/jpcoles/mosaic", + "url": " https://rseng.github.io/software/repository/github/jpcoles/mosaic", + "content": "Multipole Operators in Symbols, Automatically Improved and Condensed" }, - 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Building quality transparent software together via peer review and open source distribution. 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Please email me with bugs, suggestions, omissions, etc. The code is citable as part of the Astrophysics Source Code Library (http://ascl.net/1501.010)." + "github/dirostri/CREPE": { + "id": "github/dirostri/CREPE", + "title": "github/dirostri/CREPE", + "url": " https://rseng.github.io/software/repository/github/dirostri/CREPE", + "content": "GitHub Repository for CREPE: A tool for Transcription Factor Cataloguing" }, - "github/oorb/oorb": { - "id": "github/oorb/oorb", - "title": "github/oorb/oorb", - "url": " https://rseng.github.io/software/repository/github/oorb/oorb", - "content": "An open-source orbit-computation package for Solar System objects." + "github/rqtl/qtl2": { + "id": "github/rqtl/qtl2", + "title": "github/rqtl/qtl2", + "url": " https://rseng.github.io/software/repository/github/rqtl/qtl2", + "content": "QTL analysis software for high-dimensional data and complex cross designs" }, - "github/MariaTsantaki/FASMA-synthesis": { - "id": "github/MariaTsantaki/FASMA-synthesis", - "title": "github/MariaTsantaki/FASMA-synthesis", - "url": " https://rseng.github.io/software/repository/github/MariaTsantaki/FASMA-synthesis", - "content": "Python code for stellar spectral analysis" + "github/danielreardon/scintools": { + "id": "github/danielreardon/scintools", + "title": "github/danielreardon/scintools", + "url": " https://rseng.github.io/software/repository/github/danielreardon/scintools", + "content": "Tools for analysing of pulsar scintillations " }, - "github/DrSoulain/PREVIS": { - "id": "github/DrSoulain/PREVIS", - "title": "github/DrSoulain/PREVIS", - "url": " https://rseng.github.io/software/repository/github/DrSoulain/PREVIS", - "content": "Python Request Engine for Virtual Interferometric Survey" + "github/mecobpsu/bacseq": { + "id": "github/mecobpsu/bacseq", + "title": "github/mecobpsu/bacseq", + "url": " https://rseng.github.io/software/repository/github/mecobpsu/bacseq", + "content": "None" }, - "github/ABM4ALL/Melodie": { - "id": "github/ABM4ALL/Melodie", - "title": "github/ABM4ALL/Melodie", - "url": " https://rseng.github.io/software/repository/github/ABM4ALL/Melodie", - "content": "A general framework for developing agent-based models in Python." + "github/AMSSwanglab/SpecVar": { + "id": "github/AMSSwanglab/SpecVar", + "title": "github/AMSSwanglab/SpecVar", + "url": " https://rseng.github.io/software/repository/github/AMSSwanglab/SpecVar", + "content": "SpecVar is a convenient tool for estimating interpretable genetic correlation of human complex traits and annotating the SNPs with context specific regulatory networks" }, - "github/r-lib/gert": { - "id": "github/r-lib/gert", - "title": "github/r-lib/gert", - "url": " https://rseng.github.io/software/repository/github/r-lib/gert", - "content": "Simple git client for R" + "github/arnikz/PIQMIe": { + "id": "github/arnikz/PIQMIe", + "title": "github/arnikz/PIQMIe", + "url": " https://rseng.github.io/software/repository/github/arnikz/PIQMIe", + "content": "Proteomics Identifications & Quantitations Data Management & Integration Service" }, - 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See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html" + "github/ipython/ipython": { + "id": "github/ipython/ipython", + "title": "github/ipython/ipython", + "url": " https://rseng.github.io/software/repository/github/ipython/ipython", + "content": "Official repository for IPython itself. 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"github/sap218/jabberwocky": { - "id": "github/sap218/jabberwocky", - "title": "github/sap218/jabberwocky", - "url": " https://rseng.github.io/software/repository/github/sap218/jabberwocky", - "content": "toolkit for those nonsensical ontologies" + "github/matthiasfabry/spinOS": { + "id": "github/matthiasfabry/spinOS", + "title": "github/matthiasfabry/spinOS", + "url": " https://rseng.github.io/software/repository/github/matthiasfabry/spinOS", + "content": "SPectroscopic and Interferometric Orbital Solution finder" }, - "github/mishioo/tesliper": { - "id": "github/mishioo/tesliper", - "title": "github/mishioo/tesliper", - "url": " https://rseng.github.io/software/repository/github/mishioo/tesliper", - "content": "Theoretical Spectroscopist's Little Helper" + "github/tanner-trickle/EXCEED-DM": { + "id": "github/tanner-trickle/EXCEED-DM", + "title": "github/tanner-trickle/EXCEED-DM", + "url": " https://rseng.github.io/software/repository/github/tanner-trickle/EXCEED-DM", + "content": "EXCEED-DM: EXtended Calculation of Electronic Excitations for Direct detection of Dark Matter" }, - "github/cochran4/GEMB": { - "id": "github/cochran4/GEMB", - "title": "github/cochran4/GEMB", - "url": " https://rseng.github.io/software/repository/github/cochran4/GEMB", - "content": "Gene-set enrichment with math biology" + "github/JulianKarlBauer/mechkit": { + "id": "github/JulianKarlBauer/mechkit", + "title": "github/JulianKarlBauer/mechkit", + "url": " https://rseng.github.io/software/repository/github/JulianKarlBauer/mechkit", + "content": "Continuum mechanics toolkit" }, - "github/WatsonGroupTCD/J2suscep": { - "id": "github/WatsonGroupTCD/J2suscep", - "title": "github/WatsonGroupTCD/J2suscep", - "url": " https://rseng.github.io/software/repository/github/WatsonGroupTCD/J2suscep", - "content": "See https://github.com/WatsonGroupTCD/J2suscep/wiki" + "github/KorfLab/SNAP": { + "id": "github/KorfLab/SNAP", + "title": "github/KorfLab/SNAP", + "url": " https://rseng.github.io/software/repository/github/KorfLab/SNAP", + "content": "Gene prediction software" }, - "github/guillochon/MOSFiT": { - "id": "github/guillochon/MOSFiT", - "title": "github/guillochon/MOSFiT", - "url": " https://rseng.github.io/software/repository/github/guillochon/MOSFiT", - "content": "Modular Open Source Fitter for Transients" + "github/Pranab-JD/LeXInt": { + "id": "github/Pranab-JD/LeXInt", + "title": "github/Pranab-JD/LeXInt", + "url": " https://rseng.github.io/software/repository/github/Pranab-JD/LeXInt", + "content": "Leja Exponential Integrators" }, - "github/vocalpy/crowsetta": { - "id": "github/vocalpy/crowsetta", - "title": "github/vocalpy/crowsetta", - "url": " https://rseng.github.io/software/repository/github/vocalpy/crowsetta", - "content": "A tool to work with any format for annotating vocalizations" + "github/hcdenbakker/sepia": { + "id": "github/hcdenbakker/sepia", + "title": "github/hcdenbakker/sepia", + "url": " https://rseng.github.io/software/repository/github/hcdenbakker/sepia", + "content": "taxonomic classifier based on the kraken2 algorithms and more" }, - "github/BoPeng/simuPOP": { - "id": "github/BoPeng/simuPOP", - "title": "github/BoPeng/simuPOP", - "url": " https://rseng.github.io/software/repository/github/BoPeng/simuPOP", - "content": "A general-purpose forward-time population genetics simulation environment." + "github/hcdenbakker/SalmID": { + "id": "github/hcdenbakker/SalmID", + "title": "github/hcdenbakker/SalmID", + "url": " https://rseng.github.io/software/repository/github/hcdenbakker/SalmID", + "content": "Rapid confirmation of Salmonella spp. and subspp. from sequence data" }, - "github/ebmonson/2DFFTUtils-Module": { - "id": "github/ebmonson/2DFFTUtils-Module", - "title": "github/ebmonson/2DFFTUtils-Module", - "url": " https://rseng.github.io/software/repository/github/ebmonson/2DFFTUtils-Module", - "content": "A Python module implementation of some tasks associated with measuring spiral galaxy pitch angle with 2DFFT. To be merged into the 2dfft_utils repository at a later date. TODO: Rename package and repository to SpiralUtils." + "github/tbisbas/PDFchem": { + "id": "github/tbisbas/PDFchem", + "title": "github/tbisbas/PDFchem", + "url": " https://rseng.github.io/software/repository/github/tbisbas/PDFchem", + "content": "Estimate the average abundance of species from Av-PDFs" }, - "github/lifs-tools/jmzTab-m": { - "id": "github/lifs-tools/jmzTab-m", - "title": "github/lifs-tools/jmzTab-m", - "url": " https://rseng.github.io/software/repository/github/lifs-tools/jmzTab-m", - "content": "Reference implementation for mzTab-M 2.0 for metabolomics" + "github/szwiep/py_SBeLT": { + "id": "github/szwiep/py_SBeLT", + "title": "github/szwiep/py_SBeLT", + "url": " https://rseng.github.io/software/repository/github/szwiep/py_SBeLT", + "content": "A Markov-type numerical model of sediment particle transport in rivers" }, - "github/Astro-Sean/escatter": { - "id": "github/Astro-Sean/escatter", - "title": "github/Astro-Sean/escatter", - "url": " https://rseng.github.io/software/repository/github/Astro-Sean/escatter", - "content": "Python script to perform Monte Carlo simulations of electron scattering events in interacting supernovae." + "github/catherinezucker/radfil": { + "id": "github/catherinezucker/radfil", + "title": "github/catherinezucker/radfil", + "url": " https://rseng.github.io/software/repository/github/catherinezucker/radfil", + "content": "Building Radial Density Profiles for Interstellar Filaments" }, - "github/Ensembl/WiggleTools": { - "id": "github/Ensembl/WiggleTools", - "title": "github/Ensembl/WiggleTools", - "url": " https://rseng.github.io/software/repository/github/Ensembl/WiggleTools", - "content": "Basic operations on the space of numerical functions defined on the genome using lazy evaluators for flexibility and efficiency" + "github/ntoles/tristan-mp-pitp": { + "id": "github/ntoles/tristan-mp-pitp", + "title": "github/ntoles/tristan-mp-pitp", + "url": " https://rseng.github.io/software/repository/github/ntoles/tristan-mp-pitp", + "content": "Particle-in-cell code TRISTAN-MP" }, - "github/Ensembl/ensembl-vep": { - "id": "github/Ensembl/ensembl-vep", - "title": "github/Ensembl/ensembl-vep", - "url": " https://rseng.github.io/software/repository/github/Ensembl/ensembl-vep", - "content": "The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants" + "github/utrillalab/repromin": { + "id": "github/utrillalab/repromin", + "title": "github/utrillalab/repromin", + "url": " https://rseng.github.io/software/repository/github/utrillalab/repromin", + "content": "None" }, - "github/citation-file-format/cff-initializer-javascript": { - "id": "github/citation-file-format/cff-initializer-javascript", - "title": "github/citation-file-format/cff-initializer-javascript", - "url": " https://rseng.github.io/software/repository/github/citation-file-format/cff-initializer-javascript", - "content": "Web form to initialize CITATION.cff files." + "github/spiketools/spiketools": { + "id": "github/spiketools/spiketools", + "title": "github/spiketools/spiketools", + "url": " https://rseng.github.io/software/repository/github/spiketools/spiketools", + "content": "Tools for analyzing spiking data." }, - "github/citation-file-format/cffconvert-github-action": { - "id": "github/citation-file-format/cffconvert-github-action", - "title": "github/citation-file-format/cffconvert-github-action", - "url": " https://rseng.github.io/software/repository/github/citation-file-format/cffconvert-github-action", - "content": "GitHub action to validate CITATION.cff files, and convert to other citation formats." + "github/shikhar249/OnionMHC": { + "id": "github/shikhar249/OnionMHC", + "title": "github/shikhar249/OnionMHC", + "url": " https://rseng.github.io/software/repository/github/shikhar249/OnionMHC", + "content": "None" }, - "github/citation-file-format/cff-converter-python": { - "id": "github/citation-file-format/cff-converter-python", - "title": "github/citation-file-format/cff-converter-python", - "url": " https://rseng.github.io/software/repository/github/citation-file-format/cff-converter-python", - "content": "Command line utility to read CITATION.cff file from a GitHub url or local file and convert it to BibTex and other formats." + "github/nwchemgit/nwchem": { + "id": "github/nwchemgit/nwchem", + "title": "github/nwchemgit/nwchem", + "url": " https://rseng.github.io/software/repository/github/nwchemgit/nwchem", + "content": "NWChem: Open Source High-Performance Computational Chemistry" }, - "github/citation-file-format/citation-file-format": { - "id": "github/citation-file-format/citation-file-format", - "title": "github/citation-file-format/citation-file-format", - "url": " https://rseng.github.io/software/repository/github/citation-file-format/citation-file-format", - "content": "The Citation File Format lets you provide citation metadata for software or datasets in plaintext files that are easy to read by both humans and machines." + "github/ericcombiolab/LRTK": { + "id": "github/ericcombiolab/LRTK", + "title": "github/ericcombiolab/LRTK", + "url": " https://rseng.github.io/software/repository/github/ericcombiolab/LRTK", + "content": "A unified and versatile toolkit for analyzing Linked-Read sequencing data" }, - "github/ConnorStoneAstro/AutoProf": { - "id": "github/ConnorStoneAstro/AutoProf", - "title": "github/ConnorStoneAstro/AutoProf", - "url": " https://rseng.github.io/software/repository/github/ConnorStoneAstro/AutoProf", - "content": "Automatic Isophotal solutions for galaxy images" + "github/smaret/astrochem": { + "id": "github/smaret/astrochem", + "title": "github/smaret/astrochem", + "url": " https://rseng.github.io/software/repository/github/smaret/astrochem", + "content": "A code to compute the abundances of chemical species in the interstellar medium" }, - "github/ladsantos/p-winds": { - "id": "github/ladsantos/p-winds", - "title": "github/ladsantos/p-winds", - "url": " https://rseng.github.io/software/repository/github/ladsantos/p-winds", - "content": "Python implementation of Parker wind models for exoplanet atmospheres" + "github/smaret/thindisk": { + "id": "github/smaret/thindisk", + "title": "github/smaret/thindisk", + "url": " https://rseng.github.io/software/repository/github/smaret/thindisk", + "content": "Compute the line emission from a geometrically thin protoplanetary disk" }, - "github/ladsantos/flatstar": { - "id": "github/ladsantos/flatstar", - "title": "github/ladsantos/flatstar", - "url": " https://rseng.github.io/software/repository/github/ladsantos/flatstar", - "content": "Make 2d intensity maps of limb-darkened stars." + "github/geodynamics/burnman": { + "id": "github/geodynamics/burnman", + "title": "github/geodynamics/burnman", + "url": " https://rseng.github.io/software/repository/github/geodynamics/burnman", + "content": "BurnMan is a library for modeling mantle thermodynamics and thermoelasticity constrained by mineral physics experiments." }, - "github/cmelab/flowerMD": { - "id": "github/cmelab/flowerMD", - "title": "github/cmelab/flowerMD", - "url": " https://rseng.github.io/software/repository/github/cmelab/flowerMD", - "content": "Flexible Library of Organic Workflows and Extensible Recipes for Molecular Dynamics." + "github/geodynamics/Rayleigh": { + "id": "github/geodynamics/Rayleigh", + "title": "github/geodynamics/Rayleigh", + "url": " https://rseng.github.io/software/repository/github/geodynamics/Rayleigh", + "content": "Rayleigh: Pseudo-spectral MHD" }, - "github/henry2004y/Vlasiator.jl": { - "id": "github/henry2004y/Vlasiator.jl", - "title": "github/henry2004y/Vlasiator.jl", - "url": " https://rseng.github.io/software/repository/github/henry2004y/Vlasiator.jl", - "content": "Data processor for Vlasiator" + "github/pmaxted/pycheops": { + "id": "github/pmaxted/pycheops", + "title": "github/pmaxted/pycheops", + "url": " https://rseng.github.io/software/repository/github/pmaxted/pycheops", + "content": "Python module for the analysis of light curves from the ESA Cheops mission" + }, + "github/FabianPlum/OmniTrax": { + "id": "github/FabianPlum/OmniTrax", + "title": "github/FabianPlum/OmniTrax", + "url": " https://rseng.github.io/software/repository/github/FabianPlum/OmniTrax", + "content": "Deep learning-driven multi animal tracking and pose estimation add-on for Blender" }, - "github/napakalas/casbert": { - "id": "github/napakalas/casbert", - "title": "github/napakalas/casbert", - "url": " https://rseng.github.io/software/repository/github/napakalas/casbert", - "content": "None" + "github/martinfleis/clustergram": { + "id": "github/martinfleis/clustergram", + "title": "github/martinfleis/clustergram", + "url": " https://rseng.github.io/software/repository/github/martinfleis/clustergram", + "content": "Clustergram - Visualization and diagnostics for cluster analysis in Python" }, - "github/maxibor/sam2lca": { - "id": "github/maxibor/sam2lca", - "title": "github/maxibor/sam2lca", - "url": " https://rseng.github.io/software/repository/github/maxibor/sam2lca", - "content": "Lowest Common Ancestor from a SAM/BAM/CRAM alignment file" + "github/cbg-ethz/PredictHaplo": { + "id": "github/cbg-ethz/PredictHaplo", + "title": "github/cbg-ethz/PredictHaplo", + "url": " https://rseng.github.io/software/repository/github/cbg-ethz/PredictHaplo", + "content": "This software aims at reconstructing haplotypes from next-generation sequencing data." }, - "github/ckay314/OSPREI": { - "id": "github/ckay314/OSPREI", - "title": "github/ckay314/OSPREI", - "url": " https://rseng.github.io/software/repository/github/ckay314/OSPREI", - "content": "Fully coupled system of ForeCAT-based models" + "github/cbg-ethz/smallgenomeutilities": { + "id": "github/cbg-ethz/smallgenomeutilities", + "title": "github/cbg-ethz/smallgenomeutilities", + "url": " https://rseng.github.io/software/repository/github/cbg-ethz/smallgenomeutilities", + "content": "smallgenomeutilities is a collection of Python scripts to convert alignments between different reference genomes." }, - "github/AdrianA-T/cytomorph": { - "id": "github/AdrianA-T/cytomorph", - "title": "github/AdrianA-T/cytomorph", - "url": " https://rseng.github.io/software/repository/github/AdrianA-T/cytomorph", - "content": "Cytomorph is a open software based on the main general features of cytoneme-meditated gradient formation. This sfotware allows to upload different experimental data to study in silico the role of different biological parameters of this type of signaling. Cytomorph can also work as an in silico tester for other biological hypotheses that are difficult to validate experimentally. In addition, the software architecture is designed in different modules that make Cytomorph an adaptive computational tool in which new advances can be integrated." + "github/cbg-ethz/LolliPop": { + "id": "github/cbg-ethz/LolliPop", + "title": "github/cbg-ethz/LolliPop", + "url": " https://rseng.github.io/software/repository/github/cbg-ethz/LolliPop", + "content": "Deconvolution for Wastewater Genomics" }, - "github/doriancazeneuve/ODNet": { - "id": "github/doriancazeneuve/ODNet", - "title": "github/doriancazeneuve/ODNet", - "url": " https://rseng.github.io/software/repository/github/doriancazeneuve/ODNet", - "content": "ODNet : Asteroid Occultation Detection Convolutional Neural Network" + "github/cbg-ethz/shorah": { + "id": "github/cbg-ethz/shorah", + "title": "github/cbg-ethz/shorah", + "url": " https://rseng.github.io/software/repository/github/cbg-ethz/shorah", + "content": "Repo for the software suite ShoRAH (Short Reads Assembly into Haplotypes)" }, - "github/zarr-developers/zarr-python": { - "id": "github/zarr-developers/zarr-python", - "title": "github/zarr-developers/zarr-python", - "url": " https://rseng.github.io/software/repository/github/zarr-developers/zarr-python", - "content": "An implementation of chunked, compressed, N-dimensional arrays for Python." + "github/cbg-ethz/V-pipe": { + "id": "github/cbg-ethz/V-pipe", + "title": "github/cbg-ethz/V-pipe", + "url": " https://rseng.github.io/software/repository/github/cbg-ethz/V-pipe", + "content": "V-pipe is a pipeline designed for analysing NGS data of short viral genomes" }, - "github/fitbenchmarking/fitbenchmarking": { - "id": "github/fitbenchmarking/fitbenchmarking", - "title": "github/fitbenchmarking/fitbenchmarking", - "url": " https://rseng.github.io/software/repository/github/fitbenchmarking/fitbenchmarking", - "content": "Tool for comparing the run time and accuracy of minimizers on fit benchmarking problems" + "github/SteveMacenski/slam_toolbox": { + "id": "github/SteveMacenski/slam_toolbox", + "title": "github/SteveMacenski/slam_toolbox", + "url": " https://rseng.github.io/software/repository/github/SteveMacenski/slam_toolbox", + "content": "Slam Toolbox for lifelong mapping and localization in potentially massive maps with ROS" }, - "github/nekokoe/Plasmer": { - "id": "github/nekokoe/Plasmer", - "title": "github/nekokoe/Plasmer", - "url": " https://rseng.github.io/software/repository/github/nekokoe/Plasmer", - "content": "An accurate and sensitive bacterial plasmid identification tool based on deep machine-learning of shared k-mers and genomic features." + "github/RTIP/artip": { + "id": "github/RTIP/artip", + "title": "github/RTIP/artip", + "url": " https://rseng.github.io/software/repository/github/RTIP/artip", + "content": "Automated Radio Telescope Imaging Pipeline" }, - "github/fabiorigamonti/bang": { - "id": "github/fabiorigamonti/bang", - "title": "github/fabiorigamonti/bang", - "url": " https://rseng.github.io/software/repository/github/fabiorigamonti/bang", - "content": "GPU/CPU optimized software for morpho-kinematic galaxy parameter estimation." + "github/ylab-hi/ScanExitronLR": { + "id": "github/ylab-hi/ScanExitronLR", + "title": "github/ylab-hi/ScanExitronLR", + "url": " https://rseng.github.io/software/repository/github/ylab-hi/ScanExitronLR", + "content": "A package for the characterization and quantification of exitron splicing events in long-read RNA-seq" }, - "github/johncwok/CategoricalTimeSeries.jl": { - "id": "github/johncwok/CategoricalTimeSeries.jl", - "title": "github/johncwok/CategoricalTimeSeries.jl", - "url": " https://rseng.github.io/software/repository/github/johncwok/CategoricalTimeSeries.jl", - "content": "Toolbox for categorical time-series analysis." + "github/ylab-hi/ScanITD": { + "id": "github/ylab-hi/ScanITD", + "title": "github/ylab-hi/ScanITD", + "url": " https://rseng.github.io/software/repository/github/ylab-hi/ScanITD", + "content": "None" }, - "github/opencollab/arpack-ng": { - "id": "github/opencollab/arpack-ng", - "title": "github/opencollab/arpack-ng", - "url": " https://rseng.github.io/software/repository/github/opencollab/arpack-ng", - "content": "Collection of Fortran77 subroutines designed to solve large scale eigenvalue problems." + "github/tmcclintock/cluster_toolkit": { + "id": "github/tmcclintock/cluster_toolkit", + "title": "github/tmcclintock/cluster_toolkit", + "url": " https://rseng.github.io/software/repository/github/tmcclintock/cluster_toolkit", + "content": "Tools for analyzing galaxy clusters." }, - "github/phenomecentre/nPYc-Toolbox": { - "id": "github/phenomecentre/nPYc-Toolbox", - "title": "github/phenomecentre/nPYc-Toolbox", - "url": " https://rseng.github.io/software/repository/github/phenomecentre/nPYc-Toolbox", - "content": "The nPYc-Toolbox defines objects for representing, and implements functions to manipulate and display, metabolic profiling datasets." + "github/tmcclintock/AReconstructionTool": { + "id": "github/tmcclintock/AReconstructionTool", + "title": "github/tmcclintock/AReconstructionTool", + "url": " https://rseng.github.io/software/repository/github/tmcclintock/AReconstructionTool", + "content": "ART: A Reconstruction Tool. For reconstructing probability distributions using Gaussian processes." }, - "github/JuliaOpt/JuMP.jl": { - "id": "github/JuliaOpt/JuMP.jl", - "title": "github/JuliaOpt/JuMP.jl", - "url": " https://rseng.github.io/software/repository/github/JuliaOpt/JuMP.jl", - "content": "Modeling language for Mathematical Optimization (linear, mixed-integer, conic, semidefinite, nonlinear)" + "github/elsner/arkcos": { + "id": "github/elsner/arkcos", + "title": "github/elsner/arkcos", + "url": " https://rseng.github.io/software/repository/github/elsner/arkcos", + "content": "Accelerated radial kernel convolution on the sphere" }, - "github/pynbody/tangos": { - "id": "github/pynbody/tangos", - "title": "github/pynbody/tangos", - "url": " https://rseng.github.io/software/repository/github/pynbody/tangos", - "content": "The Agile Numerical Galaxy Organisation System" + "github/qboxcode/qbox-public": { + "id": "github/qboxcode/qbox-public", + "title": "github/qboxcode/qbox-public", + "url": " https://rseng.github.io/software/repository/github/qboxcode/qbox-public", + "content": "Qbox public repository" }, - "github/pynbody/pynbody": { - "id": "github/pynbody/pynbody", - "title": "github/pynbody/pynbody", - "url": " https://rseng.github.io/software/repository/github/pynbody/pynbody", - "content": "N-body and hydro analysis tools for Python 3. (Older versions support Python 2.)" + "github/cumbof/honto": { + "id": "github/cumbof/honto", + "title": "github/cumbof/honto", + "url": " https://rseng.github.io/software/repository/github/cumbof/honto", + "content": "A novel method for assessing and measuring homophily in networks" }, - "github/pynbody/genetIC": { - "id": "github/pynbody/genetIC", - "title": "github/pynbody/genetIC", - "url": " https://rseng.github.io/software/repository/github/pynbody/genetIC", - "content": "The GM initial conditions generator" + "github/raspishake/rsudp": { + "id": "github/raspishake/rsudp", + "title": "github/raspishake/rsudp", + "url": " https://rseng.github.io/software/repository/github/raspishake/rsudp", + "content": "Continuous visual display, sudden motion monitoring, and historical replay of Raspberry Shake data" }, - "github/jsobeck/MOOG_SCAT": { - "id": "github/jsobeck/MOOG_SCAT", - "title": "github/jsobeck/MOOG_SCAT", - "url": " https://rseng.github.io/software/repository/github/jsobeck/MOOG_SCAT", - "content": "Repository for the latest version of the MOOG_SCAT code" + "github/veragluscevic/dmdd": { + "id": "github/veragluscevic/dmdd", + "title": "github/veragluscevic/dmdd", + "url": " https://rseng.github.io/software/repository/github/veragluscevic/dmdd", + "content": "A python package that enables simple simulation and Bayesian posterior analysis of nuclear-recoil data from dark matter direct detection experiments for a wide variety of theories of dark matter-nucleon interactions." }, - "github/johnveitch/cpnest": { - "id": "github/johnveitch/cpnest", - "title": "github/johnveitch/cpnest", - "url": " https://rseng.github.io/software/repository/github/johnveitch/cpnest", - "content": "Parallel nested sampling" + "github/DrSoulain/PREVIS": { + "id": "github/DrSoulain/PREVIS", + "title": "github/DrSoulain/PREVIS", + "url": " https://rseng.github.io/software/repository/github/DrSoulain/PREVIS", + "content": "Python Request Engine for Virtual Interferometric Survey" }, - "github/Munroe-Meyer-Institute-VR-Laboratory/Biosensor-Framework": { - "id": "github/Munroe-Meyer-Institute-VR-Laboratory/Biosensor-Framework", - "title": "github/Munroe-Meyer-Institute-VR-Laboratory/Biosensor-Framework", - "url": " https://rseng.github.io/software/repository/github/Munroe-Meyer-Institute-VR-Laboratory/Biosensor-Framework", - "content": "C# library that handles the full process of gathering biometric data from a body-worn sensor, transforming it into handcrafted feature vectors, and delivering an inferencing result in thirty-five lines of code. " + "github/HannahMDoherty/ChemGAPP": { + "id": "github/HannahMDoherty/ChemGAPP", + "title": "github/HannahMDoherty/ChemGAPP", + "url": " https://rseng.github.io/software/repository/github/HannahMDoherty/ChemGAPP", + "content": "A package and series of Streamlit apps for analysing chemical genomic screen data" }, - "github/RaRe-Technologies/gensim": { - "id": "github/RaRe-Technologies/gensim", - "title": "github/RaRe-Technologies/gensim", - "url": " https://rseng.github.io/software/repository/github/RaRe-Technologies/gensim", - "content": "Topic Modelling for Humans" + "github/BarquistLab/mason_paper": { + "id": "github/BarquistLab/mason_paper", + "title": "github/BarquistLab/mason_paper", + "url": " https://rseng.github.io/software/repository/github/BarquistLab/mason_paper", + "content": "Code and analysis for MASON paper" }, - "github/mdsteiner/EFAtools": { - "id": "github/mdsteiner/EFAtools", - "title": "github/mdsteiner/EFAtools", - "url": " https://rseng.github.io/software/repository/github/mdsteiner/EFAtools", - "content": "None" + "github/MillionConcepts/lhorizon": { + "id": "github/MillionConcepts/lhorizon", + "title": "github/MillionConcepts/lhorizon", + "url": " https://rseng.github.io/software/repository/github/MillionConcepts/lhorizon", + "content": "lhorizon helps you find things in the Solar System." }, - "github/rvaser/thread_pool": { - "id": "github/rvaser/thread_pool", - "title": "github/rvaser/thread_pool", - "url": " https://rseng.github.io/software/repository/github/rvaser/thread_pool", - "content": "C++ thread pool library" + "github/dstndstn/astrometry.net": { + "id": "github/dstndstn/astrometry.net", + "title": "github/dstndstn/astrometry.net", + "url": " https://rseng.github.io/software/repository/github/dstndstn/astrometry.net", + "content": "Astrometry.net -- automatic recognition of astronomical images" }, - "github/rvaser/bioparser": { - "id": "github/rvaser/bioparser", - "title": "github/rvaser/bioparser", - "url": " https://rseng.github.io/software/repository/github/rvaser/bioparser", - "content": "C++ library for parsing several formats in bioinformatics" + "github/dstndstn/tractor": { + "id": "github/dstndstn/tractor", + "title": "github/dstndstn/tractor", + "url": " https://rseng.github.io/software/repository/github/dstndstn/tractor", + "content": "The Tractor: measuring astronomical sources via probabilistic inference" }, - "github/rvaser/rampler": { - "id": "github/rvaser/rampler", - "title": "github/rvaser/rampler", - "url": " https://rseng.github.io/software/repository/github/rvaser/rampler", - "content": "module for sampling genomic sequences" + "github/hamers/secularmultiple": { + "id": "github/hamers/secularmultiple", + "title": "github/hamers/secularmultiple", + "url": " https://rseng.github.io/software/repository/github/hamers/secularmultiple", + "content": "Code to model the secular evolution of a hierarchical multiple system" }, - "github/rvaser/sword": { - "id": "github/rvaser/sword", - "title": "github/rvaser/sword", - "url": " https://rseng.github.io/software/repository/github/rvaser/sword", - "content": "SWORD - a highly efficient protein database search" + "github/hamers/tpi": { + "id": "github/hamers/tpi", + "title": "github/hamers/tpi", + "url": " https://rseng.github.io/software/repository/github/hamers/tpi", + "content": "Test Particle Integrator: integrate test particles around a massive black hole" + }, + "github/TeamLEGWORK/LEGWORK": { + "id": "github/TeamLEGWORK/LEGWORK", + "title": "github/TeamLEGWORK/LEGWORK", + "url": " https://rseng.github.io/software/repository/github/TeamLEGWORK/LEGWORK", + "content": "simple package for gravitational wave calculations " }, - "github/rvaser/spoa": { - "id": "github/rvaser/spoa", - "title": "github/rvaser/spoa", - "url": " https://rseng.github.io/software/repository/github/rvaser/spoa", - "content": "SIMD partial order alignment tool/library" + "github/dkoboldt/varscan": { + "id": "github/dkoboldt/varscan", + "title": "github/dkoboldt/varscan", + "url": " https://rseng.github.io/software/repository/github/dkoboldt/varscan", + "content": "Variant calling and somatic mutation/CNV detection for next-generation sequencing data" }, - "github/szhorvat/IGraphM": { - "id": "github/szhorvat/IGraphM", - "title": "github/szhorvat/IGraphM", - "url": " https://rseng.github.io/software/repository/github/szhorvat/IGraphM", - "content": "IGraph/M is the igraph interface for Mathematica" + "github/CisnerosResearch/LICHEM": { + "id": "github/CisnerosResearch/LICHEM", + "title": "github/CisnerosResearch/LICHEM", + "url": " https://rseng.github.io/software/repository/github/CisnerosResearch/LICHEM", + "content": "This package is an open-source (GPLv3) interface between QM and MM software so that QM/MM calculations can be performed with polarizable and frozen electron density force fields. Functionality is also present for standard point-charge based force fields, pure MM, and pure QM calculations." }, - "github/prashjet/popkinmocks": { - "id": "github/prashjet/popkinmocks", - "title": "github/prashjet/popkinmocks", - "url": " https://rseng.github.io/software/repository/github/prashjet/popkinmocks", - "content": "Create mock IFU datacubes for stellar population and kinematic modelling." + "github/deezer/spleeter": { + "id": "github/deezer/spleeter", + "title": "github/deezer/spleeter", + "url": " https://rseng.github.io/software/repository/github/deezer/spleeter", + "content": "Deezer source separation library including pretrained models." }, - "github/akdeniz-uzay/A-Track": { - "id": "github/akdeniz-uzay/A-Track", - "title": "github/akdeniz-uzay/A-Track", - "url": " https://rseng.github.io/software/repository/github/akdeniz-uzay/A-Track", - "content": "A-Track: Detecting Moving Objects in FITS images." + "github/fritzsedlazeck/Sniffles": { + "id": "github/fritzsedlazeck/Sniffles", + "title": "github/fritzsedlazeck/Sniffles", + "url": " https://rseng.github.io/software/repository/github/fritzsedlazeck/Sniffles", + "content": "Structural variation caller using third generation sequencing" }, - "github/milicolazo/Pyedra": { - "id": "github/milicolazo/Pyedra", - "title": "github/milicolazo/Pyedra", - "url": " https://rseng.github.io/software/repository/github/milicolazo/Pyedra", - "content": "None" + "github/fritzsedlazeck/SURVIVOR": { + "id": "github/fritzsedlazeck/SURVIVOR", + "title": "github/fritzsedlazeck/SURVIVOR", + "url": " https://rseng.github.io/software/repository/github/fritzsedlazeck/SURVIVOR", + "content": "Toolset for SV simulation, comparison and filtering" }, - "github/qiime2/q2-vsearch": { - "id": "github/qiime2/q2-vsearch", - "title": "github/qiime2/q2-vsearch", - "url": " https://rseng.github.io/software/repository/github/qiime2/q2-vsearch", - "content": "vsearch plugin for QIIME 2" + "github/zooniverse/starpy": { + "id": "github/zooniverse/starpy", + "title": "github/zooniverse/starpy", + "url": " https://rseng.github.io/software/repository/github/zooniverse/starpy", + "content": "Code to determine sfh parameters of galaxy populations with emcee" }, - "github/rribeiro-sci/pygomodo": { - "id": "github/rribeiro-sci/pygomodo", - "title": "github/rribeiro-sci/pygomodo", - "url": " https://rseng.github.io/software/repository/github/rribeiro-sci/pygomodo", - "content": "GPCRs modeling and docking with python" + "github/erikbern/ann-benchmarks": { + "id": "github/erikbern/ann-benchmarks", + "title": "github/erikbern/ann-benchmarks", + "url": " https://rseng.github.io/software/repository/github/erikbern/ann-benchmarks", + "content": "Benchmarks of approximate nearest neighbor libraries in Python" }, - "github/McPHAC/McPHAC": { - "id": "github/McPHAC/McPHAC", - "title": "github/McPHAC/McPHAC", - "url": " https://rseng.github.io/software/repository/github/McPHAC/McPHAC", - "content": "The McGill Planar Hydrogen Atmosphere Code" + "github/lmfit/lmfit-py": { + "id": "github/lmfit/lmfit-py", + "title": "github/lmfit/lmfit-py", + "url": " https://rseng.github.io/software/repository/github/lmfit/lmfit-py", + "content": "Non-Linear Least Squares Minimization, with flexible Parameter settings, based on scipy.optimize, and with many additional classes and methods for curve fitting. " }, - "github/SpaceOdyssey/Blobby3D": { - "id": "github/SpaceOdyssey/Blobby3D", - "title": "github/SpaceOdyssey/Blobby3D", - "url": " https://rseng.github.io/software/repository/github/SpaceOdyssey/Blobby3D", - "content": "Blobby3D is a tool to perform Bayesian inference for gas kinematics on emission line observations of galaxies using Integral Field Spectroscopy." + "github/carlodev/SyntheticEddyMethod.jl": { + "id": "github/carlodev/SyntheticEddyMethod.jl", + "title": "github/carlodev/SyntheticEddyMethod.jl", + "url": " https://rseng.github.io/software/repository/github/carlodev/SyntheticEddyMethod.jl", + "content": "None" }, - "github/kpenev/poet": { - "id": "github/kpenev/poet", - "title": "github/kpenev/poet", - "url": " https://rseng.github.io/software/repository/github/kpenev/poet", - "content": "Documentation at:" + "github/logological/gpp": { + "id": "github/logological/gpp", + "title": "github/logological/gpp", + "url": " https://rseng.github.io/software/repository/github/logological/gpp", + "content": "GPP, a generic preprocessor" }, - 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"id": "github/Peppags/CNN-SVR", - "title": "github/Peppags/CNN-SVR", - "url": " https://rseng.github.io/software/repository/github/Peppags/CNN-SVR", - "content": "CNN-SVR: A deep learning approach for predicting CRISPR/Cas9 guide RNA on-target activity" + "github/ahmedmoustafa/JAligner": { + "id": "github/ahmedmoustafa/JAligner", + "title": "github/ahmedmoustafa/JAligner", + "url": " https://rseng.github.io/software/repository/github/ahmedmoustafa/JAligner", + "content": "Biological Sequence Alignment" }, - "github/aschafu/PSSH2": { - "id": "github/aschafu/PSSH2", - "title": "github/aschafu/PSSH2", - "url": " https://rseng.github.io/software/repository/github/aschafu/PSSH2", - "content": "Scripts for generating pssh2" + "github/jean-pierreBoth/gsearch": { + "id": "github/jean-pierreBoth/gsearch", + "title": "github/jean-pierreBoth/gsearch", + "url": " https://rseng.github.io/software/repository/github/jean-pierreBoth/gsearch", + "content": "Approximate nearest neighbour search for microbial genomes based on hash metric" }, - "github/aprsa/ebai": { - "id": "github/aprsa/ebai", - "title": "github/aprsa/ebai", - "url": " https://rseng.github.io/software/repository/github/aprsa/ebai", - "content": "Eclipsing Binaries with Artificial Intelligence" + "github/zd1/telseq": { + "id": "github/zd1/telseq", + "title": "github/zd1/telseq", + "url": " https://rseng.github.io/software/repository/github/zd1/telseq", + "content": "A software for calculating telomere length" }, - "github/aprsa/dips": { - "id": "github/aprsa/dips", - "title": "github/aprsa/dips", - "url": " https://rseng.github.io/software/repository/github/aprsa/dips", - "content": "dips: detrending periodic signals in timeseries." + "github/henrikju/resolve": { + "id": "github/henrikju/resolve", + "title": "github/henrikju/resolve", + "url": " https://rseng.github.io/software/repository/github/henrikju/resolve", + "content": "A Bayesian radio aperture synthesis algorithm." }, - "github/gvilitechltd/LibSWIFFT": { - "id": "github/gvilitechltd/LibSWIFFT", - "title": "github/gvilitechltd/LibSWIFFT", - "url": " https://rseng.github.io/software/repository/github/gvilitechltd/LibSWIFFT", - "content": "LibSWIFFT - A fast C/C++ library for the SWIFFT secure homomorphic hash function" + "github/jeaadams/ExoPix": { + "id": "github/jeaadams/ExoPix", + "title": "github/jeaadams/ExoPix", + "url": " https://rseng.github.io/software/repository/github/jeaadams/ExoPix", + "content": "None" }, - "github/TeamLEGWORK/LEGWORK": { - "id": "github/TeamLEGWORK/LEGWORK", - "title": "github/TeamLEGWORK/LEGWORK", - "url": " https://rseng.github.io/software/repository/github/TeamLEGWORK/LEGWORK", - "content": "simple package for gravitational wave calculations " + "github/ExeClim/Isca": { + "id": "github/ExeClim/Isca", + "title": "github/ExeClim/Isca", + "url": " https://rseng.github.io/software/repository/github/ExeClim/Isca", + "content": "Idealized GCM from the University of Exeter" }, - "github/ryokbys/nap": { - "id": "github/ryokbys/nap", - "title": "github/ryokbys/nap", - "url": " https://rseng.github.io/software/repository/github/ryokbys/nap", - "content": "Nagoya Atomistic-simulation Package (NAP). Why don't you take a NAP? ;)" + "github/swiftsim/swiftsimio": { + "id": "github/swiftsim/swiftsimio", + "title": "github/swiftsim/swiftsimio", + "url": " https://rseng.github.io/software/repository/github/swiftsim/swiftsimio", + "content": "Python library for reading SWIFT data. Uses unyt and h5py." + }, + "github/TeraTrees/TIPP": { + "id": "github/TeraTrees/TIPP", + "title": "github/TeraTrees/TIPP", + "url": " https://rseng.github.io/software/repository/github/TeraTrees/TIPP", + "content": "tool for Taxonomic Identification and Phylogenetic Profiling" }, - "github/xdqso/xdqso": { - "id": "github/xdqso/xdqso", - "title": "github/xdqso/xdqso", - "url": " https://rseng.github.io/software/repository/github/xdqso/xdqso", - "content": "Quasar classification with XD" + "github/hveerten/katu": { + "id": "github/hveerten/katu", + "title": "github/hveerten/katu", + "url": " https://rseng.github.io/software/repository/github/hveerten/katu", + "content": "None" }, - "github/DICP1810/ComMap": { - "id": "github/DICP1810/ComMap", - "title": "github/DICP1810/ComMap", - "url": " https://rseng.github.io/software/repository/github/DICP1810/ComMap", - "content": "CXMS generated cross-linking pairs mapping to structures" + "github/hveerten/boxfit": { + "id": "github/hveerten/boxfit", + "title": "github/hveerten/boxfit", + "url": " https://rseng.github.io/software/repository/github/hveerten/boxfit", + "content": "boxfit, a gamma-ray burst afterglow light curve generator based on two-dimensional hydrodynamics simulations" }, - "github/DICP1810/SpotLink": { - "id": "github/DICP1810/SpotLink", - "title": "github/DICP1810/SpotLink", - "url": " https://rseng.github.io/software/repository/github/DICP1810/SpotLink", - "content": "SpotLinkTest" + "github/teoxxx/nemiss_proper": { + "id": "github/teoxxx/nemiss_proper", + "title": "github/teoxxx/nemiss_proper", + "url": " https://rseng.github.io/software/repository/github/teoxxx/nemiss_proper", + "content": "nemiss code repo 2023" }, - "github/johentsch/ms3": { - "id": "github/johentsch/ms3", - "title": "github/johentsch/ms3", - "url": " https://rseng.github.io/software/repository/github/johentsch/ms3", - "content": "A parser for annotated MuseScore 3 files." + "github/teoxxx/nemiss_pbl": { + "id": "github/teoxxx/nemiss_pbl", + "title": "github/teoxxx/nemiss_pbl", + "url": " https://rseng.github.io/software/repository/github/teoxxx/nemiss_pbl", + "content": "nemiss neutrino emission from hydrocode data describing a simulated stellar binary system" }, - "github/sbraden/circle-craters": { - "id": "github/sbraden/circle-craters", - "title": "github/sbraden/circle-craters", - "url": " https://rseng.github.io/software/repository/github/sbraden/circle-craters", - "content": "A planetary science crater-counting plugin for QGIS " + "github/teoxxx/rlos": { + "id": "github/teoxxx/rlos", + "title": "github/teoxxx/rlos", + "url": " https://rseng.github.io/software/repository/github/teoxxx/rlos", + "content": "RLOS Relativistic Line of Sight, time-resolved imaging of model astrophysical jets" }, - "github/flu-crew/smot": { - "id": "github/flu-crew/smot", - "title": "github/flu-crew/smot", - "url": " https://rseng.github.io/software/repository/github/flu-crew/smot", - "content": "Simple Manipulation Of Trees" + "github/computational-chemical-biology/ChemWalker": { + "id": "github/computational-chemical-biology/ChemWalker", + "title": "github/computational-chemical-biology/ChemWalker", + "url": " https://rseng.github.io/software/repository/github/computational-chemical-biology/ChemWalker", + "content": "None" }, - "github/cistrome/MIRA": { - "id": "github/cistrome/MIRA", - "title": "github/cistrome/MIRA", - "url": " https://rseng.github.io/software/repository/github/cistrome/MIRA", - "content": "Python package for analysis of multiomic single cell RNA-seq and ATAC-seq." + "github/yuguangchen1/KcwiKit": { + "id": "github/yuguangchen1/KcwiKit", + "title": "github/yuguangchen1/KcwiKit", + "url": " https://rseng.github.io/software/repository/github/yuguangchen1/KcwiKit", + "content": "Improving KCWI/KDERP pipeline." }, - "github/jboynyc/textnets": { - "id": "github/jboynyc/textnets", - "title": "github/jboynyc/textnets", - "url": " https://rseng.github.io/software/repository/github/jboynyc/textnets", - "content": "Text analysis with networks." + "github/linbox-team/linbox": { + "id": "github/linbox-team/linbox", + "title": "github/linbox-team/linbox", + "url": " https://rseng.github.io/software/repository/github/linbox-team/linbox", + "content": "LinBox - C++ library for exact, high-performance linear algebra " }, - "github/nhejazi/txshift": { - "id": "github/nhejazi/txshift", - "title": "github/nhejazi/txshift", - "url": " https://rseng.github.io/software/repository/github/nhejazi/txshift", - "content": ":package: :game_die: R/txshift: Efficient Estimation of the Causal Effects of Stochastic Interventions, with Two-Phase Sampling Corrections" + "github/votca/xtp": { + "id": "github/votca/xtp", + "title": "github/votca/xtp", + "url": " https://rseng.github.io/software/repository/github/votca/xtp", + "content": "GW-BSE for excited state Quantum Chemistry in a Gaussian Orbital basis, electronic spectroscopy with QM/MM, charge and energy dynamics in complex molecular systems" }, - "github/nhejazi/medoutcon": { - "id": "github/nhejazi/medoutcon", - "title": "github/nhejazi/medoutcon", - "url": " https://rseng.github.io/software/repository/github/nhejazi/medoutcon", - "content": ":package: R/medoutcon: Efficient Causal Mediation Analysis with Natural and Interventional Direct/Indirect Effects" + "github/atomec-project/atoMEC": { + "id": "github/atomec-project/atoMEC", + "title": "github/atomec-project/atoMEC", + "url": " https://rseng.github.io/software/repository/github/atomec-project/atoMEC", + "content": "Python-based average-atom code for simulations of high energy density phenomena such as in warm dense matter." }, - "github/nhejazi/haldensify": { - "id": "github/nhejazi/haldensify", - "title": "github/nhejazi/haldensify", - "url": " https://rseng.github.io/software/repository/github/nhejazi/haldensify", - "content": ":package: R/haldensify: Highly Adaptive Lasso Conditional Density Estimation" + "github/mkelley/zchecker": { + "id": "github/mkelley/zchecker", + "title": "github/mkelley/zchecker", + "url": " https://rseng.github.io/software/repository/github/mkelley/zchecker", + "content": "ZTF moving target checker for short lists of moving targets" }, - "github/carpyncho/carpyncho-py": { - "id": "github/carpyncho/carpyncho-py", - "title": "github/carpyncho/carpyncho-py", - "url": " https://rseng.github.io/software/repository/github/carpyncho/carpyncho-py", - "content": "Carpyncho client for python" + "github/mkelley/calviacat": { + "id": "github/mkelley/calviacat", + "title": "github/mkelley/calviacat", + "url": " https://rseng.github.io/software/repository/github/mkelley/calviacat", + "content": "Calibrate star photometry by comparison to a catalog." }, - "github/EMBL-Hentze-group/htseq-clip": { - "id": "github/EMBL-Hentze-group/htseq-clip", - "title": "github/EMBL-Hentze-group/htseq-clip", - "url": " https://rseng.github.io/software/repository/github/EMBL-Hentze-group/htseq-clip", - "content": "a toolset designed for the processing and analysis of eCLIP/iCLIP dataset" + "github/libdynd/dynd-python": { + "id": "github/libdynd/dynd-python", + "title": "github/libdynd/dynd-python", + "url": " https://rseng.github.io/software/repository/github/libdynd/dynd-python", + "content": "Python exposure of dynd" }, - "github/KBNLresearch/ochre": { - "id": "github/KBNLresearch/ochre", - "title": "github/KBNLresearch/ochre", - "url": " https://rseng.github.io/software/repository/github/KBNLresearch/ochre", - "content": "Toolbox for OCR post-correction" + "github/mlpack/mlpack": { + "id": "github/mlpack/mlpack", + "title": "github/mlpack/mlpack", + "url": " https://rseng.github.io/software/repository/github/mlpack/mlpack", + "content": "mlpack: a scalable C++ machine learning library -- " }, - "github/astrom-tom/specstack": { - "id": "github/astrom-tom/specstack", - "title": "github/astrom-tom/specstack", - "url": " https://rseng.github.io/software/repository/github/astrom-tom/specstack", - "content": "Simple spectral stacking from command line interface" + "github/comprna/reorientexpress": { + "id": "github/comprna/reorientexpress", + "title": "github/comprna/reorientexpress", + "url": " https://rseng.github.io/software/repository/github/comprna/reorientexpress", + "content": "Transcriptome long-read orientation with Deep Learning" }, - "github/astrom-tom/dfitspy": { - "id": "github/astrom-tom/dfitspy", - "title": "github/astrom-tom/dfitspy", - "url": " https://rseng.github.io/software/repository/github/astrom-tom/dfitspy", + "github/comprna/SUPPA": { + "id": "github/comprna/SUPPA", + "title": "github/comprna/SUPPA", + "url": " https://rseng.github.io/software/repository/github/comprna/SUPPA", + "content": " SUPPA2: Fast quantification of differential splicing " + }, + "github/sihanjiao/j-comb": { + "id": "github/sihanjiao/j-comb", + "title": "github/sihanjiao/j-comb", + "url": " https://rseng.github.io/software/repository/github/sihanjiao/j-comb", "content": "None" }, - "github/ihrke/pypillometry": { - "id": "github/ihrke/pypillometry", - "title": "github/ihrke/pypillometry", - "url": " https://rseng.github.io/software/repository/github/ihrke/pypillometry", - "content": "pupillometry with python" + "github/freemed/freeshim": { + "id": "github/freemed/freeshim", + "title": "github/freemed/freeshim", + "url": " https://rseng.github.io/software/repository/github/freemed/freeshim", + "content": "opensource multiplatform medical device interface" }, - "github/hposborn/MonoTools": { - "id": "github/hposborn/MonoTools", - "title": "github/hposborn/MonoTools", - "url": " https://rseng.github.io/software/repository/github/hposborn/MonoTools", - "content": "A package for detecting, vetting, and modelling transiting exoplanets on uncertain periods" + "github/SeamusClarke/FragMent": { + "id": "github/SeamusClarke/FragMent", + "title": "github/SeamusClarke/FragMent", + "url": " https://rseng.github.io/software/repository/github/SeamusClarke/FragMent", + "content": "A collection of fragmentation techniques for studying filaments" }, - "github/pierrepo/autoclassweb": { - "id": "github/pierrepo/autoclassweb", - "title": "github/pierrepo/autoclassweb", - "url": " https://rseng.github.io/software/repository/github/pierrepo/autoclassweb", - "content": "AutoClassWeb: a web app to run AutoClass C Bayesian clustering :package: :rocket:" + "github/SeamusClarke/BTS": { + "id": "github/SeamusClarke/BTS", + "title": "github/SeamusClarke/BTS", + "url": " https://rseng.github.io/software/repository/github/SeamusClarke/BTS", + "content": "Behind The Spectrum (BTS) fitter " }, - "github/BIMSBbioinfo/pigx_scrnaseq": { - "id": "github/BIMSBbioinfo/pigx_scrnaseq", - "title": "github/BIMSBbioinfo/pigx_scrnaseq", - "url": " https://rseng.github.io/software/repository/github/BIMSBbioinfo/pigx_scrnaseq", - "content": "Pipeline for analysis of Dropseq single cell data" + "github/jGetMove/jGetMove": { + "id": "github/jGetMove/jGetMove", + "title": "github/jGetMove/jGetMove", + "url": " https://rseng.github.io/software/repository/github/jGetMove/jGetMove", + "content": "GetMove algorithm in java" }, - "github/BIMSBbioinfo/pigx_rnaseq": { - "id": "github/BIMSBbioinfo/pigx_rnaseq", - "title": "github/BIMSBbioinfo/pigx_rnaseq", - "url": " https://rseng.github.io/software/repository/github/BIMSBbioinfo/pigx_rnaseq", - "content": "Pipeline for RNAseq" + "github/epruesse/SINA": { + "id": "github/epruesse/SINA", + "title": "github/epruesse/SINA", + "url": " https://rseng.github.io/software/repository/github/epruesse/SINA", + "content": "SINA - Reference based multiple sequence alignment" }, - "github/barentsen/dave": { - "id": "github/barentsen/dave", - "title": "github/barentsen/dave", - "url": " https://rseng.github.io/software/repository/github/barentsen/dave", - "content": "Discovery And Vetting of K2 Exoplanets" + "github/snek5000/snek5000": { + "id": "github/snek5000/snek5000", + "title": "github/snek5000/snek5000", + "url": " https://rseng.github.io/software/repository/github/snek5000/snek5000", + "content": ":snake: Python framework for Nek5000 :rocket:" }, - "github/barentsen/k2flix": { - "id": "github/barentsen/k2flix", - "title": "github/barentsen/k2flix", - "url": " https://rseng.github.io/software/repository/github/barentsen/k2flix", - "content": "Create beautiful quicklook movies from the pixel data observed by NASA's Kepler/K2/TESS spacecraft." + "github/ZhenjiangFan/DAG-deepVASE": { + "id": "github/ZhenjiangFan/DAG-deepVASE", + "title": "github/ZhenjiangFan/DAG-deepVASE", + "url": " https://rseng.github.io/software/repository/github/ZhenjiangFan/DAG-deepVASE", + "content": "None" }, - "github/msm550/DMATIS": { - "id": "github/msm550/DMATIS", - "title": "github/msm550/DMATIS", - "url": " https://rseng.github.io/software/repository/github/msm550/DMATIS", - "content": "Dark Matter ATtenuation Importance Sampling" + "github/Gaiana/nirdust": { + "id": "github/Gaiana/nirdust", + "title": "github/Gaiana/nirdust", + "url": " https://rseng.github.io/software/repository/github/Gaiana/nirdust", + "content": "Nirdust is a python package that uses K-band (2.2 micrometers) spectra to measure the temperature of the dust heated by a type 2 Active Galactic Nuclei (AGN) accretion disk." + }, + "github/nvalimak/fsm-lite": { + "id": "github/nvalimak/fsm-lite", + "title": "github/nvalimak/fsm-lite", + "url": " https://rseng.github.io/software/repository/github/nvalimak/fsm-lite", + "content": "frequency-based string mining (lite)" + }, + "github/realfastvla/rfpipe": { + "id": "github/realfastvla/rfpipe", + "title": "github/realfastvla/rfpipe", + "url": " https://rseng.github.io/software/repository/github/realfastvla/rfpipe", + "content": "Fast radio interferometric transient search pipeline" }, - 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"github/laristra/flecsph": { - "id": "github/laristra/flecsph", - "title": "github/laristra/flecsph", - "url": " https://rseng.github.io/software/repository/github/laristra/flecsph", - "content": "A Parallel and Distributed SPH Implementation Based on the FleCSI" + "github/BU-ISCIII/plasmidID": { + "id": "github/BU-ISCIII/plasmidID", + "title": "github/BU-ISCIII/plasmidID", + "url": " https://rseng.github.io/software/repository/github/BU-ISCIII/plasmidID", + "content": "PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identification." }, - "github/tkchafin/autostreamtree": { - "id": "github/tkchafin/autostreamtree", - "title": "github/tkchafin/autostreamtree", - "url": " https://rseng.github.io/software/repository/github/tkchafin/autostreamtree", - "content": "Stream trees for SNP datasets" + "github/BU-ISCIII/taranis": { + "id": "github/BU-ISCIII/taranis", + "title": "github/BU-ISCIII/taranis", + "url": " https://rseng.github.io/software/repository/github/BU-ISCIII/taranis", + "content": "cg/wgMLST allele calling software, schema evaluation and allele distance estimation for outbreak reserch." }, - 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"github/tomasstolker/pycrires": { - "id": "github/tomasstolker/pycrires", - "title": "github/tomasstolker/pycrires", - "url": " https://rseng.github.io/software/repository/github/tomasstolker/pycrires", - "content": "Data reduction pipeline for VLT/CRIRES+" + "github/fkeruzore/panco2": { + "id": "github/fkeruzore/panco2", + "title": "github/fkeruzore/panco2", + "url": " https://rseng.github.io/software/repository/github/fkeruzore/panco2", + "content": "A Python library for pressure profile measurements in SZ observations of galaxy clusters." }, - "github/tomasstolker/ARTES": { - "id": "github/tomasstolker/ARTES", - "title": "github/tomasstolker/ARTES", - "url": " https://rseng.github.io/software/repository/github/tomasstolker/ARTES", - "content": "Radiative transfer of polarized light in 3D exoplanet atmospheres" + "github/BenWibking/quokka": { + "id": "github/BenWibking/quokka", + "title": "github/BenWibking/quokka", + "url": " https://rseng.github.io/software/repository/github/BenWibking/quokka", + "content": "Two-moment AMR radiation hydrodynamics on GPUs for astrophysics" }, - 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A fast C/C++ library for the SWIFFT secure homomorphic hash function" }, - "github/barklem/hlinop": { - "id": "github/barklem/hlinop", - "title": "github/barklem/hlinop", - "url": " https://rseng.github.io/software/repository/github/barklem/hlinop", - "content": "Codes for modelling hydrogen line opacity in stellar atmospheres. 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Made with tries." }, - "github/PabloVD/CosmoGraphNet": { - "id": "github/PabloVD/CosmoGraphNet", - "title": "github/PabloVD/CosmoGraphNet", - "url": " https://rseng.github.io/software/repository/github/PabloVD/CosmoGraphNet", - "content": "Graph Neural Networks to predict the cosmological parameters or the galaxy power spectrum from galaxy catalogs." + "github/kdmurray91/libqcpp": { + "id": "github/kdmurray91/libqcpp", + "title": "github/kdmurray91/libqcpp", + "url": " https://rseng.github.io/software/repository/github/kdmurray91/libqcpp", + "content": "libqc++: C++11 library for next-gen sequence quality control and assessment." }, - "github/ksahlin/strobealign": { - "id": "github/ksahlin/strobealign", - "title": "github/ksahlin/strobealign", - "url": " https://rseng.github.io/software/repository/github/ksahlin/strobealign", - "content": "Aligns short reads using dynamic seed size with strobemers" + "github/kdmurray91/libqes": { + "id": "github/kdmurray91/libqes", + "title": "github/kdmurray91/libqes", + "url": " https://rseng.github.io/software/repository/github/kdmurray91/libqes", + "content": "A small C library, with a bioinformatic focus. 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The method implements marginalization across a series of models to represent stochastic models for observatory and instrument systematics. This is primarily for HST WFC3, however, may be extened to STIS in the future. " }, - "github/CMU-SAFARI/BLEND": { - "id": "github/CMU-SAFARI/BLEND", - "title": "github/CMU-SAFARI/BLEND", - "url": " https://rseng.github.io/software/repository/github/CMU-SAFARI/BLEND", - "content": "BLEND is a mechanism that can efficiently find fuzzy seed matches between sequences to significantly improve the performance and accuracy while reducing the memory space usage of two important applications: 1) finding overlapping reads and 2) read mapping. Described by Firtina et al. (published in NARGAB https://doi.org/10.1093/nargab/lqad004)" + "github/grahambell/pymoc": { + "id": "github/grahambell/pymoc", + "title": "github/grahambell/pymoc", + "url": " https://rseng.github.io/software/repository/github/grahambell/pymoc", + "content": "Multi-Order Coverage map module for Python" }, - "github/DrafProject/elmada": { - "id": "github/DrafProject/elmada", - "title": "github/DrafProject/elmada", - "url": " https://rseng.github.io/software/repository/github/DrafProject/elmada", - "content": "elmada: Dynamic electricity carbon emission factors and prices for Europe" + "github/ElectionDataAnalysis/electiondata": { + "id": "github/ElectionDataAnalysis/electiondata", + "title": "github/ElectionDataAnalysis/electiondata", + "url": " https://rseng.github.io/software/repository/github/ElectionDataAnalysis/electiondata", + "content": "Tools for consolidation and analysis of raw election results from the most reliable sources -- the election agencies themselves." }, - "github/MrOlm/drep": { - "id": "github/MrOlm/drep", - "title": "github/MrOlm/drep", - "url": " https://rseng.github.io/software/repository/github/MrOlm/drep", - "content": "a python program for rapidly comparing large numbers of genomes, dRep can also "de-replicate" a genome set by identifying groups of highly similar genomes and choosing the best representative genome for each genome set." + "github/RomainFeron/mwga-utils": { + "id": "github/RomainFeron/mwga-utils", + "title": "github/RomainFeron/mwga-utils", + "url": " https://rseng.github.io/software/repository/github/RomainFeron/mwga-utils", + "content": "Collection of utilities for processing Multispecies Whole Genome Alignments " + }, + "github/LangeLab/SQuAPP": { + "id": "github/LangeLab/SQuAPP", + "title": "github/LangeLab/SQuAPP", + "url": " https://rseng.github.io/software/repository/github/LangeLab/SQuAPP", + "content": "Shiny App allows streamlined analysis of multiple levels of proteomics data." }, "github/luinix/pesco": { "id": "github/luinix/pesco", @@ -23589,341 +23565,377 @@ "url": " https://rseng.github.io/software/repository/github/luinix/pesco", "content": "Cognitive stimulation tool for elderly or cognitively impaired" }, - "github/Taywee/args": { - "id": "github/Taywee/args", - "title": "github/Taywee/args", - "url": " https://rseng.github.io/software/repository/github/Taywee/args", - "content": " A simple header-only C++ argument parser library. Supposed to be flexible and powerful, and attempts to be compatible with the functionality of the Python standard argparse library (though not necessarily the API)." + "github/mtakahiro/gsf": { + "id": "github/mtakahiro/gsf", + "title": "github/mtakahiro/gsf", + "url": " https://rseng.github.io/software/repository/github/mtakahiro/gsf", + "content": "Grism SED Fitting package" }, - "github/tpapp/MCMCDiagnostics.jl": { - "id": "github/tpapp/MCMCDiagnostics.jl", - "title": "github/tpapp/MCMCDiagnostics.jl", - "url": " https://rseng.github.io/software/repository/github/tpapp/MCMCDiagnostics.jl", - "content": "Markov Chain Monte Carlo convergence diagnostics in Julia" + "github/AFD-Illinois/ebhlight": { + "id": "github/AFD-Illinois/ebhlight", + "title": "github/AFD-Illinois/ebhlight", + "url": " https://rseng.github.io/software/repository/github/AFD-Illinois/ebhlight", + "content": "Two-temperature General Relativistic Radiation Magnetohydrodynamics" }, - "github/ColdThunder/NR-code": { - "id": "github/ColdThunder/NR-code", - "title": "github/ColdThunder/NR-code", - "url": " https://rseng.github.io/software/repository/github/ColdThunder/NR-code", - "content": "Nonlinear reconstruction code" + "github/AFD-Illinois/iharm3d": { + "id": "github/AFD-Illinois/iharm3d", + "title": "github/AFD-Illinois/iharm3d", + "url": " https://rseng.github.io/software/repository/github/AFD-Illinois/iharm3d", + "content": "Hybrid MPI/OpenMP 3D HARM with vectorization" }, - "github/johnh2o2/cuvarbase": { - "id": "github/johnh2o2/cuvarbase", - "title": "github/johnh2o2/cuvarbase", - "url": " https://rseng.github.io/software/repository/github/johnh2o2/cuvarbase", - "content": "Python library for fast time-series analysis on CUDA GPUs" + "github/babelomics/impuSARS": { + "id": "github/babelomics/impuSARS", + "title": "github/babelomics/impuSARS", + "url": " https://rseng.github.io/software/repository/github/babelomics/impuSARS", + "content": "Software tool for the imputation of whole-genome SARS-CoV-2 sequences." + }, + "github/Via-Appia/via-appia-online-viewer": { + "id": "github/Via-Appia/via-appia-online-viewer", + "title": "github/Via-Appia/via-appia-online-viewer", + "url": " https://rseng.github.io/software/repository/github/Via-Appia/via-appia-online-viewer", + "content": "Via Appia viewer application" + }, + "github/biboyd/SALSA": { + "id": "github/biboyd/SALSA", + "title": "github/biboyd/SALSA", + "url": " https://rseng.github.io/software/repository/github/biboyd/SALSA", + "content": "Salsa is a Python package for constructing synthetic absorber catalogs from astrophysical hydrodynamic simulations" + }, + "github/ahoward-cf/ppmap": { + "id": "github/ahoward-cf/ppmap", + "title": "github/ahoward-cf/ppmap", + "url": " https://rseng.github.io/software/repository/github/ahoward-cf/ppmap", + "content": "Code for column density mapping with extra dimensions (temperature and dust opacity index)." + }, + "github/maxbernyk/lightcone": { + "id": "github/maxbernyk/lightcone", + "title": "github/maxbernyk/lightcone", + "url": " https://rseng.github.io/software/repository/github/maxbernyk/lightcone", + "content": "light-cone generating script" }, - "github/kdeck/TTVFast": { - "id": "github/kdeck/TTVFast", - "title": "github/kdeck/TTVFast", - "url": " https://rseng.github.io/software/repository/github/kdeck/TTVFast", - "content": "TTVFast efficiently calculates transit times for n-planet systems and the corresponding radial velocities." + "github/agree019/DarkCapPy": { + "id": "github/agree019/DarkCapPy", + "title": "github/agree019/DarkCapPy", + "url": " https://rseng.github.io/software/repository/github/agree019/DarkCapPy", + "content": "None" }, - "github/DarkQuestCosmology/dark_emulator_public": { - "id": "github/DarkQuestCosmology/dark_emulator_public", - "title": "github/DarkQuestCosmology/dark_emulator_public", - "url": " https://rseng.github.io/software/repository/github/DarkQuestCosmology/dark_emulator_public", - "content": "A cosmological tool for emulation of various basic statistics of dark matter haloes based on Dark Quest project (https://darkquestcosmology.github.io/)." + "github/sina-cb/Tn-seqExplorer": { + "id": "github/sina-cb/Tn-seqExplorer", + "title": "github/sina-cb/Tn-seqExplorer", + "url": " https://rseng.github.io/software/repository/github/sina-cb/Tn-seqExplorer", + "content": "Tn-seq Explorer allows users to explore and analyze Tn-seq data for prokaryotic (bacterial or archaeal) genomes. It implements two alternative methods for identification of essential genes and provides additional tools to investigate the Tn-seq data. The primary goal of the data analysis is to study fitness by identifying genes that are essential or beneficial under specific growth conditions." }, - "github/devitocodes/pyrevolve": { - "id": "github/devitocodes/pyrevolve", - "title": "github/devitocodes/pyrevolve", - "url": " https://rseng.github.io/software/repository/github/devitocodes/pyrevolve", - "content": "Python library to manage checkpointing for adjoints" + "github/dnonatar/Sequoia": { + "id": "github/dnonatar/Sequoia", + "title": "github/dnonatar/Sequoia", + "url": " https://rseng.github.io/software/repository/github/dnonatar/Sequoia", + "content": "None" }, - "github/devitocodes/devito": { - "id": "github/devitocodes/devito", - "title": "github/devitocodes/devito", - "url": " https://rseng.github.io/software/repository/github/devitocodes/devito", - "content": "Code generation framework for automated finite difference computation" + "github/qmarcou/IGoR": { + "id": "github/qmarcou/IGoR", + "title": "github/qmarcou/IGoR", + "url": " https://rseng.github.io/software/repository/github/qmarcou/IGoR", + "content": "IGoR is a C++ software designed to infer V(D)J recombination related processes from sequencing data. Find full documentation at:" }, - "github/nlesc-ave/ave-rest-service": { - "id": "github/nlesc-ave/ave-rest-service", - "title": "github/nlesc-ave/ave-rest-service", - "url": " https://rseng.github.io/software/repository/github/nlesc-ave/ave-rest-service", - "content": "visualize (clustered) single-nucleotide variants across genomes" + "github/OceanGenomics/mudskipper": { + "id": "github/OceanGenomics/mudskipper", + "title": "github/OceanGenomics/mudskipper", + "url": " https://rseng.github.io/software/repository/github/OceanGenomics/mudskipper", + "content": "A tool for projecting genomic alignments to transcriptomic coordinates" }, - "github/llt1836/TE-HI-GCN": { - "id": "github/llt1836/TE-HI-GCN", - "title": "github/llt1836/TE-HI-GCN", - "url": " https://rseng.github.io/software/repository/github/llt1836/TE-HI-GCN", + "github/qianlivan/RPPPS": { + "id": "github/qianlivan/RPPPS", + "title": "github/qianlivan/RPPPS", + "url": " https://rseng.github.io/software/repository/github/qianlivan/RPPPS", "content": "None" }, - "github/dondi/GRNsight": { - "id": "github/dondi/GRNsight", - "title": "github/dondi/GRNsight", - "url": " https://rseng.github.io/software/repository/github/dondi/GRNsight", - "content": "Web app and service for modeling and visualizing gene regulatory networks." + "github/muLAn-project/muLAn": { + "id": "github/muLAn-project/muLAn", + "title": "github/muLAn-project/muLAn", + "url": " https://rseng.github.io/software/repository/github/muLAn-project/muLAn", + "content": "muLAn: MICROlensing Analysis software" }, - "github/kingyin3613/RingsPy": { - "id": "github/kingyin3613/RingsPy", - "title": "github/kingyin3613/RingsPy", - "url": " https://rseng.github.io/software/repository/github/kingyin3613/RingsPy", - "content": "A Python automated geometric generation tool that generates 3D meshes of prismatic cellular solids with radial growth rules based on Voronoi diagrams." + "github/BoPeng/simuPOP": { + "id": "github/BoPeng/simuPOP", + "title": "github/BoPeng/simuPOP", + "url": " https://rseng.github.io/software/repository/github/BoPeng/simuPOP", + "content": "A general-purpose forward-time population genetics simulation environment." }, - "github/neuroanatomy/reorient": { - "id": "github/neuroanatomy/reorient", - "title": "github/neuroanatomy/reorient", - "url": " https://rseng.github.io/software/repository/github/neuroanatomy/reorient", - "content": "A tool for reorienting and cropping MRI data" + "github/IFB-ElixirFr/edam-browser": { + "id": "github/IFB-ElixirFr/edam-browser", + "title": "github/IFB-ElixirFr/edam-browser", + "url": " https://rseng.github.io/software/repository/github/IFB-ElixirFr/edam-browser", + "content": "Stand alone js browser for EDAM Ontology" }, - "github/ParBLiSS/FastANI": { - "id": "github/ParBLiSS/FastANI", - "title": "github/ParBLiSS/FastANI", - "url": " https://rseng.github.io/software/repository/github/ParBLiSS/FastANI", - "content": "Fast Whole-Genome Similarity (ANI) Estimation" + "github/egstrom/cluster-in-a-box": { + "id": "github/egstrom/cluster-in-a-box", + "title": "github/egstrom/cluster-in-a-box", + "url": " https://rseng.github.io/software/repository/github/egstrom/cluster-in-a-box", + "content": "Statistical model of protostellar clusters" }, - "github/lpantano/seqbuster": { - "id": "github/lpantano/seqbuster", - "title": "github/lpantano/seqbuster", - "url": " https://rseng.github.io/software/repository/github/lpantano/seqbuster", - "content": "pipeline for the analysis of small RNA data" + "github/mentatpsi/OSGenome": { + "id": "github/mentatpsi/OSGenome", + "title": "github/mentatpsi/OSGenome", + "url": " https://rseng.github.io/software/repository/github/mentatpsi/OSGenome", + "content": "An Open Source Web Application for Genetic Data (SNPs) using 23AndMe and Data Crawling Technologies" }, - "github/lpantano/seqcluster": { - "id": "github/lpantano/seqcluster", - "title": "github/lpantano/seqcluster", - "url": " https://rseng.github.io/software/repository/github/lpantano/seqcluster", - "content": "small RNA analysis from NGS data" + "github/sunnyvagnozzi/Braneworld-extra-dimensions": { + "id": "github/sunnyvagnozzi/Braneworld-extra-dimensions", + "title": "github/sunnyvagnozzi/Braneworld-extra-dimensions", + "url": " https://rseng.github.io/software/repository/github/sunnyvagnozzi/Braneworld-extra-dimensions", + "content": "None" }, - "github/brainglobe/bg-atlasapi": { - "id": "github/brainglobe/bg-atlasapi", - "title": "github/brainglobe/bg-atlasapi", - "url": " https://rseng.github.io/software/repository/github/brainglobe/bg-atlasapi", - "content": "A lightweight python module to interact with atlases for systems neuroscience" + "github/epic-astronomy/EPIC": { + "id": "github/epic-astronomy/EPIC", + "title": "github/epic-astronomy/EPIC", + "url": " https://rseng.github.io/software/repository/github/epic-astronomy/EPIC", + "content": "None" }, - "github/eucp-project/storyboards": { - "id": "github/eucp-project/storyboards", - "title": "github/eucp-project/storyboards", - "url": " https://rseng.github.io/software/repository/github/eucp-project/storyboards", - "content": "Simple web application to show example use cases with some interactivity. (visitors via old url will be redirected to the website with new url)" + "github/fkiwy/unTimely_Catalog_explorer": { + "id": "github/fkiwy/unTimely_Catalog_explorer", + "title": "github/fkiwy/unTimely_Catalog_explorer", + "url": " https://rseng.github.io/software/repository/github/fkiwy/unTimely_Catalog_explorer", + "content": "A search and visualization tool for the unTimely Catalog" }, - "github/eucp-project/atlas": { - "id": "github/eucp-project/atlas", - "title": "github/eucp-project/atlas", - "url": " https://rseng.github.io/software/repository/github/eucp-project/atlas", - "content": "prototype result browser" + "github/fkiwy/AstroToolBox": { + "id": "github/fkiwy/AstroToolBox", + "title": "github/fkiwy/AstroToolBox", + "url": " https://rseng.github.io/software/repository/github/fkiwy/AstroToolBox", + "content": "Java tool set for the identification and classification of astronomical objects with a focus on low-mass stars and ultra-cool dwarfs" }, - "github/ni1o1/transbigdata": { - "id": "github/ni1o1/transbigdata", - "title": "github/ni1o1/transbigdata", - "url": " https://rseng.github.io/software/repository/github/ni1o1/transbigdata", - "content": "A Python package develop for transportation spatio-temporal big data processing, analysis and visualization." + "github/fkiwy/Finder_charts": { + "id": "github/fkiwy/Finder_charts", + "title": "github/fkiwy/Finder_charts", + "url": " https://rseng.github.io/software/repository/github/fkiwy/Finder_charts", + "content": "A Python module to create finder charts from image data of various sky surveys" }, - "github/SSDataLab/vetting": { - "id": "github/SSDataLab/vetting", - "title": "github/SSDataLab/vetting", - "url": " https://rseng.github.io/software/repository/github/SSDataLab/vetting", - "content": "Simple, stand-alone tools for vetting transit signals in Kepler, K2 and TESS data" + "github/gymreklab/chips": { + "id": "github/gymreklab/chips", + "title": "github/gymreklab/chips", + "url": " https://rseng.github.io/software/repository/github/gymreklab/chips", + "content": "Simulation tool for ChIP- and other -seq experiments" }, - "github/SSDataLab/psfmachine": { - "id": "github/SSDataLab/psfmachine", - "title": "github/SSDataLab/psfmachine", - "url": " https://rseng.github.io/software/repository/github/SSDataLab/psfmachine", - "content": "Tool kit for doing PSF photometry" + "github/gymreklab/GangSTR": { + "id": "github/gymreklab/GangSTR", + "title": "github/gymreklab/GangSTR", + "url": " https://rseng.github.io/software/repository/github/gymreklab/GangSTR", + "content": "A tool for profiling long STRs from short reads" }, - "github/icesat2py/icepyx": { - "id": "github/icesat2py/icepyx", - "title": "github/icesat2py/icepyx", - "url": " https://rseng.github.io/software/repository/github/icesat2py/icepyx", - "content": "Python tools for obtaining and working with ICESat-2 data" + "github/BDI-pathogens/OpenABM-Covid19-model-paper": { + "id": "github/BDI-pathogens/OpenABM-Covid19-model-paper", + "title": "github/BDI-pathogens/OpenABM-Covid19-model-paper", + "url": " https://rseng.github.io/software/repository/github/BDI-pathogens/OpenABM-Covid19-model-paper", + "content": "Figures for the paper describing the OpenABM-Covid19 model" }, - "github/xxsds/DYNAMIC": { - "id": "github/xxsds/DYNAMIC", - "title": "github/xxsds/DYNAMIC", - "url": " https://rseng.github.io/software/repository/github/xxsds/DYNAMIC", - "content": "Dynamic succinct/compressed data structures" + "github/EigenDev/simbi": { + "id": "github/EigenDev/simbi", + "title": "github/EigenDev/simbi", + "url": " https://rseng.github.io/software/repository/github/EigenDev/simbi", + "content": "SIMBI is a 3D Heterogeneous Relativistic Gas Dynamics Code using the Cython framework to blend together C++, CUDA, HIP, and Python." }, - "github/birnstiel/two-pop-py": { - "id": "github/birnstiel/two-pop-py", - "title": "github/birnstiel/two-pop-py", - "url": " https://rseng.github.io/software/repository/github/birnstiel/two-pop-py", - "content": "Implementation of the 2-population model for dust evolution in protoplanetary disks after Birnstiel, Klahr, & Ercolano, A&A 2012" + "github/mikekatz04/BOWIE": { + "id": "github/mikekatz04/BOWIE", + "title": "github/mikekatz04/BOWIE", + "url": " https://rseng.github.io/software/repository/github/mikekatz04/BOWIE", + "content": "BOWIE - Binary Observability With Illustrative Exploration" }, - "github/ashleefv/ACEInhibPKPD": { - "id": "github/ashleefv/ACEInhibPKPD", - "title": "github/ashleefv/ACEInhibPKPD", - "url": " https://rseng.github.io/software/repository/github/ashleefv/ACEInhibPKPD", - "content": "PKPD model for ACE inhibition; educational drug dosing app for treatment of high blood pressure" + "github/ahudde/greeks": { + "id": "github/ahudde/greeks", + "title": "github/ahudde/greeks", + "url": " https://rseng.github.io/software/repository/github/ahudde/greeks", + "content": "Sensitivities of Prices of Financial Options and Implied Volatilites" }, - "github/mjshao06/pdifFinder": { - "id": "github/mjshao06/pdifFinder", - "title": "github/mjshao06/pdifFinder", - "url": " https://rseng.github.io/software/repository/github/mjshao06/pdifFinder", - "content": "None" + "github/exomishra/kobe": { + "id": "github/exomishra/kobe", + "title": "github/exomishra/kobe", + "url": " https://rseng.github.io/software/repository/github/exomishra/kobe", + "content": "A program to add geometrical limitations and detection biases of a transit survey to theoretical planetary systems." }, - "github/nemesiscode/radtrancode": { - "id": "github/nemesiscode/radtrancode", - "title": "github/nemesiscode/radtrancode", - "url": " https://rseng.github.io/software/repository/github/nemesiscode/radtrancode", - "content": "This is the repository of the NEMESIS/RADTRANS project. It is described on the associated web page listed here." + "github/ArenA-Crowds/Crowds": { + "id": "github/ArenA-Crowds/Crowds", + "title": "github/ArenA-Crowds/Crowds", + "url": " https://rseng.github.io/software/repository/github/ArenA-Crowds/Crowds", + "content": "Jupyter python notebooks related to the ArenA project" }, - "github/yangyanli/DO-Conv": { - "id": "github/yangyanli/DO-Conv", - "title": "github/yangyanli/DO-Conv", - "url": " https://rseng.github.io/software/repository/github/yangyanli/DO-Conv", - "content": "Depthwise Over-parameterized Convolutional Layer" + "github/bommert/stabm": { + "id": "github/bommert/stabm", + "title": "github/bommert/stabm", + "url": " https://rseng.github.io/software/repository/github/bommert/stabm", + "content": "Stability measures" + }, + "github/ShixiangWang/sigminer": { + "id": "github/ShixiangWang/sigminer", + "title": "github/ShixiangWang/sigminer", + "url": " https://rseng.github.io/software/repository/github/ShixiangWang/sigminer", + "content": "🌲 An easy-to-use and scalable toolkit for genomic alteration (mutational) signature analysis and visualization in R" }, - "github/bcgov/shinyssdtools": { - "id": "github/bcgov/shinyssdtools", - "title": "github/bcgov/shinyssdtools", - "url": " https://rseng.github.io/software/repository/github/bcgov/shinyssdtools", - "content": "Shiny interface to ssdtools R package" + "github/pec27/smerfs": { + "id": "github/pec27/smerfs", + "title": "github/pec27/smerfs", + "url": " https://rseng.github.io/software/repository/github/pec27/smerfs", + "content": "Creating large realisations of random fields on the sphere" }, - "github/bcgov/bcdata": { - "id": "github/bcgov/bcdata", - "title": "github/bcgov/bcdata", - "url": " https://rseng.github.io/software/repository/github/bcgov/bcdata", - "content": "An R package for searching & retrieving data from the B.C. Data Catalogue" + "github/pec27/hfof": { + "id": "github/pec27/hfof", + "title": "github/pec27/hfof", + "url": " https://rseng.github.io/software/repository/github/pec27/hfof", + "content": "Friends-of-Friends via spatial hashing" }, - "github/MICCoM/SSAGES-public": { - "id": "github/MICCoM/SSAGES-public", - "title": "github/MICCoM/SSAGES-public", - "url": " https://rseng.github.io/software/repository/github/MICCoM/SSAGES-public", - "content": "Software Suite for Advanced General Ensemble Simulations" + "github/pec27/lizard": { + "id": "github/pec27/lizard", + "title": "github/pec27/lizard", + "url": " https://rseng.github.io/software/repository/github/pec27/lizard", + "content": "lizard is an open-source code for the creation of particle initial conditions for cosmological simulations" }, - "github/sunpy/ndcube": { - "id": "github/sunpy/ndcube", - "title": "github/sunpy/ndcube", - "url": " https://rseng.github.io/software/repository/github/sunpy/ndcube", - "content": "A base package for multi-dimensional contiguous and non-contiguous coordinate-aware arrays. Maintainers: @danryanirish & @Cadair" + "github/gerddie/maxflow": { + "id": "github/gerddie/maxflow", + "title": "github/gerddie/maxflow", + "url": " https://rseng.github.io/software/repository/github/gerddie/maxflow", + "content": "A library that implements the maxflow-mincut algorithm. 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It supports all source models including points, Gaussians and Shapelets. Distributed calibration using MPI and consensus optimization is enabled. Tools to build/restore sky models are included." + "github/jdber1/opendrop": { + "id": "github/jdber1/opendrop", + "title": "github/jdber1/opendrop", + "url": " https://rseng.github.io/software/repository/github/jdber1/opendrop", + "content": "OpenDrop pendant drop tensiometry software" }, - "github/jgagneastro/CoMover": { - "id": "github/jgagneastro/CoMover", - "title": "github/jgagneastro/CoMover", - "url": " https://rseng.github.io/software/repository/github/jgagneastro/CoMover", - "content": "None" + "github/JEFworks-Lab/STdeconvolve": { + "id": "github/JEFworks-Lab/STdeconvolve", + "title": "github/JEFworks-Lab/STdeconvolve", + "url": " https://rseng.github.io/software/repository/github/JEFworks-Lab/STdeconvolve", + "content": "Reference-free cell-type deconvolution of multi-cellular spatially resolved transcriptomics data" }, - "github/natashabatalha/picaso": { - "id": "github/natashabatalha/picaso", - "title": "github/natashabatalha/picaso", - "url": " https://rseng.github.io/software/repository/github/natashabatalha/picaso", - "content": "A Planetary Intensity Code for Atmospheric Spectroscopy Observations" + "github/s4hts/HTStream": { + "id": "github/s4hts/HTStream", + "title": "github/s4hts/HTStream", + "url": " https://rseng.github.io/software/repository/github/s4hts/HTStream", + "content": "A high throughput sequence read toolset using a streaming approach facilitated by Linux pipes" }, - "github/natashabatalha/PandExo": { - "id": "github/natashabatalha/PandExo", - "title": "github/natashabatalha/PandExo", - "url": " https://rseng.github.io/software/repository/github/natashabatalha/PandExo", - "content": "A Community Tool for Transiting Exoplanet Science with the JWST & HST" + "github/mihanke/athos": { + "id": "github/mihanke/athos", + "title": "github/mihanke/athos", + "url": " https://rseng.github.io/software/repository/github/mihanke/athos", + "content": "ATHOS: On-the-fly stellar parameter determination of FGK stars based on flux ratios from optical spectra" }, - "github/mirapy-org/mirapy": { - "id": "github/mirapy-org/mirapy", - "title": "github/mirapy-org/mirapy", - "url": " https://rseng.github.io/software/repository/github/mirapy-org/mirapy", - "content": "MiraPy: A Python package for Deep Learning in Astronomy" + "github/undark-lab/albatross": { + "id": "github/undark-lab/albatross", + "title": "github/undark-lab/albatross", + "url": " https://rseng.github.io/software/repository/github/undark-lab/albatross", + "content": "A simulation-based Inference (SBI) library designed to perform analysis on stellar streams in the Milky Way" }, - "github/jhkorhonen/MOODS": { - "id": "github/jhkorhonen/MOODS", - "title": "github/jhkorhonen/MOODS", - "url": " https://rseng.github.io/software/repository/github/jhkorhonen/MOODS", - "content": "MOODS: Motif Occurrence Detection Suite" + "github/undark-lab/sstrax": { + "id": "github/undark-lab/sstrax", + "title": "github/undark-lab/sstrax", + "url": " https://rseng.github.io/software/repository/github/undark-lab/sstrax", + "content": "A jax-accelerated modelling code for Milky Way stellar streams" }, - 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"title": "github/vgteam/vg#vg", - "url": " https://rseng.github.io/software/repository/github/vgteam/vg#vg", - "content": "tools for working with genome variation graphs" + "github/arumugamlab/msamtools": { + "id": "github/arumugamlab/msamtools", + "title": "github/arumugamlab/msamtools", + "url": " https://rseng.github.io/software/repository/github/arumugamlab/msamtools", + "content": "Metagenomics-related extended functionalities to samtools" }, - "github/vgteam/vg": { - "id": "github/vgteam/vg", - "title": "github/vgteam/vg", - "url": " https://rseng.github.io/software/repository/github/vgteam/vg", - "content": "tools for working with genome variation graphs" + "github/PaulKuin/uvotpy": { + "id": "github/PaulKuin/uvotpy", + "title": "github/PaulKuin/uvotpy", + "url": " https://rseng.github.io/software/repository/github/PaulKuin/uvotpy", + "content": "Swift UVOT grisms - spectral extraction" }, - "github/FINNGEN/lavaa-react": { - "id": "github/FINNGEN/lavaa-react", - "title": "github/FINNGEN/lavaa-react", - "url": " https://rseng.github.io/software/repository/github/FINNGEN/lavaa-react", - "content": "lavaa-react" + "github/918particle/AskaryanModule": { + "id": "github/918particle/AskaryanModule", + "title": "github/918particle/AskaryanModule", + "url": " https://rseng.github.io/software/repository/github/918particle/AskaryanModule", + "content": "None" + }, + "github/IMS-MAXIMS/openMAXIMS": { + "id": "github/IMS-MAXIMS/openMAXIMS", + "title": "github/IMS-MAXIMS/openMAXIMS", + "url": " https://rseng.github.io/software/repository/github/IMS-MAXIMS/openMAXIMS", + "content": "Home of the openMAXIMS PAS and EPR" }, - "github/prdm0/ropenblas": { - "id": "github/prdm0/ropenblas", - "title": "github/prdm0/ropenblas", - "url": " https://rseng.github.io/software/repository/github/prdm0/ropenblas", - "content": "Package to link R language to OpenBLAS library" + "github/JD2112/methylr": { + "id": "github/JD2112/methylr", + "title": "github/JD2112/methylr", + "url": " https://rseng.github.io/software/repository/github/JD2112/methylr", + "content": "methylR: a single shiny solution from sequencer data to pathway analysis" }, - 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(2011) XDGMM methods." + "github/DLR-RM/BlenderProc": { + "id": "github/DLR-RM/BlenderProc", + "title": "github/DLR-RM/BlenderProc", + "url": " https://rseng.github.io/software/repository/github/DLR-RM/BlenderProc", + "content": "A procedural Blender pipeline for photorealistic training image generation" }, - "github/tholoien/empiriciSN": { - "id": "github/tholoien/empiriciSN", - "title": "github/tholoien/empiriciSN", - "url": " https://rseng.github.io/software/repository/github/tholoien/empiriciSN", - "content": "Generate realistic parameters for a SN given host galaxy observations based on empirical correlations from SN datasets" + "github/AdmiralenOla/Scoary": { + "id": "github/AdmiralenOla/Scoary", + "title": "github/AdmiralenOla/Scoary", + "url": " https://rseng.github.io/software/repository/github/AdmiralenOla/Scoary", + "content": "Pan-genome wide association studies" }, - "github/seqcode/allo": { - "id": "github/seqcode/allo", - "title": "github/seqcode/allo", - "url": " https://rseng.github.io/software/repository/github/seqcode/allo", - "content": "Allo: a multi-mapped read rescue strategy for peak based gene regulatory analyses" + "github/daehwankimlab/hisat2": { + "id": "github/daehwankimlab/hisat2", + "title": "github/daehwankimlab/hisat2", + "url": " https://rseng.github.io/software/repository/github/daehwankimlab/hisat2", + "content": "Graph-based alignment (Hierarchical Graph FM index)" }, - "github/cjneely10/EukMetaSanity": { - "id": "github/cjneely10/EukMetaSanity", - "title": "github/cjneely10/EukMetaSanity", - "url": " https://rseng.github.io/software/repository/github/cjneely10/EukMetaSanity", - "content": "Structural and functional annotation of eukaryotic metagenome-assembled genomes" + "github/hytrac/amber": { + "id": "github/hytrac/amber", + "title": "github/hytrac/amber", + "url": " https://rseng.github.io/software/repository/github/hytrac/amber", + "content": "The Abundance Matching Box for the Epoch of Reionization (AMBER) is a semi-numerical code for modeling the cosmic dawn and reionization." }, - "github/aabdurrouf/piXedfit": { - "id": "github/aabdurrouf/piXedfit", - "title": "github/aabdurrouf/piXedfit", - "url": " https://rseng.github.io/software/repository/github/aabdurrouf/piXedfit", - "content": "piXedfit is a Python package designed for analyzing spatially resolved SEDs of galaxies " + "github/Kambrian/HBTplus": { + "id": "github/Kambrian/HBTplus", + "title": "github/Kambrian/HBTplus", + "url": " https://rseng.github.io/software/repository/github/Kambrian/HBTplus", + "content": "HBT+ subhalo finder and merger tree builder, the tool to get you out of mess and back to physics." + }, + "github/andreaminio/haplosync": { + "id": "github/andreaminio/haplosync", + "title": "github/andreaminio/haplosync", + "url": " https://rseng.github.io/software/repository/github/andreaminio/haplosync", + "content": "Tools for haplotype-wise reconstruction of pseudomolecules" + }, + "github/danielemelini/ALMA3": { + "id": "github/danielemelini/ALMA3", + "title": "github/danielemelini/ALMA3", + "url": " https://rseng.github.io/software/repository/github/danielemelini/ALMA3", + "content": "the plAnetary Love nuMbers cAlculator" + }, + "github/freebayes/freebayes": { + "id": "github/freebayes/freebayes", + "title": "github/freebayes/freebayes", + "url": " https://rseng.github.io/software/repository/github/freebayes/freebayes", + "content": "Bayesian haplotype-based genetic polymorphism discovery and genotyping." }, "github/ewels/MultiQC": { "id": "github/ewels/MultiQC", @@ -23973,3653 +24003,3761 @@ "url": " https://rseng.github.io/software/repository/github/ewels/MultiQC", "content": "Aggregate results from bioinformatics analyses across many samples into a single report." }, - "github/jianhuupenn/SpaGCN": { - "id": "github/jianhuupenn/SpaGCN", - "title": "github/jianhuupenn/SpaGCN", - "url": " https://rseng.github.io/software/repository/github/jianhuupenn/SpaGCN", - "content": "SpaGCN: Integrating gene expression, spatial location and histology to identify spatial domains and spatially variable genes by graph convolutional network" - }, - "github/karel-brinda/ococo": { - "id": "github/karel-brinda/ococo", - "title": "github/karel-brinda/ococo", - "url": " https://rseng.github.io/software/repository/github/karel-brinda/ococo", - "content": "Ococo: the first online variant and consensus caller. Call genomic consensus directly from an unsorted SAM/BAM stream." - }, - "github/ElsevierSoftwareX/SOFTX_2020_119": { - "id": "github/ElsevierSoftwareX/SOFTX_2020_119", - "title": "github/ElsevierSoftwareX/SOFTX_2020_119", - "url": " https://rseng.github.io/software/repository/github/ElsevierSoftwareX/SOFTX_2020_119", - "content": "Python/Octave wrapper generation for LALSuite" - }, - "github/ruanjue/wtdbg2": { - "id": "github/ruanjue/wtdbg2", - "title": "github/ruanjue/wtdbg2", - "url": " https://rseng.github.io/software/repository/github/ruanjue/wtdbg2", - "content": "Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly" - }, - "github/constantAmateur/SoupX": { - "id": "github/constantAmateur/SoupX", - "title": "github/constantAmateur/SoupX", - "url": " https://rseng.github.io/software/repository/github/constantAmateur/SoupX", - "content": "R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data" - }, - "github/micbia/SubgridClumping": { - "id": "github/micbia/SubgridClumping", - "title": "github/micbia/SubgridClumping", - "url": " https://rseng.github.io/software/repository/github/micbia/SubgridClumping", - "content": "None" - }, - "github/Yingjie4Science/SDGdetector": { - "id": "github/Yingjie4Science/SDGdetector", - "title": "github/Yingjie4Science/SDGdetector", - "url": " https://rseng.github.io/software/repository/github/Yingjie4Science/SDGdetector", - "content": "A novel R package that can identify and visualize 17 Sustainable Development Goals and associated 169 Targets in text" - }, - "github/fgbuster/fgbuster": { - "id": "github/fgbuster/fgbuster", - "title": "github/fgbuster/fgbuster", - "url": " https://rseng.github.io/software/repository/github/fgbuster/fgbuster", - "content": "Parametric component separation for Cosmic Microwave Background observations" - }, - "github/0xCoto/Virgo": { - "id": "github/0xCoto/Virgo", - "title": "github/0xCoto/Virgo", - "url": " https://rseng.github.io/software/repository/github/0xCoto/Virgo", - "content": "📡 Virgo: A Versatile Spectrometer for Radio Astronomy" - 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"url": " https://rseng.github.io/software/repository/github/rickhelmus/patRoon", - "content": "Workflow solutions for mass-spectrometry based non-target analysis." + "github/mattyowl/fitScalingRelation": { + "id": "github/mattyowl/fitScalingRelation", + "title": "github/mattyowl/fitScalingRelation", + "url": " https://rseng.github.io/software/repository/github/mattyowl/fitScalingRelation", + "content": "Code for fitting galaxy cluster scaling relations using MCMC" }, - "github/nextstrain/auspice": { - "id": "github/nextstrain/auspice", - "title": "github/nextstrain/auspice", - "url": " https://rseng.github.io/software/repository/github/nextstrain/auspice", - "content": "Web app for visualizing pathogen evolution" + "github/getzlab/rnaseqc": { + "id": "github/getzlab/rnaseqc", + "title": "github/getzlab/rnaseqc", + "url": " https://rseng.github.io/software/repository/github/getzlab/rnaseqc", + "content": "Fast, efficient RNA-Seq metrics for quality control and process optimization" }, - 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It has a suite of IMEX time integration schemes." + "github/jts/sga": { + "id": "github/jts/sga", + "title": "github/jts/sga", + "url": " https://rseng.github.io/software/repository/github/jts/sga", + "content": "de novo sequence assembler using string graphs" }, - "github/odlomax/spamcart-dev": { - "id": "github/odlomax/spamcart-dev", - "title": "github/odlomax/spamcart-dev", - "url": " https://rseng.github.io/software/repository/github/odlomax/spamcart-dev", - "content": "Development repository for SPAMCART radiative transfer code" + "github/jts/nanopolish": { + "id": "github/jts/nanopolish", + "title": "github/jts/nanopolish", + "url": " https://rseng.github.io/software/repository/github/jts/nanopolish", + "content": "Signal-level algorithms for MinION data" }, - "github/myfang2021/VIPPID": { - "id": "github/myfang2021/VIPPID", - "title": "github/myfang2021/VIPPID", - "url": " https://rseng.github.io/software/repository/github/myfang2021/VIPPID", - "content": "None" + "github/akikuno/cstag": { + "id": "github/akikuno/cstag", + "title": "github/akikuno/cstag", + "url": " https://rseng.github.io/software/repository/github/akikuno/cstag", + "content": "Python module to manipulate and visualize minimap2's cs tag" }, - "github/gromacs/gromacs": { - "id": "github/gromacs/gromacs", - "title": "github/gromacs/gromacs", - "url": " https://rseng.github.io/software/repository/github/gromacs/gromacs", - "content": "Public/backup repository of the GROMACS molecular simulation toolkit. Please do not mine the metadata blindly; we use https://gitlab.com/gromacs/gromacs for code review and issue tracking." + "github/mayuresh159/starsense_algorithms": { + "id": "github/mayuresh159/starsense_algorithms", + "title": "github/mayuresh159/starsense_algorithms", + "url": " https://rseng.github.io/software/repository/github/mayuresh159/starsense_algorithms", + "content": "This is a software package for testing and performance evaluation of different star sensors. The algorithms used for calculating quaternions from star field images are : centroiding, geometric voting and QUEST algorithms. The physical parameters of a star sensor are parametrized and by changing these parameters various performance estimators like sky coverage, memory requirement, timing requirements etc can be estimated for the selected star sensor. 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"id": "github/fenderglass/Ragout", - "title": "github/fenderglass/Ragout", - "url": " https://rseng.github.io/software/repository/github/fenderglass/Ragout", - "content": "Chromosome-level scaffolding using multiple references" + "github/lberaldoesilva/naif": { + "id": "github/lberaldoesilva/naif", + "title": "github/lberaldoesilva/naif", + "url": " https://rseng.github.io/software/repository/github/lberaldoesilva/naif", + "content": "pure-python package for numerical analysis of frequencies of numerically integrated orbits" }, - "github/fenderglass/Flye": { - "id": "github/fenderglass/Flye", - "title": "github/fenderglass/Flye", - "url": " https://rseng.github.io/software/repository/github/fenderglass/Flye", - "content": "De novo assembler for single molecule sequencing reads using repeat graphs" + "github/auranic/ClinTrajan": { + "id": "github/auranic/ClinTrajan", + "title": "github/auranic/ClinTrajan", + "url": " https://rseng.github.io/software/repository/github/auranic/ClinTrajan", + "content": "Finding trajectories, bifurcations and quantifying pseudotime in large clinical datasets" }, - 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"id": "github/m-a-d-n-e-s-s/madness", - "title": "github/m-a-d-n-e-s-s/madness", - "url": " https://rseng.github.io/software/repository/github/m-a-d-n-e-s-s/madness", - "content": "Multiresolution Adaptive Numerical Environment for Scientific Simulation" + "github/RECETOX/RIAssigner": { + "id": "github/RECETOX/RIAssigner", + "title": "github/RECETOX/RIAssigner", + "url": " https://rseng.github.io/software/repository/github/RECETOX/RIAssigner", + "content": "RIAssigner is a python tool for retention index (RI) computation for GC-MS data." }, - "github/pratheesh3780/grapesAgri1": { - "id": "github/pratheesh3780/grapesAgri1", - "title": "github/pratheesh3780/grapesAgri1", - "url": " https://rseng.github.io/software/repository/github/pratheesh3780/grapesAgri1", - "content": "Collection of shiny apps for Agricultural research Data Analysis. Allows user to have graphical user interface to perform analysis of Agricultural experimental data. On using the functions in this package a Graphical User Interface will pop up. Apps Works by simple upload of files in CSV format." + "github/RECETOX/MSMetaEnhancer": { + "id": "github/RECETOX/MSMetaEnhancer", + "title": "github/RECETOX/MSMetaEnhancer", + "url": " https://rseng.github.io/software/repository/github/RECETOX/MSMetaEnhancer", + "content": "Tool for mass spectra metadata annotation." }, - "github/NLeSC/xtas": { - "id": "github/NLeSC/xtas", - "title": "github/NLeSC/xtas", - "url": " https://rseng.github.io/software/repository/github/NLeSC/xtas", - "content": "Distributed text analysis suite based on Celery" + "github/LoganAMorrison/Hazma": { + "id": "github/LoganAMorrison/Hazma", + "title": "github/LoganAMorrison/Hazma", + "url": " https://rseng.github.io/software/repository/github/LoganAMorrison/Hazma", + "content": "Python package for computing indirect detection constraints on sub-GeV dark matter." }, - "github/NLeSC/structure-from-motion": { - "id": "github/NLeSC/structure-from-motion", - "title": "github/NLeSC/structure-from-motion", - "url": " https://rseng.github.io/software/repository/github/NLeSC/structure-from-motion", - "content": "Structure from Motion Pipeline" + "github/MDAnalysis/mdanalysis": { + "id": "github/MDAnalysis/mdanalysis", + "title": "github/MDAnalysis/mdanalysis", + "url": " https://rseng.github.io/software/repository/github/MDAnalysis/mdanalysis", + "content": "MDAnalysis is a Python library to analyze molecular dynamics trajectories." }, - "github/NLeSC/Massive-PotreeConverter": { - "id": "github/NLeSC/Massive-PotreeConverter", - "title": "github/NLeSC/Massive-PotreeConverter", - "url": " https://rseng.github.io/software/repository/github/NLeSC/Massive-PotreeConverter", - "content": "Convert massive pointcloud, for example ahn2 (640 Billion points) to potree format." + "github/lcpp-org/RustBCA": { + "id": "github/lcpp-org/RustBCA", + "title": "github/lcpp-org/RustBCA", + "url": " https://rseng.github.io/software/repository/github/lcpp-org/RustBCA", + "content": "A Binary Collision Approximation (BCA) code for arbitrary ion-material interactions" }, - "github/NLeSC/esibayes": { - "id": "github/NLeSC/esibayes", - "title": "github/NLeSC/esibayes", - "url": " https://rseng.github.io/software/repository/github/NLeSC/esibayes", - "content": "Optimization and state estimation of dynamic models" + "github/MelanieKahl/MechAnalyze": { + "id": "github/MelanieKahl/MechAnalyze", + "title": "github/MelanieKahl/MechAnalyze", + "url": " https://rseng.github.io/software/repository/github/MelanieKahl/MechAnalyze", + "content": "an algorithm for standardization and automation of unconfined compression test analysis" }, - "github/NLeSC/xenon-flow": { - "id": "github/NLeSC/xenon-flow", - "title": "github/NLeSC/xenon-flow", - "url": " https://rseng.github.io/software/repository/github/NLeSC/xenon-flow", - "content": "Run CWL workflows using Xenon" + "github/vanheeringen-lab/gimmemotifs": { + "id": "github/vanheeringen-lab/gimmemotifs", + "title": "github/vanheeringen-lab/gimmemotifs", + "url": " https://rseng.github.io/software/repository/github/vanheeringen-lab/gimmemotifs", + "content": "Suite of motif tools, including a motif prediction pipeline for ChIP-seq experiments. See full GimmeMotifs documentation for detailed installation instructions and usage examples." }, - "github/NLeSC/noodles": { - "id": "github/NLeSC/noodles", - "title": "github/NLeSC/noodles", - "url": " https://rseng.github.io/software/repository/github/NLeSC/noodles", - "content": "Computational workflow engine, making distributed computing in Python easy!" + "github/ryneches/SuchTree": { + "id": "github/ryneches/SuchTree", + "title": "github/ryneches/SuchTree", + "url": " https://rseng.github.io/software/repository/github/ryneches/SuchTree", + "content": "A Python library for fast, thread-safe computations on phylogenetic trees" }, - "github/NLeSC/osmium": { - "id": "github/NLeSC/osmium", - "title": "github/NLeSC/osmium", - "url": " https://rseng.github.io/software/repository/github/NLeSC/osmium", - "content": "Xenon Job Webservice" + "github/pokynmr/ipick": { + "id": "github/pokynmr/ipick", + "title": "github/pokynmr/ipick", + "url": " https://rseng.github.io/software/repository/github/pokynmr/ipick", + "content": "Multiprocessing Peak Picking Software for UCSF NMR Spectra" }, - "github/NLeSC/boatswain": { - "id": "github/NLeSC/boatswain", - "title": "github/NLeSC/boatswain", - "url": " https://rseng.github.io/software/repository/github/NLeSC/boatswain", - "content": "A simple build system for docker images" + "github/fzagaria/COpops": { + "id": "github/fzagaria/COpops", + "title": "github/fzagaria/COpops", + "url": " https://rseng.github.io/software/repository/github/fzagaria/COpops", + "content": "A Jupyter notebook with a simple class to compute CO sizes and fluxes using the semi-analytical method developed by Zagaria et al. (2023b)." }, - "github/NLeSC/lokum": { - "id": "github/NLeSC/lokum", - "title": "github/NLeSC/lokum", - "url": " https://rseng.github.io/software/repository/github/NLeSC/lokum", - "content": "Deploy GlusterFS, Docker, Spark and JupyterHub services on bare-metal cluster." + "github/JCGonzS/mechnetor": { + "id": "github/JCGonzS/mechnetor", + "title": "github/JCGonzS/mechnetor", + "url": " https://rseng.github.io/software/repository/github/JCGonzS/mechnetor", + "content": "Protein Interaction Visualization" }, - "github/NLeSC/cptm": { - "id": "github/NLeSC/cptm", - "title": "github/NLeSC/cptm", - "url": " https://rseng.github.io/software/repository/github/NLeSC/cptm", - "content": "Cross-Perspective Topic Modeling" + "github/j-faria/kima": { + "id": "github/j-faria/kima", + "title": "github/j-faria/kima", + "url": " https://rseng.github.io/software/repository/github/j-faria/kima", + "content": "Exoplanet detection in RVs with DNest4 and GPs" }, - "github/NLeSC/eEcology-Annotation-WS": { - "id": "github/NLeSC/eEcology-Annotation-WS", - "title": "github/NLeSC/eEcology-Annotation-WS", - "url": " https://rseng.github.io/software/repository/github/NLeSC/eEcology-Annotation-WS", - "content": "Webservice for eEcology Annotation project." + "github/walaj/svaba": { + "id": "github/walaj/svaba", + "title": "github/walaj/svaba", + "url": " https://rseng.github.io/software/repository/github/walaj/svaba", + "content": "Structural variation and indel detection by local assembly" }, - "github/NLeSC/eEcology-Classification": { - "id": "github/NLeSC/eEcology-Classification", - "title": "github/NLeSC/eEcology-Classification", - "url": " https://rseng.github.io/software/repository/github/NLeSC/eEcology-Classification", - "content": "Classification tool" + "github/walaj/SeqLib": { + "id": "github/walaj/SeqLib", + "title": "github/walaj/SeqLib", + "url": " https://rseng.github.io/software/repository/github/walaj/SeqLib", + "content": "C++ htslib/bwa-mem/fermi interface for interrogating sequence data" }, - "github/NLeSC/xenon-cli": { - "id": "github/NLeSC/xenon-cli", - "title": "github/NLeSC/xenon-cli", - "url": " https://rseng.github.io/software/repository/github/NLeSC/xenon-cli", - "content": "Perform files and jobs operations with Xenon library from command line" + "github/ckm3/Py-PDM": { + "id": "github/ckm3/Py-PDM", + "title": "github/ckm3/Py-PDM", + "url": " https://rseng.github.io/software/repository/github/ckm3/Py-PDM", + "content": "A Python wrapper of the Phase Dispersion Minimization (PDM), which is a C code written by Stellingwerf." + }, + "github/davemlz/eemont": { + "id": "github/davemlz/eemont", + "title": "github/davemlz/eemont", + "url": " https://rseng.github.io/software/repository/github/davemlz/eemont", + "content": "A python package that extends Google Earth Engine." + }, + "github/martinjzhang/scDRS": { + "id": "github/martinjzhang/scDRS", + "title": "github/martinjzhang/scDRS", + "url": " https://rseng.github.io/software/repository/github/martinjzhang/scDRS", + "content": "Single-cell disease relevance score (scDRS)" + }, + "github/ncbi/SKESA": { + "id": "github/ncbi/SKESA", + "title": "github/ncbi/SKESA", + "url": " https://rseng.github.io/software/repository/github/ncbi/SKESA", + "content": "SKESA assembler" }, - 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"url": " https://rseng.github.io/software/repository/github/NLeSC/ShiCo", - "content": "Netherlands eScience Center - Shifting Concepts Through Time project" + "github/ncbi/igblast": { + "id": "github/ncbi/igblast", + "title": "github/ncbi/igblast", + "url": " https://rseng.github.io/software/repository/github/ncbi/igblast", + "content": "Immunoglobulin and T cell receptor variable domain sequence analysis" }, - "github/NLeSC/fairdatapoint": { - "id": "github/NLeSC/fairdatapoint", - "title": "github/NLeSC/fairdatapoint", - "url": " https://rseng.github.io/software/repository/github/NLeSC/fairdatapoint", - "content": "Provide machine-readable descriptions of your data assets" + "github/ncbi/sra-tools": { + "id": "github/ncbi/sra-tools", + "title": "github/ncbi/sra-tools", + "url": " https://rseng.github.io/software/repository/github/ncbi/sra-tools", + "content": "SRA Tools" }, - "github/NLeSC/eSalsa-MPI": { - "id": "github/NLeSC/eSalsa-MPI", - "title": "github/NLeSC/eSalsa-MPI", - "url": " https://rseng.github.io/software/repository/github/NLeSC/eSalsa-MPI", - "content": "This project contains the wide area MPI used in the eSalsa project" + "github/ncbi/TPMCalculator": { + "id": "github/ncbi/TPMCalculator", + "title": "github/ncbi/TPMCalculator", + "url": " https://rseng.github.io/software/repository/github/ncbi/TPMCalculator", + "content": "TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files" }, - "github/NLeSC/compressing-the-sky": { - "id": "github/NLeSC/compressing-the-sky", - "title": "github/NLeSC/compressing-the-sky", - "url": " https://rseng.github.io/software/repository/github/NLeSC/compressing-the-sky", - "content": "Compressing the Sky project with CWI DA" + "github/ncbi/ngs": { + "id": "github/ncbi/ngs", + "title": "github/ncbi/ngs", + "url": " https://rseng.github.io/software/repository/github/ncbi/ngs", + "content": "NGS Language Bindings" }, - "github/NLeSC/PattyData": { - "id": "github/NLeSC/PattyData", - "title": "github/NLeSC/PattyData", - "url": " https://rseng.github.io/software/repository/github/NLeSC/PattyData", - "content": "None" + "github/ncbi/datasets": { + "id": "github/ncbi/datasets", + "title": "github/ncbi/datasets", + "url": " https://rseng.github.io/software/repository/github/ncbi/datasets", + "content": "NCBI Datasets is an experimental resource for finding and building datasets" }, - "github/NLeSC/OCTSegmentation": { - "id": "github/NLeSC/OCTSegmentation", - "title": "github/NLeSC/OCTSegmentation", - "url": " https://rseng.github.io/software/repository/github/NLeSC/OCTSegmentation", - "content": "EYR4-OCTSEG " + "github/ncbi/ncbi-vdb": { + "id": "github/ncbi/ncbi-vdb", + "title": "github/ncbi/ncbi-vdb", + "url": " https://rseng.github.io/software/repository/github/ncbi/ncbi-vdb", + "content": "ncbi-vdb" }, - "github/NLeSC/docker-couch-admin": { - "id": "github/NLeSC/docker-couch-admin", - "title": "github/NLeSC/docker-couch-admin", - "url": " https://rseng.github.io/software/repository/github/NLeSC/docker-couch-admin", - "content": "Configures a web service using angular-schema-form and CouchDB" + "github/ncbi/BAMscale": { + "id": "github/ncbi/BAMscale", + "title": "github/ncbi/BAMscale", + "url": " https://rseng.github.io/software/repository/github/ncbi/BAMscale", + "content": "BAMscale is a one-step tool for either 1) quantifying and normalizing the coverage of peaks or 2) generated scaled BigWig files for easy visualization of commonly used DNA-seq capture based methods." }, - "github/NLeSC/xenon-grpc": { - "id": "github/NLeSC/xenon-grpc", - "title": "github/NLeSC/xenon-grpc", - "url": " https://rseng.github.io/software/repository/github/NLeSC/xenon-grpc", - "content": "Xenon grpc based server" + "github/ajshajib/LensingETC": { + "id": "github/ajshajib/LensingETC", + "title": "github/ajshajib/LensingETC", + "url": " https://rseng.github.io/software/repository/github/ajshajib/LensingETC", + "content": "Lensing Exposure Time Calculator" }, - "github/NLeSC/pattyvis": { - "id": "github/NLeSC/pattyvis", - "title": "github/NLeSC/pattyvis", - "url": " https://rseng.github.io/software/repository/github/NLeSC/pattyvis", - "content": "Webgl pointcloud visualization of the Via Appia based on potree" + "github/ajshajib/dolphin": { + "id": "github/ajshajib/dolphin", + "title": "github/ajshajib/dolphin", + "url": " https://rseng.github.io/software/repository/github/ajshajib/dolphin", + "content": "Automated pipeline for lens modelling based on lenstronomy." }, - "github/NLeSC/eEcology-SMS-reciever": { - "id": "github/NLeSC/eEcology-SMS-reciever", - "title": "github/NLeSC/eEcology-SMS-reciever", - "url": " https://rseng.github.io/software/repository/github/NLeSC/eEcology-SMS-reciever", - "content": "Webservice to store SMS messages into a database table" + "github/sebhaan/geobo": { + "id": "github/sebhaan/geobo", + "title": "github/sebhaan/geobo", + "url": " https://rseng.github.io/software/repository/github/sebhaan/geobo", + "content": "Python package for Multi-Objective Bayesian Optimisation and Joint Inversion" }, - "github/NLeSC/MAGMa": { - "id": "github/NLeSC/MAGMa", - "title": "github/NLeSC/MAGMa", - "url": " https://rseng.github.io/software/repository/github/NLeSC/MAGMa", - "content": "eMetabolomics project: Mass Annotation based on in silico Generated Metabolites" + "github/musoke/UltraDark.jl": { + "id": "github/musoke/UltraDark.jl", + "title": "github/musoke/UltraDark.jl", + "url": " https://rseng.github.io/software/repository/github/musoke/UltraDark.jl", + "content": "Simulations of cosmological scalar fields" }, - "github/NLeSC/case-law-app": { - "id": "github/NLeSC/case-law-app", - "title": "github/NLeSC/case-law-app", - "url": " https://rseng.github.io/software/repository/github/NLeSC/case-law-app", + "github/khowe/quick": { + "id": "github/khowe/quick", + "title": "github/khowe/quick", + "url": " https://rseng.github.io/software/repository/github/khowe/quick", + "content": "an efficient implementation of the Neighbor-Joining algorithm." + }, + "github/gdefazio/kMetaShot": { + "id": "github/gdefazio/kMetaShot", + "title": "github/gdefazio/kMetaShot", + "url": " https://rseng.github.io/software/repository/github/gdefazio/kMetaShot", "content": "None" }, - "github/NLeSC/eAstroViz": { - "id": "github/NLeSC/eAstroViz", - "title": "github/NLeSC/eAstroViz", - "url": " https://rseng.github.io/software/repository/github/NLeSC/eAstroViz", + "github/AarhusCosmology/connect_public": { + "id": "github/AarhusCosmology/connect_public", + "title": "github/AarhusCosmology/connect_public", + "url": " https://rseng.github.io/software/repository/github/AarhusCosmology/connect_public", + "content": "Public branch of CONNECT" + }, + "github/AarhusCosmology/prospect_public": { + "id": "github/AarhusCosmology/prospect_public", + "title": "github/AarhusCosmology/prospect_public", + "url": " https://rseng.github.io/software/repository/github/AarhusCosmology/prospect_public", "content": "None" }, - 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Includes segmentation, registration, file format conversion. 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For a Linux release of a complete embedding+visualization pipeline please visit https://github.com/sonjageorgievska/Embed-Dive." + "github/dib-lab/sourmash": { + "id": "github/dib-lab/sourmash", + "title": "github/dib-lab/sourmash", + "url": " https://rseng.github.io/software/repository/github/dib-lab/sourmash", + "content": "Quickly search, compare, and analyze genomic and metagenomic data sets." }, - "github/NLeSC/ExtJS-DateTime": { - "id": "github/NLeSC/ExtJS-DateTime", - "title": "github/NLeSC/ExtJS-DateTime", - "url": " https://rseng.github.io/software/repository/github/NLeSC/ExtJS-DateTime", - "content": "DateTime input field for Ext JS" + "github/rribeiro-sci/pygomodo": { + "id": "github/rribeiro-sci/pygomodo", + "title": "github/rribeiro-sci/pygomodo", + "url": " https://rseng.github.io/software/repository/github/rribeiro-sci/pygomodo", + "content": "GPCRs modeling and docking with python" }, - "github/NLeSC/UncertaintyVisualization": { - "id": "github/NLeSC/UncertaintyVisualization", - "title": "github/NLeSC/UncertaintyVisualization", - "url": " https://rseng.github.io/software/repository/github/NLeSC/UncertaintyVisualization", - "content": "None" + "github/domschrei/mallob": { + "id": "github/domschrei/mallob", + "title": "github/domschrei/mallob", + "url": " https://rseng.github.io/software/repository/github/domschrei/mallob", + "content": "Malleable Load Balancer. 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"title": "github/changliao1025/pyflowline", - "url": " https://rseng.github.io/software/repository/github/changliao1025/pyflowline", - "content": "A mesh independent river network generator for hydrologic models" + "github/liuhong-jia/scAnno": { + "id": "github/liuhong-jia/scAnno", + "title": "github/liuhong-jia/scAnno", + "url": " https://rseng.github.io/software/repository/github/liuhong-jia/scAnno", + "content": "None" }, - "github/mwoodbri/MRIdb": { - "id": "github/mwoodbri/MRIdb", - "title": "github/mwoodbri/MRIdb", - "url": " https://rseng.github.io/software/repository/github/mwoodbri/MRIdb", - "content": "An end-to-end data management system for MRI" + "github/pepamengual/UEP": { + "id": "github/pepamengual/UEP", + "title": "github/pepamengual/UEP", + "url": " https://rseng.github.io/software/repository/github/pepamengual/UEP", + "content": "None" }, - "github/AlexanderLabWHOI/EUKulele": { - "id": "github/AlexanderLabWHOI/EUKulele", - "title": "github/AlexanderLabWHOI/EUKulele", - 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Java library of data structures and algorithms" }, - "github/3D-e-Chem/knime-sstea": { - "id": "github/3D-e-Chem/knime-sstea", - "title": "github/3D-e-Chem/knime-sstea", - "url": " https://rseng.github.io/software/repository/github/3D-e-Chem/knime-sstea", - "content": "Knime node to calculate ss-TEA score of sequence alignment and subfamily members." + "github/danielhuson/megan-ce": { + "id": "github/danielhuson/megan-ce", + "title": "github/danielhuson/megan-ce", + "url": " https://rseng.github.io/software/repository/github/danielhuson/megan-ce", + "content": "MEGAN Community Edition" }, - "github/3D-e-Chem/knime-gpcrdb": { - "id": "github/3D-e-Chem/knime-gpcrdb", - "title": "github/3D-e-Chem/knime-gpcrdb", - "url": " https://rseng.github.io/software/repository/github/3D-e-Chem/knime-gpcrdb", - "content": "GPCRDB nodes for Knime" + "github/danielhuson/dendroscope3": { + "id": "github/danielhuson/dendroscope3", + "title": "github/danielhuson/dendroscope3", + "url": " https://rseng.github.io/software/repository/github/danielhuson/dendroscope3", + "content": "Dendroscope program for analyzing and visualizing rooted phylogenetic trees and networks" }, - 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"content": "Manycore platform Simulation tool for NoC-based platform at a Cycle-accurate level" + "github/mlarichardson/ramses2hsim": { + "id": "github/mlarichardson/ramses2hsim", + "title": "github/mlarichardson/ramses2hsim", + "url": " https://rseng.github.io/software/repository/github/mlarichardson/ramses2hsim", + "content": "A simulation pipeline for converting cosmological RAMSES simulations into input FITS cubes for the hsim pipeline." }, - "github/DreamCloud-Project/AMALTHEA-Microworkload-Generator": { - "id": "github/DreamCloud-Project/AMALTHEA-Microworkload-Generator", - "title": "github/DreamCloud-Project/AMALTHEA-Microworkload-Generator", - "url": " https://rseng.github.io/software/repository/github/DreamCloud-Project/AMALTHEA-Microworkload-Generator", - "content": "Command line tool generating micro workloads from an AMALTHEA application" + "github/simd-everywhere/simde": { + "id": "github/simd-everywhere/simde", + "title": "github/simd-everywhere/simde", + "url": " https://rseng.github.io/software/repository/github/simd-everywhere/simde", + "content": "Implementations of SIMD instruction sets for systems which don't natively support them." }, - 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These relativistic correction are calculated by doing the convolution with the relativistic transfer code KYCONV (Dovciak, Karas & Yaqoob 2004) at each radial annulus" + "github/JuliaAI/Imbalance.jl": { + "id": "github/JuliaAI/Imbalance.jl", + "title": "github/JuliaAI/Imbalance.jl", + "url": " https://rseng.github.io/software/repository/github/JuliaAI/Imbalance.jl", + "content": "A Julia toolbox with resampling methods to correct for class imbalance." + }, + "github/zarr-developers/zarr-python": { + "id": "github/zarr-developers/zarr-python", + "title": "github/zarr-developers/zarr-python", + "url": " https://rseng.github.io/software/repository/github/zarr-developers/zarr-python", + "content": "An implementation of chunked, compressed, N-dimensional arrays for Python." + }, + "github/yangyongsan-bio/GREAP": { + "id": "github/yangyongsan-bio/GREAP", + "title": "github/yangyongsan-bio/GREAP", + "url": " https://rseng.github.io/software/repository/github/yangyongsan-bio/GREAP", + "content": "None" }, - 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Based on graphosaurus.js (https://github.com/frewsxcv/graphosaurus), which runs on Three.js. 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This tool was developed alongside the paper by Amendola, Rodrigues, Kumar, and Quartin, published in MNRAS in 2024" }, - "github/NickMilsonPhysics/BinaryStarSolver": { - "id": "github/NickMilsonPhysics/BinaryStarSolver", - "title": "github/NickMilsonPhysics/BinaryStarSolver", - "url": " https://rseng.github.io/software/repository/github/NickMilsonPhysics/BinaryStarSolver", - "content": "BinaryStarSolver is a Python 3 program which solves for the orbital elements of binary stars, given radial velocity time series" + "github/davi-rodrigues/NAVanalysis": { + "id": "github/davi-rodrigues/NAVanalysis", + "title": "github/davi-rodrigues/NAVanalysis", + "url": " https://rseng.github.io/software/repository/github/davi-rodrigues/NAVanalysis", + "content": "Normalized Additional Velocity analysis" }, - "github/egpbos/barcode": { - "id": "github/egpbos/barcode", - "title": "github/egpbos/barcode", - "url": " https://rseng.github.io/software/repository/github/egpbos/barcode", - "content": "Bayesian reconstruction of cosmic density fields" + "github/galaxyproject/ansible-tiaas2": { + "id": "github/galaxyproject/ansible-tiaas2", + "title": "github/galaxyproject/ansible-tiaas2", + "url": " https://rseng.github.io/software/repository/github/galaxyproject/ansible-tiaas2", + "content": "Ansible role for deploying TIaaS2" }, - "github/njcuk9999/apero-drs": { - "id": "github/njcuk9999/apero-drs", - "title": "github/njcuk9999/apero-drs", - "url": " https://rseng.github.io/software/repository/github/njcuk9999/apero-drs", - "content": "A PipelinE to Reduce Observations - The DRS for SPIRou (CFHT)" + "github/galaxyproject/galaxy-lib": { + "id": "github/galaxyproject/galaxy-lib", + "title": "github/galaxyproject/galaxy-lib", + "url": " https://rseng.github.io/software/repository/github/galaxyproject/galaxy-lib", + "content": "Subset of Galaxy (http://galaxyproject.org/) core code designed to be used as a library." }, - "github/Degiacomi-Lab/molearn": { - "id": "github/Degiacomi-Lab/molearn", - "title": "github/Degiacomi-Lab/molearn", - "url": " https://rseng.github.io/software/repository/github/Degiacomi-Lab/molearn", - "content": "protein conformational spaces meet machine learning" + "github/swiftbiosciences/primerclip": { + "id": "github/swiftbiosciences/primerclip", + "title": "github/swiftbiosciences/primerclip", + "url": " https://rseng.github.io/software/repository/github/swiftbiosciences/primerclip", + "content": "Swift Accel-Amplicon primer trimming tool for fast alignment-based primer trimming" }, - "github/phineasng/DECODE": { - "id": "github/phineasng/DECODE", - "title": "github/phineasng/DECODE", - "url": " https://rseng.github.io/software/repository/github/phineasng/DECODE", - "content": "Code Release for the DECODE submission (ISMB2022)" + "github/astrogilda/mirkwood": { + "id": "github/astrogilda/mirkwood", + "title": "github/astrogilda/mirkwood", + "url": " https://rseng.github.io/software/repository/github/astrogilda/mirkwood", + "content": "None" }, - "github/uclchem/Chemulator": { - "id": "github/uclchem/Chemulator", - "title": "github/uclchem/Chemulator", - "url": " https://rseng.github.io/software/repository/github/uclchem/Chemulator", - "content": "The thermochemical emulator for hydrodynamical modelling" + "github/daeken/Emokit": { + "id": "github/daeken/Emokit", + "title": "github/daeken/Emokit", + "url": " https://rseng.github.io/software/repository/github/daeken/Emokit", + "content": "Python library for the Emotiv EPOC headset" }, - "github/thachnguyen/CRISPRnano": { - "id": "github/thachnguyen/CRISPRnano", - "title": "github/thachnguyen/CRISPRnano", - "url": " https://rseng.github.io/software/repository/github/thachnguyen/CRISPRnano", - "content": "A simple website analyzes CRISPR experiment for Oxford Nanopore Sequencing data." + "github/sPaMFouR/RedPipe": { + "id": "github/sPaMFouR/RedPipe", + "title": "github/sPaMFouR/RedPipe", + "url": " https://rseng.github.io/software/repository/github/sPaMFouR/RedPipe", + "content": "Python Scripts for Data Reduction and Analysis" }, - "github/Yomguithereal/talisman": { - "id": "github/Yomguithereal/talisman", - "title": "github/Yomguithereal/talisman", - "url": " https://rseng.github.io/software/repository/github/Yomguithereal/talisman", - "content": "Straightforward fuzzy matching, information retrieval and NLP building blocks for JavaScript." + "github/hyosubkim/bayes-toolbox": { + "id": "github/hyosubkim/bayes-toolbox", + "title": "github/hyosubkim/bayes-toolbox", + "url": " https://rseng.github.io/software/repository/github/hyosubkim/bayes-toolbox", + "content": "bayes-toolbox" }, - "github/jonschwenk/RivGraph": { - "id": "github/jonschwenk/RivGraph", - "title": "github/jonschwenk/RivGraph", - "url": " https://rseng.github.io/software/repository/github/jonschwenk/RivGraph", - "content": "Extracting and quantifying graphical representations of river and delta channel networks from binary masks" + "github/meinardmueller/synctoolbox": { + "id": "github/meinardmueller/synctoolbox", + "title": "github/meinardmueller/synctoolbox", + "url": " https://rseng.github.io/software/repository/github/meinardmueller/synctoolbox", + "content": "Sync Toolbox - Python package with reference implementations for efficient, robust, and accurate music synchronization based on dynamic time warping (DTW)" }, - "github/cbg-ethz/V-pipe": { - "id": "github/cbg-ethz/V-pipe", - "title": "github/cbg-ethz/V-pipe", - "url": " https://rseng.github.io/software/repository/github/cbg-ethz/V-pipe", - "content": "V-pipe is a pipeline designed for analysing NGS data of short viral genomes" + "github/meinardmueller/libfmp": { + "id": "github/meinardmueller/libfmp", + "title": "github/meinardmueller/libfmp", + "url": " https://rseng.github.io/software/repository/github/meinardmueller/libfmp", + "content": "None" }, - "github/cbg-ethz/LolliPop": { - "id": "github/cbg-ethz/LolliPop", - "title": "github/cbg-ethz/LolliPop", - "url": " https://rseng.github.io/software/repository/github/cbg-ethz/LolliPop", - "content": "Deconvolution for Wastewater Genomics" + "github/FastMLC/fMLC": { + "id": "github/FastMLC/fMLC", + "title": "github/FastMLC/fMLC", + "url": " https://rseng.github.io/software/repository/github/FastMLC/fMLC", + "content": "None" }, - "github/cbg-ethz/smallgenomeutilities": { - "id": "github/cbg-ethz/smallgenomeutilities", - "title": "github/cbg-ethz/smallgenomeutilities", - "url": " https://rseng.github.io/software/repository/github/cbg-ethz/smallgenomeutilities", - "content": "smallgenomeutilities is a collection of Python scripts to convert alignments between different reference genomes." + "github/SIOSlab/exodetbox": { + "id": "github/SIOSlab/exodetbox", + "title": "github/SIOSlab/exodetbox", + "url": " https://rseng.github.io/software/repository/github/SIOSlab/exodetbox", + "content": "Methods for finding planets sharing a common (s,dmag)" }, - "github/cbg-ethz/shorah": { - "id": "github/cbg-ethz/shorah", - "title": "github/cbg-ethz/shorah", - "url": " https://rseng.github.io/software/repository/github/cbg-ethz/shorah", - "content": "Repo for the software suite ShoRAH (Short Reads Assembly into Haplotypes)" + "github/heuermh/dishevelled-bio": { + "id": "github/heuermh/dishevelled-bio", + "title": "github/heuermh/dishevelled-bio", + "url": " https://rseng.github.io/software/repository/github/heuermh/dishevelled-bio", + "content": "dishevelled.org bio" + }, + "github/FlowModelingControl/flowtorch": { + "id": "github/FlowModelingControl/flowtorch", + "title": "github/FlowModelingControl/flowtorch", + "url": " https://rseng.github.io/software/repository/github/FlowModelingControl/flowtorch", + "content": "flowTorch - a Python library for analysis and reduced-order modeling of fluid flows" }, - "github/cbg-ethz/PredictHaplo": { - "id": "github/cbg-ethz/PredictHaplo", - "title": "github/cbg-ethz/PredictHaplo", - "url": " https://rseng.github.io/software/repository/github/cbg-ethz/PredictHaplo", - "content": "This software aims at reconstructing haplotypes from next-generation sequencing data." + "github/PaulMcMillan-Astro/Torus": { + "id": "github/PaulMcMillan-Astro/Torus", + "title": "github/PaulMcMillan-Astro/Torus", + "url": " https://rseng.github.io/software/repository/github/PaulMcMillan-Astro/Torus", + "content": "Torus Code" }, - "github/nilearn/nilearnhub.io": { - "id": "github/nilearn/nilearnhub.io", - "title": "github/nilearn/nilearnhub.io", - "url": " https://rseng.github.io/software/repository/github/nilearn/nilearnhub.io", - "content": "a Python module for fast and easy statistical learning on NeuroImaging data. It leverages the scikit-learn Python toolbox for multivariate statistics with applications such as predictive modelling, classification, decoding, or connectivity analysis." + "github/PaulMcMillan-Astro/GalPot": { + "id": "github/PaulMcMillan-Astro/GalPot", + "title": "github/PaulMcMillan-Astro/GalPot", + "url": " https://rseng.github.io/software/repository/github/PaulMcMillan-Astro/GalPot", + "content": "A stand-alone version of Dehnen's GalaxyPotential code." }, - "github/dtcc-platform/dtcc-builder": { - "id": "github/dtcc-platform/dtcc-builder", - "title": "github/dtcc-platform/dtcc-builder", - "url": " https://rseng.github.io/software/repository/github/dtcc-platform/dtcc-builder", - "content": "None" + "github/lucydot/effmass": { + "id": "github/lucydot/effmass", + "title": "github/lucydot/effmass", + "url": " https://rseng.github.io/software/repository/github/lucydot/effmass", + "content": "Calculates various definitions of effective mass from the electronic bandstructure of a semiconductor." }, - "github/ltlancas/walter": { - "id": "github/ltlancas/walter", - "title": "github/ltlancas/walter", - "url": " https://rseng.github.io/software/repository/github/ltlancas/walter", - "content": "A code to make predictions for the number of resolved stars in a given observation with the future Nancy Grace Roman Space Telescope (RST)" + "github/tgrimes/SeqNet": { + "id": "github/tgrimes/SeqNet", + "title": "github/tgrimes/SeqNet", + "url": " https://rseng.github.io/software/repository/github/tgrimes/SeqNet", + "content": "An R package for simulating RNA-sequence datasets from regulatory networks" }, - "github/ddarriba/prottest3": { - "id": "github/ddarriba/prottest3", - "title": "github/ddarriba/prottest3", - "url": " https://rseng.github.io/software/repository/github/ddarriba/prottest3", - "content": "Automatically exported from code.google.com/p/prottest3" + "github/gmarcais/Quorum": { + "id": "github/gmarcais/Quorum", + "title": "github/gmarcais/Quorum", + "url": " https://rseng.github.io/software/repository/github/gmarcais/Quorum", + "content": "QUality Optimized Reads from the University of Maryland" }, - "github/alexander-pastukhov/bistablehistory": { - "id": "github/alexander-pastukhov/bistablehistory", - "title": "github/alexander-pastukhov/bistablehistory", - "url": " https://rseng.github.io/software/repository/github/alexander-pastukhov/bistablehistory", - "content": "A package to compute a cumulative history for time-series of perceptual dominance in bistable displays." + "github/gmarcais/Jellyfish": { + "id": "github/gmarcais/Jellyfish", + "title": "github/gmarcais/Jellyfish", + "url": " https://rseng.github.io/software/repository/github/gmarcais/Jellyfish", + "content": "A fast multi-threaded k-mer counter" }, - "github/STAR-Fusion/STAR-Fusion": { - "id": "github/STAR-Fusion/STAR-Fusion", - "title": "github/STAR-Fusion/STAR-Fusion", - "url": " https://rseng.github.io/software/repository/github/STAR-Fusion/STAR-Fusion", - "content": "STAR-Fusion codebase" + "github/abrupt-climate/hyper-canny": { + "id": "github/abrupt-climate/hyper-canny", + "title": "github/abrupt-climate/hyper-canny", + "url": " https://rseng.github.io/software/repository/github/abrupt-climate/hyper-canny", + "content": "High dimensional Canny edge detection" }, - "github/mrirecon/bart": { - "id": "github/mrirecon/bart", - "title": "github/mrirecon/bart", - "url": " https://rseng.github.io/software/repository/github/mrirecon/bart", - "content": "BART: Toolbox for Computational Magnetic Resonance Imaging" + "github/joshspeagle/dynesty": { + "id": "github/joshspeagle/dynesty", + "title": "github/joshspeagle/dynesty", + "url": " https://rseng.github.io/software/repository/github/joshspeagle/dynesty", + "content": "Dynamic Nested Sampling package for computing Bayesian posteriors and evidences" }, - "github/mrirecon/view": { - "id": "github/mrirecon/view", - "title": "github/mrirecon/view", - "url": " https://rseng.github.io/software/repository/github/mrirecon/view", - "content": "Image Viewer for BART" + "github/ci-for-science/self-hosted-runners": { + "id": "github/ci-for-science/self-hosted-runners", + "title": "github/ci-for-science/self-hosted-runners", + "url": " https://rseng.github.io/software/repository/github/ci-for-science/self-hosted-runners", + "content": "Recipe to install and configure a GitHub action runner using Ansible" }, - "github/tlancian/bio_cs": { - "id": "github/tlancian/bio_cs", - "title": "github/tlancian/bio_cs", - "url": " https://rseng.github.io/software/repository/github/tlancian/bio_cs", - "content": ""Contrast Subgraphs Allow Comparing Homogeneous and Heterogeneous Networks Derived from Omics Data" - T. Lanciano, A. Savino, F. Porcu, D. Cittaro, F. Bonchi, P. Provero" + "github/vatlab/sos-notebook": { + "id": "github/vatlab/sos-notebook", + "title": "github/vatlab/sos-notebook", + "url": " https://rseng.github.io/software/repository/github/vatlab/sos-notebook", + "content": "Multi-language Jupyter Notebook" }, - "github/lnasellentin/DALI": { - "id": "github/lnasellentin/DALI", - "title": "github/lnasellentin/DALI", - "url": " https://rseng.github.io/software/repository/github/lnasellentin/DALI", - "content": "Non-Gaussian Likelihood Approximations" + "github/teamPSG/kNN_Sleep_Scorer_kNNSS": { + "id": "github/teamPSG/kNN_Sleep_Scorer_kNNSS", + "title": "github/teamPSG/kNN_Sleep_Scorer_kNNSS", + "url": " https://rseng.github.io/software/repository/github/teamPSG/kNN_Sleep_Scorer_kNNSS", + "content": "A matlab package for automated sleep scoring using the k-nearest neighbors algorithm" }, - "github/natelust/least_asymmetry": { - "id": "github/natelust/least_asymmetry", - "title": "github/natelust/least_asymmetry", - "url": " https://rseng.github.io/software/repository/github/natelust/least_asymmetry", - "content": "This code is to find the center of a distribution of light in an image using the least asymmetry method. The code also contains center of light and fitting a Gaussian routines as well. All functions are designed to take optional weights" + "github/ChrisBeaumont/brut": { + "id": "github/ChrisBeaumont/brut", + "title": "github/ChrisBeaumont/brut", + "url": " https://rseng.github.io/software/repository/github/ChrisBeaumont/brut", + "content": "Machine Learning on the Milky Way Project DR1" }, - "github/qpv-research-group/solcore5": { - "id": "github/qpv-research-group/solcore5", - "title": "github/qpv-research-group/solcore5", - "url": " https://rseng.github.io/software/repository/github/qpv-research-group/solcore5", - "content": "A multi-scale, python-based library for the modelling of solar cells and semiconductor materials" + "github/JonasRieger/ldaPrototype": { + "id": "github/JonasRieger/ldaPrototype", + "title": "github/JonasRieger/ldaPrototype", + "url": " https://rseng.github.io/software/repository/github/JonasRieger/ldaPrototype", + "content": "Determine a Prototype from a number of runs of Latent Dirichlet Allocation (LDA) measuring its similarities with S-CLOP: A procedure to select the LDA run with highest mean pairwise similarity, which is measured by S-CLOP (Similarity of multiple sets by Clustering with Local Pruning), to all other runs." }, - "github/neuroneural/brainchop": { - "id": "github/neuroneural/brainchop", - "title": "github/neuroneural/brainchop", - "url": " https://rseng.github.io/software/repository/github/neuroneural/brainchop", - "content": "Brainchop: In-browser 3D MRI rendering and segmentation" + "github/pyranges/pyrle": { + "id": "github/pyranges/pyrle", + "title": "github/pyranges/pyrle", + "url": " https://rseng.github.io/software/repository/github/pyranges/pyrle", + "content": "Numerical Run Length Encoding and Arithmetic in Cython" }, - "github/nanoporetech/scrappie": { - "id": "github/nanoporetech/scrappie", - "title": "github/nanoporetech/scrappie", - "url": " https://rseng.github.io/software/repository/github/nanoporetech/scrappie", - "content": "Scrappie is a technology demonstrator for the Oxford Nanopore Research Algorithms group" + "github/AMReX-Combustion/PeleLMeX": { + "id": "github/AMReX-Combustion/PeleLMeX", + "title": "github/AMReX-Combustion/PeleLMeX", + "url": " https://rseng.github.io/software/repository/github/AMReX-Combustion/PeleLMeX", + "content": "An adaptive mesh hydrodynamics simulation code for low Mach number reacting flows without level sub-cycling." }, - "github/nanoporetech/qcat": { - "id": "github/nanoporetech/qcat", - "title": "github/nanoporetech/qcat", - "url": " https://rseng.github.io/software/repository/github/nanoporetech/qcat", - "content": " qcat is a Python command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files." + "github/jonaselgammal/GPry": { + "id": "github/jonaselgammal/GPry", + "title": "github/jonaselgammal/GPry", + "url": " https://rseng.github.io/software/repository/github/jonaselgammal/GPry", + "content": "A Package for Bayesian inference of expensive likelihoods with Gaussian Processes" }, - "github/nanoporetech/pychopper": { - "id": "github/nanoporetech/pychopper", - "title": "github/nanoporetech/pychopper", - "url": " https://rseng.github.io/software/repository/github/nanoporetech/pychopper", - "content": "A tool to identify, orient, trim and rescue full length cDNA reads" + "github/hallamlab/TreeSAPP": { + "id": "github/hallamlab/TreeSAPP", + "title": "github/hallamlab/TreeSAPP", + "url": " https://rseng.github.io/software/repository/github/hallamlab/TreeSAPP", + "content": "A Python package for gene-centric taxonomic and functional classification using phylogenetic placement" }, - "github/nanoporetech/medaka": { - "id": "github/nanoporetech/medaka", - "title": "github/nanoporetech/medaka", - "url": " https://rseng.github.io/software/repository/github/nanoporetech/medaka", - "content": "Sequence correction provided by ONT Research" + "github/Dfupa/meTAline": { + "id": "github/Dfupa/meTAline", + "title": "github/Dfupa/meTAline", + "url": " https://rseng.github.io/software/repository/github/Dfupa/meTAline", + "content": "WGS pipeline implementation in Snakemake" }, - "github/nanoporetech/pinfish": { - "id": "github/nanoporetech/pinfish", - "title": "github/nanoporetech/pinfish", - "url": " https://rseng.github.io/software/repository/github/nanoporetech/pinfish", - "content": "Tools to annotate genomes using long read transcriptomics data" + "github/nextflow-io/nextflow": { + "id": "github/nextflow-io/nextflow", + "title": "github/nextflow-io/nextflow", + "url": " https://rseng.github.io/software/repository/github/nextflow-io/nextflow", + "content": "A DSL for data-driven computational pipelines" }, - "github/nanoporetech/tombo": { - "id": "github/nanoporetech/tombo", - "title": "github/nanoporetech/tombo", - "url": " https://rseng.github.io/software/repository/github/nanoporetech/tombo", - "content": "Tombo is a suite of tools primarily for the identification of modified nucleotides from raw nanopore sequencing data. " + "github/tool-bin/ukbcc": { + "id": "github/tool-bin/ukbcc", + "title": "github/tool-bin/ukbcc", + "url": " https://rseng.github.io/software/repository/github/tool-bin/ukbcc", + "content": "UKBB Cohort Curator. " }, - "github/nanoporetech/pomoxis": { - "id": "github/nanoporetech/pomoxis", - "title": "github/nanoporetech/pomoxis", - "url": " https://rseng.github.io/software/repository/github/nanoporetech/pomoxis", - "content": "Analysis components from Oxford Nanopore Research" + "github/mirnylab/cooler": { + "id": "github/mirnylab/cooler", + "title": "github/mirnylab/cooler", + "url": " https://rseng.github.io/software/repository/github/mirnylab/cooler", + "content": "is a support library for a sparse, compressed, binary persistent storage format, also called cooler, used to store genomic interaction data, such as Hi-C contact matrices." }, - "github/nanoporetech/megalodon": { - "id": "github/nanoporetech/megalodon", - "title": "github/nanoporetech/megalodon", - "url": " https://rseng.github.io/software/repository/github/nanoporetech/megalodon", - "content": " Megalodon is a research command line tool to extract high accuracy modified base and sequence variant calls from raw nanopore reads by anchoring the information rich basecalling neural network output to a reference genome/transriptome." + "github/mirnylab/pairtools": { + "id": "github/mirnylab/pairtools", + "title": "github/mirnylab/pairtools", + "url": " https://rseng.github.io/software/repository/github/mirnylab/pairtools", + "content": "CLI tools to process mapped Hi-C data" }, - 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"github/natir/rustyread": { - "id": "github/natir/rustyread", - "title": "github/natir/rustyread", - "url": " https://rseng.github.io/software/repository/github/natir/rustyread", - "content": "A long read simulator based on badread idea" + "github/ECP-WarpX/WarpX": { + "id": "github/ECP-WarpX/WarpX", + "title": "github/ECP-WarpX/WarpX", + "url": " https://rseng.github.io/software/repository/github/ECP-WarpX/WarpX", + "content": "WarpX is an advanced, time-based electromagnetic & electrostatic Particle-In-Cell code." }, - "github/CGATOxford/UMI-tools": { - "id": "github/CGATOxford/UMI-tools", - "title": "github/CGATOxford/UMI-tools", - "url": " https://rseng.github.io/software/repository/github/CGATOxford/UMI-tools", - "content": "Tools for handling Unique Molecular Identifiers in NGS data sets" + "github/sdnjly/WSDL-AD": { + "id": "github/sdnjly/WSDL-AD", + "title": "github/sdnjly/WSDL-AD", + "url": " https://rseng.github.io/software/repository/github/sdnjly/WSDL-AD", + "content": "None" }, - "github/hfarias/mask_galaxy": { - "id": "github/hfarias/mask_galaxy", - "title": "github/hfarias/mask_galaxy", - "url": " https://rseng.github.io/software/repository/github/hfarias/mask_galaxy", - "content": "Morphological segmentation of Galaxies" + "github/Schulik/aiolos": { + "id": "github/Schulik/aiolos", + "title": "github/Schulik/aiolos", + "url": " https://rseng.github.io/software/repository/github/Schulik/aiolos", + "content": "1-D hydrodynamics code for planetary atmosphere accretion and escape simulations" }, - "github/lbcb-sci/graphmap2": { - "id": "github/lbcb-sci/graphmap2", - "title": "github/lbcb-sci/graphmap2", - "url": " https://rseng.github.io/software/repository/github/lbcb-sci/graphmap2", - "content": "GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1" + "github/mfem/mfem": { + "id": "github/mfem/mfem", + "title": "github/mfem/mfem", + "url": " https://rseng.github.io/software/repository/github/mfem/mfem", + "content": "Lightweight, general, scalable C++ library for finite element methods" }, - "github/lbcb-sci/raven": { - "id": "github/lbcb-sci/raven", - "title": "github/lbcb-sci/raven", - "url": " https://rseng.github.io/software/repository/github/lbcb-sci/raven", - "content": "De novo genome assembler for long uncorrected reads" + "github/C0PEP0D/otto": { + "id": "github/C0PEP0D/otto", + "title": "github/C0PEP0D/otto", + "url": " https://rseng.github.io/software/repository/github/C0PEP0D/otto", + "content": "a Python package to simulate, solve and visualize the source-tracking POMDP" }, - "github/lbcb-sci/racon": { - "id": "github/lbcb-sci/racon", - "title": "github/lbcb-sci/racon", - "url": " https://rseng.github.io/software/repository/github/lbcb-sci/racon", - "content": "Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads" + "github/spokenlanguage/platalea": { + "id": "github/spokenlanguage/platalea", + "title": "github/spokenlanguage/platalea", + "url": " https://rseng.github.io/software/repository/github/spokenlanguage/platalea", + "content": "Library for training visually-grounded models of spoken language understanding." }, - 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Solves for the orbital elements of any single companion, provided observed radial velocity and/or astrometry." }, - "github/c-zhou/yahs": { - "id": "github/c-zhou/yahs", - "title": "github/c-zhou/yahs", - "url": " https://rseng.github.io/software/repository/github/c-zhou/yahs", - "content": "Yet another Hi-C scaffolding tool" + "github/mkplummer/Imber": { + "id": "github/mkplummer/Imber", + "title": "github/mkplummer/Imber", + "url": " https://rseng.github.io/software/repository/github/mkplummer/Imber", + "content": "Python module for both numerical simulation of stellar/substellar surfaces and fitting the resulting spectral line profiles and photometric light curves with analytical models." }, - "github/mayuresh159/starsense_algorithms": { - "id": "github/mayuresh159/starsense_algorithms", - "title": "github/mayuresh159/starsense_algorithms", - "url": " https://rseng.github.io/software/repository/github/mayuresh159/starsense_algorithms", - "content": "This is a software package for testing and performance evaluation of different star sensors. The algorithms used for calculating quaternions from star field images are : centroiding, geometric voting and QUEST algorithms. The physical parameters of a star sensor are parametrized and by changing these parameters various performance estimators like sky coverage, memory requirement, timing requirements etc can be estimated for the selected star sensor. 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educational drug dosing app for treatment of high blood pressure" }, - "github/OP2/PyOP2": { - "id": "github/OP2/PyOP2", - "title": "github/OP2/PyOP2", - "url": " https://rseng.github.io/software/repository/github/OP2/PyOP2", - "content": "Framework for performance-portable parallel computations on unstructured meshes" + "github/gdalle/HiddenMarkovModels.jl": { + "id": "github/gdalle/HiddenMarkovModels.jl", + "title": "github/gdalle/HiddenMarkovModels.jl", + "url": " https://rseng.github.io/software/repository/github/gdalle/HiddenMarkovModels.jl", + "content": "A Julia package for simulation, inference and learning of Hidden Markov Models." }, - "github/AemulusProject/bias_emulator": { - "id": "github/AemulusProject/bias_emulator", - "title": "github/AemulusProject/bias_emulator", - "url": " https://rseng.github.io/software/repository/github/AemulusProject/bias_emulator", - "content": "Emulator for the halo bias from The Aemulus Project." + "github/Social-Evolution-and-Behavior/anTraX": { + "id": "github/Social-Evolution-and-Behavior/anTraX", + "title": "github/Social-Evolution-and-Behavior/anTraX", + "url": " https://rseng.github.io/software/repository/github/Social-Evolution-and-Behavior/anTraX", + "content": "anTraX: high throughput tracking of color-tagged insects" }, - "github/mikaelLEROY/AxionNS_RayTracing": { - "id": "github/mikaelLEROY/AxionNS_RayTracing", - "title": "github/mikaelLEROY/AxionNS_RayTracing", - "url": " https://rseng.github.io/software/repository/github/mikaelLEROY/AxionNS_RayTracing", - "content": "None" + "github/darrencroton/sage": { + "id": "github/darrencroton/sage", + "title": "github/darrencroton/sage", + "url": " https://rseng.github.io/software/repository/github/darrencroton/sage", + "content": "Home of the Semi-Analytic Galaxy Evolution (SAGE) galaxy formation model" }, - "github/nkallima/sim-universal-construction": { - "id": "github/nkallima/sim-universal-construction", - "title": "github/nkallima/sim-universal-construction", - "url": " https://rseng.github.io/software/repository/github/nkallima/sim-universal-construction", - "content": "An open-source framework for concurrent data-structures and benchmarks. " + "github/HWang-Summit/HCGrid": { + "id": "github/HWang-Summit/HCGrid", + "title": "github/HWang-Summit/HCGrid", + "url": " https://rseng.github.io/software/repository/github/HWang-Summit/HCGrid", + "content": "HCGrid is a convolution-based gridding framework for radio astronomy on hybrid computing environments" }, - "github/slzarate/parliament2": { - "id": "github/slzarate/parliament2", - "title": "github/slzarate/parliament2", - "url": " https://rseng.github.io/software/repository/github/slzarate/parliament2", - "content": "Runs a combination of tools to generate structural variant calls on short-read whole-genome sequencing data" + "github/rzellem/EXOTIC": { + "id": "github/rzellem/EXOTIC", + "title": "github/rzellem/EXOTIC", + "url": " https://rseng.github.io/software/repository/github/rzellem/EXOTIC", + "content": "EXOplanet Transit Interpretation Code" }, - "github/jaimerzp/limberjack.jl": { - "id": "github/jaimerzp/limberjack.jl", - "title": "github/jaimerzp/limberjack.jl", - "url": " https://rseng.github.io/software/repository/github/jaimerzp/limberjack.jl", - "content": "Auto-differentiable methods for Cosmology" + "github/dask/dask": { + "id": "github/dask/dask", + "title": "github/dask/dask", + "url": " https://rseng.github.io/software/repository/github/dask/dask", + "content": "Parallel computing with task scheduling" }, - "github/SCECcode/pycsep": { - "id": "github/SCECcode/pycsep", - "title": "github/SCECcode/pycsep", - "url": " https://rseng.github.io/software/repository/github/SCECcode/pycsep", - "content": "Tools to help earthquake forecast model developers build and evaluate their forecasts" + "github/RangamaniLabUCSD/smart": { + "id": "github/RangamaniLabUCSD/smart", + "title": "github/RangamaniLabUCSD/smart", + "url": " https://rseng.github.io/software/repository/github/RangamaniLabUCSD/smart", + "content": "None" }, - "github/wjakethompson/measr": { - "id": "github/wjakethompson/measr", - "title": "github/wjakethompson/measr", - "url": " https://rseng.github.io/software/repository/github/wjakethompson/measr", - "content": "R package for the Bayesian estimation of diagnostic classification models using Stan" + "github/locasto/libdisorder": { + "id": "github/locasto/libdisorder", + "title": "github/locasto/libdisorder", + "url": " https://rseng.github.io/software/repository/github/locasto/libdisorder", + "content": "A simple C library for entropy measurement of byte streams and other data." }, - "github/OpenDA-Association/OpenDA": { - "id": "github/OpenDA-Association/OpenDA", - "title": "github/OpenDA-Association/OpenDA", - "url": " https://rseng.github.io/software/repository/github/OpenDA-Association/OpenDA", - "content": "Open data assimilation toolbox" + "github/GoelandProver/Goeland": { + "id": "github/GoelandProver/Goeland", + "title": "github/GoelandProver/Goeland", + "url": " https://rseng.github.io/software/repository/github/GoelandProver/Goeland", + "content": "A first-order concurrent automated theorem prover" }, - "github/plazar/coast_guard": { - "id": "github/plazar/coast_guard", - "title": "github/plazar/coast_guard", - "url": " https://rseng.github.io/software/repository/github/plazar/coast_guard", - "content": "A python/PSRCHIVE-based timing pipeline for reducing Effelsberg data." + "github/BU-hammerTeam/PyHammer": { + "id": "github/BU-hammerTeam/PyHammer", + "title": "github/BU-hammerTeam/PyHammer", + "url": " https://rseng.github.io/software/repository/github/BU-hammerTeam/PyHammer", + "content": "A Python Spectral Typing Suite" }, - "github/plazar/TOASTER": { - "id": "github/plazar/TOASTER", - "title": "github/plazar/TOASTER", - "url": " https://rseng.github.io/software/repository/github/plazar/TOASTER", - "content": "A framework for generating, storing and tracking high-precision TOAs for PTAs as well as observation meta data and processing details." + "github/HajimeKawahara/exojax": { + "id": "github/HajimeKawahara/exojax", + "title": "github/HajimeKawahara/exojax", + "url": " https://rseng.github.io/software/repository/github/HajimeKawahara/exojax", + "content": "🐈 Automatic differentiable spectrum modeling of exoplanets/brown dwarfs using JAX, compatible with NumPyro and JAXopt" }, - 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"github/bmorris3/aesop": { - "id": "github/bmorris3/aesop", - "title": "github/bmorris3/aesop", - "url": " https://rseng.github.io/software/repository/github/bmorris3/aesop", - "content": "ARC Echelle Spectroscopic Observation Pipeline (aesop)" + "github/RudolfCardinal/camcops": { + "id": "github/RudolfCardinal/camcops", + "title": "github/RudolfCardinal/camcops", + "url": " https://rseng.github.io/software/repository/github/RudolfCardinal/camcops", + "content": "Cambridge Cognitive and Psychiatric Test Kit (CamCOPS)" }, - "github/alesantuz/musclesyneRgies": { - "id": "github/alesantuz/musclesyneRgies", - "title": "github/alesantuz/musclesyneRgies", - "url": " https://rseng.github.io/software/repository/github/alesantuz/musclesyneRgies", - "content": "R package to extract muscle synergies from electromyogram" + "github/adriancorrendo/metrica": { + "id": "github/adriancorrendo/metrica", + "title": "github/adriancorrendo/metrica", + "url": " https://rseng.github.io/software/repository/github/adriancorrendo/metrica", + "content": "Prediction Performance Metrics" }, - "github/daddeptr/Needlets": { - "id": "github/daddeptr/Needlets", - "title": "github/daddeptr/Needlets", - "url": " https://rseng.github.io/software/repository/github/daddeptr/Needlets", + "github/ngbusca/QuasarNET": { + "id": "github/ngbusca/QuasarNET", + "title": "github/ngbusca/QuasarNET", + "url": " https://rseng.github.io/software/repository/github/ngbusca/QuasarNET", "content": "None" }, - "github/vinisalazar/metaphor": { - "id": "github/vinisalazar/metaphor", - "title": "github/vinisalazar/metaphor", - "url": " https://rseng.github.io/software/repository/github/vinisalazar/metaphor", - "content": "Metaphor: a general-purpose workflow for assembly and binning of metagenomes" - }, - "github/Basvanstein/GSAreport": { - "id": "github/Basvanstein/GSAreport", - "title": "github/Basvanstein/GSAreport", - "url": " https://rseng.github.io/software/repository/github/Basvanstein/GSAreport", - "content": "Global Sensitivity reporting for Explainable AI" + "github/JelfsMaterialsGroup/stk": { + "id": "github/JelfsMaterialsGroup/stk", + "title": "github/JelfsMaterialsGroup/stk", + "url": " https://rseng.github.io/software/repository/github/JelfsMaterialsGroup/stk", + "content": "Mirror of lukasturcani/stk - please file issues / fork / star that repo. " }, - "github/skiehl/polarizationtools": { - "id": "github/skiehl/polarizationtools", - "title": "github/skiehl/polarizationtools", - "url": " https://rseng.github.io/software/repository/github/skiehl/polarizationtools", - "content": "Tools to deal with astrophysical polarization data in python3" + "github/biod/sambamba": { + "id": "github/biod/sambamba", + "title": "github/biod/sambamba", + "url": " https://rseng.github.io/software/repository/github/biod/sambamba", + "content": "Tools for working with SAM/BAM data" }, - "github/skiehl/wwz": { - "id": "github/skiehl/wwz", - "title": "github/skiehl/wwz", - "url": " https://rseng.github.io/software/repository/github/skiehl/wwz", - "content": "Weighted wavelet z-transform (WWZ) analysis package" + "github/diCenzo-GC/Tn-Core-webserver": { + "id": "github/diCenzo-GC/Tn-Core-webserver", + "title": "github/diCenzo-GC/Tn-Core-webserver", + "url": " https://rseng.github.io/software/repository/github/diCenzo-GC/Tn-Core-webserver", + "content": "Help files and sample data for the Tn-Core webserver. The code supporting the web server is also included." }, - "github/skiehl/lcsim": { - "id": "github/skiehl/lcsim", - "title": "github/skiehl/lcsim", - "url": " https://rseng.github.io/software/repository/github/skiehl/lcsim", - "content": "Blazar light curve simulation package" + "github/MRChemSoft/mrchem": { + "id": "github/MRChemSoft/mrchem", + "title": "github/MRChemSoft/mrchem", + "url": " https://rseng.github.io/software/repository/github/MRChemSoft/mrchem", + "content": "MultiResolution Chemistry" }, - "github/mikessh/oncofuse": { - "id": "github/mikessh/oncofuse", - "title": "github/mikessh/oncofuse", - "url": " https://rseng.github.io/software/repository/github/mikessh/oncofuse", - "content": "Predicting oncogenic potential of gene fusions" + "github/jkimlab/msPIPE": { + "id": "github/jkimlab/msPIPE", + "title": "github/jkimlab/msPIPE", + "url": " https://rseng.github.io/software/repository/github/jkimlab/msPIPE", + "content": "None" }, - "github/mikessh/vdjtools": { - "id": "github/mikessh/vdjtools", - "title": "github/mikessh/vdjtools", - "url": " https://rseng.github.io/software/repository/github/mikessh/vdjtools", - "content": "Post-analysis of immune repertoire sequencing data" + "github/nextstrain/nextclade": { + "id": "github/nextstrain/nextclade", + "title": "github/nextstrain/nextclade", + "url": " https://rseng.github.io/software/repository/github/nextstrain/nextclade", + "content": "Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement" }, - "github/streamlit/streamlit": { - "id": "github/streamlit/streamlit", - "title": "github/streamlit/streamlit", - "url": " https://rseng.github.io/software/repository/github/streamlit/streamlit", - "content": "Streamlit — The fastest way to build data apps in Python" + "github/nextstrain/auspice": { + "id": "github/nextstrain/auspice", + "title": "github/nextstrain/auspice", + "url": " https://rseng.github.io/software/repository/github/nextstrain/auspice", + "content": "Web app for visualizing pathogen evolution" }, - "github/yair111/AnalyticLC": { - "id": "github/yair111/AnalyticLC", - "title": "github/yair111/AnalyticLC", - "url": " https://rseng.github.io/software/repository/github/yair111/AnalyticLC", - "content": "None" + "github/nextstrain/augur": { + "id": "github/nextstrain/augur", + "title": "github/nextstrain/augur", + "url": " https://rseng.github.io/software/repository/github/nextstrain/augur", + "content": "Pipeline components for real-time phylodynamic analysis" }, - "github/rudolffu/pyfosc": { - "id": "github/rudolffu/pyfosc", - "title": "github/rudolffu/pyfosc", - "url": " https://rseng.github.io/software/repository/github/rudolffu/pyfosc", - "content": "PyFOSC is a pipeline toolbox for spectroscopic data reduction written in Python. It can be used for FOSC data from Xinglong/Lijiang 2-meter telescopes." + "github/arabic-digital-humanities/adhtools": { + "id": "github/arabic-digital-humanities/adhtools", + "title": "github/arabic-digital-humanities/adhtools", + "url": " https://rseng.github.io/software/repository/github/arabic-digital-humanities/adhtools", + "content": "Scripts for manipulating Arabic texts" }, - "github/Starlink/starjava": { - "id": "github/Starlink/starjava", - "title": "github/Starlink/starjava", - "url": " https://rseng.github.io/software/repository/github/Starlink/starjava", - "content": "Java applications initially developed for the Starlink Project but now developed independently" + "github/remi-adam/minot": { + "id": "github/remi-adam/minot", + "title": "github/remi-adam/minot", + "url": " https://rseng.github.io/software/repository/github/remi-adam/minot", + "content": "minot: Modeling of the ICM (Non-)thermal content and Observables prediction Tools" }, - "github/Starlink/aspic": { - "id": "github/Starlink/aspic", - "title": "github/Starlink/aspic", - "url": " https://rseng.github.io/software/repository/github/Starlink/aspic", - "content": "Starlink Image processing programs from the 1980s" + "github/webbjj/m2mcluster": { + "id": "github/webbjj/m2mcluster", + "title": "github/webbjj/m2mcluster", + "url": " https://rseng.github.io/software/repository/github/webbjj/m2mcluster", + "content": "A code for made to measure modelling of star clusters" }, - "github/Starlink/ORAC-DR": { - "id": "github/Starlink/ORAC-DR", - "title": "github/Starlink/ORAC-DR", - "url": " https://rseng.github.io/software/repository/github/Starlink/ORAC-DR", - "content": "The ORAC-DR astronomy data reduction pipeline" + "github/webbjj/clustertools": { + "id": "github/webbjj/clustertools", + "title": "github/webbjj/clustertools", + "url": " https://rseng.github.io/software/repository/github/webbjj/clustertools", + "content": "A Python package with tools for analysing star clusters." }, - "github/Starlink/pal": { - "id": "github/Starlink/pal", - "title": "github/Starlink/pal", - "url": " https://rseng.github.io/software/repository/github/Starlink/pal", - "content": "Positional Astronomy Library" + "github/valeriabonapersona/repair": { + "id": "github/valeriabonapersona/repair", + "title": "github/valeriabonapersona/repair", + "url": " https://rseng.github.io/software/repository/github/valeriabonapersona/repair", + "content": "Reduction from Prior Animal Informed Research" }, - "github/Starlink/hds-v5": { - "id": "github/Starlink/hds-v5", - "title": "github/Starlink/hds-v5", - "url": " https://rseng.github.io/software/repository/github/Starlink/hds-v5", - "content": "HDS API implemented using HDF5" + "github/aconley/simple_cosfitter": { + "id": "github/aconley/simple_cosfitter", + "title": "github/aconley/simple_cosfitter", + "url": " https://rseng.github.io/software/repository/github/aconley/simple_cosfitter", + "content": "Grid based SN cosmology fitting code" }, - "github/Starlink/starlink": { - "id": "github/Starlink/starlink", - "title": "github/Starlink/starlink", - "url": " https://rseng.github.io/software/repository/github/Starlink/starlink", - "content": "Starlink Software Collection" + "github/aconley/mbb_emcee": { + "id": "github/aconley/mbb_emcee", + "title": "github/aconley/mbb_emcee", + "url": " https://rseng.github.io/software/repository/github/aconley/mbb_emcee", + "content": "Modified blackbody MCMC code" }, - "github/Starlink/perl-Starlink-Autoastrom": { - "id": "github/Starlink/perl-Starlink-Autoastrom", - "title": "github/Starlink/perl-Starlink-Autoastrom", - "url": " https://rseng.github.io/software/repository/github/Starlink/perl-Starlink-Autoastrom", - "content": "Starlink Auto astrometry software" + "github/vimc/dettl": { + "id": "github/vimc/dettl", + "title": "github/vimc/dettl", + "url": " https://rseng.github.io/software/repository/github/vimc/dettl", + "content": ":bar_chart::shower: Data extract, transform, test and load" }, - "github/DrDaveShaw/INCHEM-Py": { - "id": "github/DrDaveShaw/INCHEM-Py", - "title": "github/DrDaveShaw/INCHEM-Py", - "url": " https://rseng.github.io/software/repository/github/DrDaveShaw/INCHEM-Py", - "content": "The INdoor CHEMical model in Python (INCHEM-Py) is an open source and accessible box-model built to give researchers deeper insight into the chemical mechanisms behind indoor air chemistry." + "github/vimc/orderly": { + "id": "github/vimc/orderly", + "title": "github/vimc/orderly", + "url": " https://rseng.github.io/software/repository/github/vimc/orderly", + "content": ":hospital::ambulance: Lightweight Reproducible Reporting for R" }, - "github/vterron/lemon": { - "id": "github/vterron/lemon", - "title": "github/vterron/lemon", - "url": " https://rseng.github.io/software/repository/github/vterron/lemon", - "content": "Differential photometry for humans (and astronomers)" + "github/vimc/vaultr": { + "id": "github/vimc/vaultr", + "title": "github/vimc/vaultr", + "url": " https://rseng.github.io/software/repository/github/vimc/vaultr", + "content": ":lock: API client for Hashicorp's vault (https://www.vaultproject.io/)" }, - "github/csabiu/kstat": { - "id": "github/csabiu/kstat", - "title": "github/csabiu/kstat", - "url": " https://rseng.github.io/software/repository/github/csabiu/kstat", - "content": "Fast KD-tree MPI correlation statistics package - Author: Cristiano Sabiu" + "github/migp11/pyfastcore": { + "id": "github/migp11/pyfastcore", + "title": "github/migp11/pyfastcore", + "url": " https://rseng.github.io/software/repository/github/migp11/pyfastcore", + "content": "A python implementation of the context-specific model extraction method FastCore by Vlassis et al. (2014)." }, - "github/toddy15/medicalterms": { - "id": "github/toddy15/medicalterms", - "title": "github/toddy15/medicalterms", - "url": " https://rseng.github.io/software/repository/github/toddy15/medicalterms", - "content": "German medical dictionary words" + "github/pilon/wiki": { + "id": "github/pilon/wiki", + "title": "github/pilon/wiki", + "url": " https://rseng.github.io/software/repository/github/pilon/wiki", + "content": "Pilon is a software tool which can be used to automatically improve draft assemblies and find variation among strains, including large event detection." }, - "github/gdefazio/kMetaShot": { - "id": "github/gdefazio/kMetaShot", - "title": "github/gdefazio/kMetaShot", - "url": " https://rseng.github.io/software/repository/github/gdefazio/kMetaShot", - "content": "None" + "github/weizhongli/cdhit": { + "id": "github/weizhongli/cdhit", + "title": "github/weizhongli/cdhit", + "url": " https://rseng.github.io/software/repository/github/weizhongli/cdhit", + "content": "clusters and compares protein or nucleotide sequences." }, - "github/Ouranosinc/xclim": { - "id": "github/Ouranosinc/xclim", - "title": "github/Ouranosinc/xclim", - "url": " https://rseng.github.io/software/repository/github/Ouranosinc/xclim", - "content": "Library of derived climate variables, ie climate indicators, based on xarray. " + "github/alphaparrot/ExoPlaSim": { + "id": "github/alphaparrot/ExoPlaSim", + "title": "github/alphaparrot/ExoPlaSim", + "url": " https://rseng.github.io/software/repository/github/alphaparrot/ExoPlaSim", + "content": "Exoplanet Planet Simulator (PlaSim extended for different planet types (including tidally-locked) and evolution on geological timescales--glaciers and carbon cycle)" }, - "github/cheerfuluser/tessreduce": { - "id": "github/cheerfuluser/tessreduce", - "title": "github/cheerfuluser/tessreduce", - "url": " https://rseng.github.io/software/repository/github/cheerfuluser/tessreduce", - "content": "Transient focused reduction for TESS data" + "github/Glogobyte/miRGalaxy": { + "id": "github/Glogobyte/miRGalaxy", + "title": "github/Glogobyte/miRGalaxy", + "url": " https://rseng.github.io/software/repository/github/Glogobyte/miRGalaxy", + "content": "miRGalaxy: a Galaxy‑based framework for interactive analysis of microRNA and isomiR sequencing data" }, - "github/nasa/K2CE": { - "id": "github/nasa/K2CE", - "title": "github/nasa/K2CE", - "url": " https://rseng.github.io/software/repository/github/nasa/K2CE", - "content": "Kepler K2 Cadence Events (K2CE) is a Python data visualization and manipulation tool for astronomers to identify and remove cadences (observations) associated with problematic thruster events, thus producing cleaner light curves. K2CE was designed to work with standard Kepler or K2 data products: long-cadence (30 min) and short-cadence (1 min) light curve files and long-cadence and short-cadence target pixel files. The tool has been modified to work with light curve files and target pixel files from the TESS mission." + "github/benhid/Sequoya": { + "id": "github/benhid/Sequoya", + "title": "github/benhid/Sequoya", + "url": " https://rseng.github.io/software/repository/github/benhid/Sequoya", + "content": "Solving Multiple Sequence Alignment (MSA) problems with multi-objective metaheuristics" }, - "github/nasa/prog_models": { - "id": "github/nasa/prog_models", - "title": "github/nasa/prog_models", - "url": " https://rseng.github.io/software/repository/github/nasa/prog_models", - "content": "The NASA Prognostic Model Package is a Python framework focused on defining and building models for prognostics (computation of remaining useful life) of engineering systems, and provides a set of prognostics models for select components developed within this framework, suitable for use in prognostics applications for these components." + "github/pelican/pelican": { + "id": "github/pelican/pelican", + "title": "github/pelican/pelican", + "url": " https://rseng.github.io/software/repository/github/pelican/pelican", + "content": "Pipeline for Extensible Lightweight Imaging and CAlibratioN" }, - "github/nasa/kepler-robovetter": { - "id": "github/nasa/kepler-robovetter", - "title": "github/nasa/kepler-robovetter", - "url": " https://rseng.github.io/software/repository/github/nasa/kepler-robovetter", - "content": "None" + "github/DataBiosphere/wdl-parsers": { + "id": "github/DataBiosphere/wdl-parsers", + "title": "github/DataBiosphere/wdl-parsers", + "url": " https://rseng.github.io/software/repository/github/DataBiosphere/wdl-parsers", + "content": "A package that provides the generated ANTLR4 WDL parsers for Python." }, - "github/nasa/KeplerPORTs": { - "id": "github/nasa/KeplerPORTs", - "title": "github/nasa/KeplerPORTs", - "url": " https://rseng.github.io/software/repository/github/nasa/KeplerPORTs", - "content": "None" + "github/PaulRitsche/DLTrack": { + "id": "github/PaulRitsche/DLTrack", + "title": "github/PaulRitsche/DLTrack", + "url": " https://rseng.github.io/software/repository/github/PaulRitsche/DLTrack", + "content": "This repositories contains code for automatic analysis of human lower limb ultrasonography images." }, - "github/nasa/simupy-flight": { - "id": "github/nasa/simupy-flight", - "title": "github/nasa/simupy-flight", - "url": " https://rseng.github.io/software/repository/github/nasa/simupy-flight", - "content": "None" + "github/zizroc/villager": { + "id": "github/zizroc/villager", + "title": "github/zizroc/villager", + "url": " https://rseng.github.io/software/repository/github/zizroc/villager", + "content": "villager is an extensible agent based modeling (ABM) framework for the R language. It supports agents, agent aggregations and their associated resources, as well as flexible data management." }, - "github/gpantel/MolPainter": { - "id": "github/gpantel/MolPainter", - "title": "github/gpantel/MolPainter", - "url": " https://rseng.github.io/software/repository/github/gpantel/MolPainter", - "content": "A Tool for Drawing Complex Planar Molecular Systems of Arbitrary Composition and Placement" + "github/ester-project/ester": { + "id": "github/ester-project/ester", + "title": "github/ester-project/ester", + "url": " https://rseng.github.io/software/repository/github/ester-project/ester", + "content": "Evolution STEllaire en Rotation." }, - "github/vsoch/gridtest": { - "id": "github/vsoch/gridtest", - "title": "github/vsoch/gridtest", - "url": " https://rseng.github.io/software/repository/github/vsoch/gridtest", - "content": "grid parameters and testing for Python modules and functions" + "github/mikejohnson51/AHGestimation": { + "id": "github/mikejohnson51/AHGestimation", + "title": "github/mikejohnson51/AHGestimation", + "url": " https://rseng.github.io/software/repository/github/mikejohnson51/AHGestimation", + "content": "Estimating robust, mass conserving AHG relationships" }, - "github/vsoch/citelang": { - "id": "github/vsoch/citelang", - "title": "github/vsoch/citelang", - "url": " https://rseng.github.io/software/repository/github/vsoch/citelang", - "content": "markdown syntax and credit system for software!" + "github/SeaIce-Math/SubZero": { + "id": "github/SeaIce-Math/SubZero", + "title": "github/SeaIce-Math/SubZero", + "url": " https://rseng.github.io/software/repository/github/SeaIce-Math/SubZero", + "content": "Discrete element sea ice model" }, - "github/gxiaolab/scAllele": { - "id": "github/gxiaolab/scAllele", - "title": "github/gxiaolab/scAllele", - "url": " https://rseng.github.io/software/repository/github/gxiaolab/scAllele", - "content": "scAllele is a versatile tool to detect and analyze nucleotide variants in scRNA-seq." + "github/zhangrengang/SubPhaser": { + "id": "github/zhangrengang/SubPhaser", + "title": "github/zhangrengang/SubPhaser", + "url": " https://rseng.github.io/software/repository/github/zhangrengang/SubPhaser", + "content": "Phase and visualize subgenomes of an allopolyploid or hybrid based on the repetitive kmers." }, - "github/mrtommyb/ktransit": { - "id": "github/mrtommyb/ktransit", - "title": "github/mrtommyb/ktransit", - "url": " https://rseng.github.io/software/repository/github/mrtommyb/ktransit", - "content": "A simple exoplanet transit modeling tool in python" + "github/BaroudLab/Griottes": { + "id": "github/BaroudLab/Griottes", + "title": "github/BaroudLab/Griottes", + "url": " https://rseng.github.io/software/repository/github/BaroudLab/Griottes", + "content": "Python program to generate NetworkX graphs from segmented images." }, - "github/HajkD/LTRpred": { - "id": "github/HajkD/LTRpred", - "title": "github/HajkD/LTRpred", - "url": " https://rseng.github.io/software/repository/github/HajkD/LTRpred", - "content": "De novo annotation of intact retrotransposons" + "github/pysat/pysat": { + "id": "github/pysat/pysat", + "title": "github/pysat/pysat", + "url": " https://rseng.github.io/software/repository/github/pysat/pysat", + "content": "Generalized satellite and space science data processing and file management. " }, - "github/hyattpd/Prodigal": { - "id": "github/hyattpd/Prodigal", - "title": "github/hyattpd/Prodigal", - "url": " https://rseng.github.io/software/repository/github/hyattpd/Prodigal", - "content": "Prodigal Gene Prediction Software" + "github/JuliaMatrices/BandedMatrices.jl": { + "id": "github/JuliaMatrices/BandedMatrices.jl", + "title": "github/JuliaMatrices/BandedMatrices.jl", + "url": " https://rseng.github.io/software/repository/github/JuliaMatrices/BandedMatrices.jl", + "content": "A Julia package for representing banded matrices" }, - "github/Leo-Simpson/c-lasso": { - "id": "github/Leo-Simpson/c-lasso", - "title": "github/Leo-Simpson/c-lasso", - "url": " https://rseng.github.io/software/repository/github/Leo-Simpson/c-lasso", - "content": "c-lasso: a Python package for constrained sparse regression and classification" + "github/JuliaMatrices/LazyBandedMatrices.jl": { + "id": "github/JuliaMatrices/LazyBandedMatrices.jl", + "title": "github/JuliaMatrices/LazyBandedMatrices.jl", + "url": " https://rseng.github.io/software/repository/github/JuliaMatrices/LazyBandedMatrices.jl", + "content": "A Julia package for lazy banded matrices" }, - "github/cdslaborg/paramonte": { - "id": "github/cdslaborg/paramonte", - "title": "github/cdslaborg/paramonte", - "url": " https://rseng.github.io/software/repository/github/cdslaborg/paramonte", - "content": "ParaMonte: Plain Powerful Parallel Monte Carlo and MCMC Library for Python, MATLAB, Fortran, C++, C." + "github/JuliaMatrices/BlockBandedMatrices.jl": { + "id": "github/JuliaMatrices/BlockBandedMatrices.jl", + "title": "github/JuliaMatrices/BlockBandedMatrices.jl", + "url": " https://rseng.github.io/software/repository/github/JuliaMatrices/BlockBandedMatrices.jl", + "content": "A Julia package for representing block-banded matrices and banded-block-banded matrices" }, - "github/simple-crypto/SCALib": { - "id": "github/simple-crypto/SCALib", - "title": "github/simple-crypto/SCALib", - "url": " https://rseng.github.io/software/repository/github/simple-crypto/SCALib", - "content": "Side-Channel Analysis Library" + "github/sbird/fake_spectra": { + "id": "github/sbird/fake_spectra", + "title": "github/sbird/fake_spectra", + "url": " https://rseng.github.io/software/repository/github/sbird/fake_spectra", + "content": "A code for generating fake spectra from a cosmological simulation" }, - "github/Washington-University/CiftiLib": { - "id": "github/Washington-University/CiftiLib", - "title": "github/Washington-University/CiftiLib", - "url": " https://rseng.github.io/software/repository/github/Washington-University/CiftiLib", - "content": "C++ Library for reading and writing CIFTI-2 and CIFTI-1 files" + "github/sbird/GenPK": { + "id": "github/sbird/GenPK", + "title": "github/sbird/GenPK", + "url": " https://rseng.github.io/software/repository/github/sbird/GenPK", + "content": "Program for finding the matter power spectrum from Gadget format files. Uses FFTW3 and GadgetReader." }, - "github/swiftsim/swiftsimio": { - "id": "github/swiftsim/swiftsimio", - "title": "github/swiftsim/swiftsimio", - "url": " https://rseng.github.io/software/repository/github/swiftsim/swiftsimio", - "content": "Python library for reading SWIFT data. Uses unyt and h5py." + "github/bpairet/mayo_hci": { + "id": "github/bpairet/mayo_hci", + "title": "github/bpairet/mayo_hci", + "url": " https://rseng.github.io/software/repository/github/bpairet/mayo_hci", + "content": "None" }, - "github/joe-antognini/kozai": { - "id": "github/joe-antognini/kozai", - "title": "github/joe-antognini/kozai", - "url": " https://rseng.github.io/software/repository/github/joe-antognini/kozai", - "content": "A Python package to evolve hierarchical triples in the secular approximation" + "github/fabian-sp/GGLasso": { + "id": "github/fabian-sp/GGLasso", + "title": "github/fabian-sp/GGLasso", + "url": " https://rseng.github.io/software/repository/github/fabian-sp/GGLasso", + "content": "Implementations for solving the Group and Fused Graphical Lasso problem" }, - "github/genouest/biomaj-cli": { - "id": "github/genouest/biomaj-cli", - "title": "github/genouest/biomaj-cli", - "url": " https://rseng.github.io/software/repository/github/genouest/biomaj-cli", - "content": "CLI for BioMAJ" + "github/rgmyr/corebreakout": { + "id": "github/rgmyr/corebreakout", + "title": "github/rgmyr/corebreakout", + "url": " https://rseng.github.io/software/repository/github/rgmyr/corebreakout", + "content": "Segmentation and depth-alignment of geological core sample image columns via Mask-RCNN" }, - "github/genouest/biomaj-daemon": { - "id": "github/genouest/biomaj-daemon", - "title": "github/genouest/biomaj-daemon", - "url": " https://rseng.github.io/software/repository/github/genouest/biomaj-daemon", - "content": "micro service to manage biomaj client requests and bank updates" + "github/candebellavita/vkompth": { + "id": "github/candebellavita/vkompth", + "title": "github/candebellavita/vkompth", + "url": " https://rseng.github.io/software/repository/github/candebellavita/vkompth", + "content": "None" }, - "github/nhcrisp/ADBSat": { - "id": "github/nhcrisp/ADBSat", - "title": "github/nhcrisp/ADBSat", - "url": " https://rseng.github.io/software/repository/github/nhcrisp/ADBSat", - "content": "Aerodynamic Database for Satellites" + "github/v-morello/riptide": { + "id": "github/v-morello/riptide", + "title": "github/v-morello/riptide", + "url": " https://rseng.github.io/software/repository/github/v-morello/riptide", + "content": "Pulsar searching with the Fast Folding Algorithm (FFA)" }, - "github/rorybarnes/EqTide": { - "id": "github/rorybarnes/EqTide", - "title": "github/rorybarnes/EqTide", - "url": " https://rseng.github.io/software/repository/github/rorybarnes/EqTide", - "content": "Source code for Equilibrium Tide calculations" + "github/v-morello/clfd": { + "id": "github/v-morello/clfd", + "title": "github/v-morello/clfd", + "url": " https://rseng.github.io/software/repository/github/v-morello/clfd", + "content": " Smart RFI removal algorithms to be used on folded pulsar search and timing data" }, - "github/Someone789/galax2d": { - "id": "github/Someone789/galax2d", - "title": "github/Someone789/galax2d", - "url": " https://rseng.github.io/software/repository/github/Someone789/galax2d", - "content": "matlab or octave code to compute the 2D stationary solution of the isothermal Euler equations of gas dynamics in a rotating galaxy with a weak bar" + "github/v-morello/iqrm": { + "id": "github/v-morello/iqrm", + "title": "github/v-morello/iqrm", + "url": " https://rseng.github.io/software/repository/github/v-morello/iqrm", + "content": "A minimal implementation of the IQRM interference flagging algorithm for radio pulsar and transient searches" }, - "github/jbrakensiek/CORBITS": { - "id": "github/jbrakensiek/CORBITS", - "title": "github/jbrakensiek/CORBITS", - "url": " https://rseng.github.io/software/repository/github/jbrakensiek/CORBITS", - "content": "None" + "github/nbarbey/TomograPy": { + "id": "github/nbarbey/TomograPy", + "title": "github/nbarbey/TomograPy", + "url": " https://rseng.github.io/software/repository/github/nbarbey/TomograPy", + "content": "Siddon tomography algorithm" }, - "github/Gaius-Augustus/GALBA": { - "id": "github/Gaius-Augustus/GALBA", - "title": "github/Gaius-Augustus/GALBA", - "url": " https://rseng.github.io/software/repository/github/Gaius-Augustus/GALBA", - "content": "GALBA is a pipeline for fully automated prediction of protein coding gene structures with AUGUSTUS in novel eukaryotic genomes for the scenario where high quality proteins from a closely related species are available." + "github/RealTimeGenomics/rtg-tools": { + "id": "github/RealTimeGenomics/rtg-tools", + "title": "github/RealTimeGenomics/rtg-tools", + "url": " https://rseng.github.io/software/repository/github/RealTimeGenomics/rtg-tools", + "content": "RTG Tools: Utilities for accurate VCF comparison and manipulation" }, - "github/Gaius-Augustus/BRAKER": { - "id": "github/Gaius-Augustus/BRAKER", - "title": "github/Gaius-Augustus/BRAKER", - "url": " https://rseng.github.io/software/repository/github/Gaius-Augustus/BRAKER", - "content": "BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes" + "github/gijut/gnucash": { + "id": "github/gijut/gnucash", + "title": "github/gijut/gnucash", + "url": " https://rseng.github.io/software/repository/github/gijut/gnucash", + "content": "Public Mirror of code.gnucash.org/gnucash" }, - "github/jan-rybizki/Chempy": { - "id": "github/jan-rybizki/Chempy", - "title": "github/jan-rybizki/Chempy", - "url": " https://rseng.github.io/software/repository/github/jan-rybizki/Chempy", - "content": "Start with the Chempy tutorial" + "github/valboz/VBBinaryLensing": { + "id": "github/valboz/VBBinaryLensing", + "title": "github/valboz/VBBinaryLensing", + "url": " https://rseng.github.io/software/repository/github/valboz/VBBinaryLensing", + "content": "Microlensing light curve calculation" }, - "github/jan-rybizki/gdr2_completeness": { - "id": "github/jan-rybizki/gdr2_completeness", - "title": "github/jan-rybizki/gdr2_completeness", - "url": " https://rseng.github.io/software/repository/github/jan-rybizki/gdr2_completeness", - "content": "This package helps with downloading GaiaDR2 data and gives approximate completeness maps over the sky and per G magntude bin. It also has a function to query the GDR2 RVS sample selection function." + "github/TheMillerLab/genetex": { + "id": "github/TheMillerLab/genetex", + "title": "github/TheMillerLab/genetex", + "url": " https://rseng.github.io/software/repository/github/TheMillerLab/genetex", + "content": "None" }, - "github/jan-rybizki/Galaxia_wrap": { - "id": "github/jan-rybizki/Galaxia_wrap", - "title": "github/jan-rybizki/Galaxia_wrap", - "url": " https://rseng.github.io/software/repository/github/jan-rybizki/Galaxia_wrap", - "content": "A few python scripts and a tutorial notebook to create and manipulate Galaxia mock catalogues" + "github/frank1010111/pywaterflood": { + "id": "github/frank1010111/pywaterflood", + "title": "github/frank1010111/pywaterflood", + "url": " https://rseng.github.io/software/repository/github/frank1010111/pywaterflood", + "content": "Capacitance resistance models for waterflood connectivity" }, - "github/pjcigan/pysymlog": { - "id": "github/pjcigan/pysymlog", - "title": "github/pjcigan/pysymlog", - "url": " https://rseng.github.io/software/repository/github/pjcigan/pysymlog", - "content": "Utilities for plotting in matplotlib, plotly, etc. using a symmetric or signed log transform. This allows the plotting of positive and negative data with a pseudo-log axis scale or stretch. " + "github/frank1010111/bluebonnet": { + "id": "github/frank1010111/bluebonnet", + "title": "github/frank1010111/bluebonnet", + "url": " https://rseng.github.io/software/repository/github/frank1010111/bluebonnet", + "content": "Scaling solutions for production analysis from unconventional oil and gas wells" }, - "github/pjcigan/obsplanning": { - "id": "github/pjcigan/obsplanning", - "title": "github/pjcigan/obsplanning", - "url": " https://rseng.github.io/software/repository/github/pjcigan/obsplanning", - "content": "Python tools for planning astronomical observations" + "github/Open-ET/flux-data-qaqc": { + "id": "github/Open-ET/flux-data-qaqc", + "title": "github/Open-ET/flux-data-qaqc", + "url": " https://rseng.github.io/software/repository/github/Open-ET/flux-data-qaqc", + "content": "Energy Balance Closure Analysis and Eddy Flux Data Post-Processing" }, - "github/pjcigan/multicolorfits": { - "id": "github/pjcigan/multicolorfits", - "title": "github/pjcigan/multicolorfits", - "url": " https://rseng.github.io/software/repository/github/pjcigan/multicolorfits", - "content": "Python tool for colorizing and combining fits images." + "github/jiahecui/SenAOReFoc": { + "id": "github/jiahecui/SenAOReFoc", + "title": "github/jiahecui/SenAOReFoc", + "url": " https://rseng.github.io/software/repository/github/jiahecui/SenAOReFoc", + "content": "A closed-loop sensorbased adaptive optics and remote focusing control software that works with a deformable mirror and a Shack-Hartmann wavefront sensor." }, - "github/benstahl92/deepSIP": { - "id": "github/benstahl92/deepSIP", - "title": "github/benstahl92/deepSIP", - "url": " https://rseng.github.io/software/repository/github/benstahl92/deepSIP", - "content": "Deep Learning of Supernova Ia Parameters" + "github/AlexanderJuestel/pyheatdemand": { + "id": "github/AlexanderJuestel/pyheatdemand", + "title": "github/AlexanderJuestel/pyheatdemand", + "url": " https://rseng.github.io/software/repository/github/AlexanderJuestel/pyheatdemand", + "content": "Processing Tool for Heat Demand Data" }, - "github/RasmussenLab/vamb": { - "id": "github/RasmussenLab/vamb", - "title": "github/RasmussenLab/vamb", - "url": " https://rseng.github.io/software/repository/github/RasmussenLab/vamb", - "content": "Variational autoencoder for metagenomic binning" + "github/koenderks/jaspAudit": { + "id": "github/koenderks/jaspAudit", + "title": "github/koenderks/jaspAudit", + "url": " https://rseng.github.io/software/repository/github/koenderks/jaspAudit", + "content": "The Audit module is developed to facilitate statistical auditing in both Bayesian and classical manifestations. The main feature is a workflow that helps guide auditors through the sampling process. Additionally, there are stand-alone analyses for planning, selecting, and evaluating a sample. The module is based on the R package jfa." }, - "github/DedalusProject/eigentools": { - "id": "github/DedalusProject/eigentools", - "title": "github/DedalusProject/eigentools", - "url": " https://rseng.github.io/software/repository/github/DedalusProject/eigentools", - "content": "The Eigentools package for Dedalus" + "github/c-martinez/BeyondTheBook": { + "id": "github/c-martinez/BeyondTheBook", + "title": "github/c-martinez/BeyondTheBook", + "url": " https://rseng.github.io/software/repository/github/c-martinez/BeyondTheBook", + "content": "Using Wikipedia to assess the translatability of text." }, - "github/JunTaoLuo/mctreesearch4j": { - "id": "github/JunTaoLuo/mctreesearch4j", - "title": "github/JunTaoLuo/mctreesearch4j", - "url": " https://rseng.github.io/software/repository/github/JunTaoLuo/mctreesearch4j", + "github/AlexandrosAntoniadis/ODUSSEAS": { + "id": "github/AlexandrosAntoniadis/ODUSSEAS", + "title": "github/AlexandrosAntoniadis/ODUSSEAS", + "url": " https://rseng.github.io/software/repository/github/AlexandrosAntoniadis/ODUSSEAS", "content": "None" }, - "github/ywx649999311/EzTao": { - "id": "github/ywx649999311/EzTao", - "title": "github/ywx649999311/EzTao", - "url": " https://rseng.github.io/software/repository/github/ywx649999311/EzTao", - "content": "A Python Toolkit for AGN Time Series Analysis using CARMA models" + "github/nickk124/RCR": { + "id": "github/nickk124/RCR", + "title": "github/nickk124/RCR", + "url": " https://rseng.github.io/software/repository/github/nickk124/RCR", + "content": "Robust Chauvenet Rejection: RCR is advanced, but easy to use, outlier rejection." }, - "github/ywx649999311/vizic": { - "id": "github/ywx649999311/vizic", - "title": "github/ywx649999311/vizic", - "url": " https://rseng.github.io/software/repository/github/ywx649999311/vizic", - "content": "A Jupyter-based Interactive Visualization Tool for Astronomical Catalogs" + "github/light-curve/light-curve-python": { + "id": "github/light-curve/light-curve-python", + "title": "github/light-curve/light-curve-python", + "url": " https://rseng.github.io/software/repository/github/light-curve/light-curve-python", + "content": "light-curve feature extraction library for Python" }, - "github/zpenoyre/OoT": { - "id": "github/zpenoyre/OoT", - "title": "github/zpenoyre/OoT", - "url": " https://rseng.github.io/software/repository/github/zpenoyre/OoT", - "content": "Out-of-Transit Light Curve Generator" + "github/light-curve/light-curve": { + "id": "github/light-curve/light-curve", + "title": "github/light-curve/light-curve", + "url": " https://rseng.github.io/software/repository/github/light-curve/light-curve", + "content": "Collection of Rust packages for time-series analysis" + }, + "github/sheneman/clearcut": { + "id": "github/sheneman/clearcut", + "title": "github/sheneman/clearcut", + "url": " https://rseng.github.io/software/repository/github/sheneman/clearcut", + "content": "This is clearcut, the reference implementation for the Relaxed Neighbor Joining algorithm." }, - "github/zpenoyre/CausticFrog": { - "id": "github/zpenoyre/CausticFrog", - "title": "github/zpenoyre/CausticFrog", - "url": " https://rseng.github.io/software/repository/github/zpenoyre/CausticFrog", - "content": "1D Lagrangian Simulation Package" + "github/JamesPaynter/PyGRB": { + "id": "github/JamesPaynter/PyGRB", + "title": "github/JamesPaynter/PyGRB", + "url": " https://rseng.github.io/software/repository/github/JamesPaynter/PyGRB", + "content": "Gamma-ray burst analysis library" }, - "github/spacepy/spacepy": { - "id": "github/spacepy/spacepy", - "title": "github/spacepy/spacepy", - "url": " https://rseng.github.io/software/repository/github/spacepy/spacepy", - "content": "Space Science library for Python - contains superposed epoch classes, drift shell tracing, access to magnetic field models, streamline tracing, bootstrap confidence limits, time and coordinate conversions, etc." + "github/Vini2/GraphBin": { + "id": "github/Vini2/GraphBin", + "title": "github/Vini2/GraphBin", + "url": " https://rseng.github.io/software/repository/github/Vini2/GraphBin", + "content": "GraphBin: Refined binning of metagenomic contigs using assembly graphs" }, - "github/JonasRieger/ldaPrototype": { - "id": "github/JonasRieger/ldaPrototype", - "title": "github/JonasRieger/ldaPrototype", - "url": " https://rseng.github.io/software/repository/github/JonasRieger/ldaPrototype", - "content": "Determine a Prototype from a number of runs of Latent Dirichlet Allocation (LDA) measuring its similarities with S-CLOP: A procedure to select the LDA run with highest mean pairwise similarity, which is measured by S-CLOP (Similarity of multiple sets by Clustering with Local Pruning), to all other runs." + "github/cespinosa/pyHIIexplorerV2": { + "id": "github/cespinosa/pyHIIexplorerV2", + "title": "github/cespinosa/pyHIIexplorerV2", + "url": " https://rseng.github.io/software/repository/github/cespinosa/pyHIIexplorerV2", + "content": "None" }, - "github/kno10/python-kmedoids": { - "id": "github/kno10/python-kmedoids", - "title": "github/kno10/python-kmedoids", - "url": " https://rseng.github.io/software/repository/github/kno10/python-kmedoids", - "content": "Fast K-Medoids clustering in Python with FasterPAM" + "github/lgrcia/prose": { + "id": "github/lgrcia/prose", + "title": "github/lgrcia/prose", + "url": " https://rseng.github.io/software/repository/github/lgrcia/prose", + "content": "A python framework to process FITS images. Built for Astronomy." }, - "github/USU-Analytics-Solution-Center/Bruno.jl": { - "id": "github/USU-Analytics-Solution-Center/Bruno.jl", - "title": "github/USU-Analytics-Solution-Center/Bruno.jl", - "url": " https://rseng.github.io/software/repository/github/USU-Analytics-Solution-Center/Bruno.jl", - "content": "Repository for the Julia package with financial tools for data generation, asset pricing and strategy testing" + "github/PyPSA/atlite": { + "id": "github/PyPSA/atlite", + "title": "github/PyPSA/atlite", + "url": " https://rseng.github.io/software/repository/github/PyPSA/atlite", + "content": "Atlite: Light-weight version of Aarhus RE Atlas for converting weather data to power systems data" }, - "github/Hoecker-Lab/atligator": { - "id": "github/Hoecker-Lab/atligator", - "title": "github/Hoecker-Lab/atligator", - "url": " https://rseng.github.io/software/repository/github/Hoecker-Lab/atligator", - "content": "Analysis and design of protein-protein or protein-peptide interactions based on atlas database." + "github/PyPSA/linopy": { + "id": "github/PyPSA/linopy", + "title": "github/PyPSA/linopy", + "url": " https://rseng.github.io/software/repository/github/PyPSA/linopy", + "content": "Linear optimization with N-D labeled arrays in Python" }, - "github/mrempel/geohexviz": { - "id": "github/mrempel/geohexviz", - "title": "github/mrempel/geohexviz", - "url": " https://rseng.github.io/software/repository/github/mrempel/geohexviz", - "content": "GeoHexViz - generating publication-quality geospatical visualization of hexagonally binned data" + "github/skiehl/lcsim": { + "id": "github/skiehl/lcsim", + "title": "github/skiehl/lcsim", + "url": " https://rseng.github.io/software/repository/github/skiehl/lcsim", + "content": "Blazar light curve simulation package" }, - "github/babinyurii/recan": { - "id": "github/babinyurii/recan", - "title": "github/babinyurii/recan", - "url": " https://rseng.github.io/software/repository/github/babinyurii/recan", - "content": "genetic distance plotting for recombination events analysis" + "github/skiehl/polarizationtools": { + "id": "github/skiehl/polarizationtools", + "title": "github/skiehl/polarizationtools", + "url": " https://rseng.github.io/software/repository/github/skiehl/polarizationtools", + "content": "Tools to deal with astrophysical polarization data in python3" }, - "github/CHES2023/PyMsOfa": { - "id": "github/CHES2023/PyMsOfa", - "title": "github/CHES2023/PyMsOfa", - "url": " https://rseng.github.io/software/repository/github/CHES2023/PyMsOfa", - "content": "a Python package for the Standards of Fundamental Astronomy (SOFA) service" + "github/skiehl/wwz": { + "id": "github/skiehl/wwz", + "title": "github/skiehl/wwz", + "url": " https://rseng.github.io/software/repository/github/skiehl/wwz", + "content": "Weighted wavelet z-transform (WWZ) analysis package" }, - "github/pybamm-team/PyBaMM": { - "id": "github/pybamm-team/PyBaMM", - "title": "github/pybamm-team/PyBaMM", - "url": " https://rseng.github.io/software/repository/github/pybamm-team/PyBaMM", - "content": "Fast and flexible physics-based battery models in Python" + "github/iomega/zenodo-upload": { + "id": "github/iomega/zenodo-upload", + "title": "github/iomega/zenodo-upload", + "url": " https://rseng.github.io/software/repository/github/iomega/zenodo-upload", + "content": "JS package to create a new version of a Zenodo upload with a file" }, - "github/pybamm-team/liionpack": { - "id": "github/pybamm-team/liionpack", - "title": "github/pybamm-team/liionpack", - "url": " https://rseng.github.io/software/repository/github/pybamm-team/liionpack", - "content": "A battery pack simulation tool that uses the PyBaMM framework" + "github/iomega/spec2vec": { + "id": "github/iomega/spec2vec", + "title": "github/iomega/spec2vec", + "url": " https://rseng.github.io/software/repository/github/iomega/spec2vec", + "content": "Word2Vec based similarity measure of mass spectrometry data." }, - "github/bsafdi/stellarWakes": { - "id": "github/bsafdi/stellarWakes", - "title": "github/bsafdi/stellarWakes", - "url": " https://rseng.github.io/software/repository/github/bsafdi/stellarWakes", - "content": "Python package for dark matter subhalo searches using stellar kinematic data" + "github/iomega/paired-data-form": { + "id": "github/iomega/paired-data-form", + "title": "github/iomega/paired-data-form", + "url": " https://rseng.github.io/software/repository/github/iomega/paired-data-form", + "content": "Linking mas spectra and genomic information to discover new chemistry" }, - "github/hasindu2008/slow5tools": { - "id": "github/hasindu2008/slow5tools", - "title": "github/hasindu2008/slow5tools", - "url": " https://rseng.github.io/software/repository/github/hasindu2008/slow5tools", - "content": "Slow5tools is a toolkit for converting (FAST5 <-> SLOW5), compressing, viewing, indexing and manipulating data in SLOW5 format." + "github/annayqho/TheCannon": { + "id": "github/annayqho/TheCannon", + "title": "github/annayqho/TheCannon", + "url": " https://rseng.github.io/software/repository/github/annayqho/TheCannon", + "content": "a data-driven method for determining stellar parameters and abundances from stellar spectra" }, - "github/horovod/horovod": { - "id": "github/horovod/horovod", - "title": "github/horovod/horovod", - "url": " https://rseng.github.io/software/repository/github/horovod/horovod", - "content": "Distributed training framework for TensorFlow, Keras, PyTorch, and Apache MXNet." + "github/mikecokina/elisa": { + "id": "github/mikecokina/elisa", + "title": "github/mikecokina/elisa", + "url": " https://rseng.github.io/software/repository/github/mikecokina/elisa", + "content": "None" }, - 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"url": " https://rseng.github.io/software/repository/github/vpc-ccg/calib", - "content": "clusters paired-end reads using their barcodes and sequences." + "github/pysal/pysal": { + "id": "github/pysal/pysal", + "title": "github/pysal/pysal", + "url": " https://rseng.github.io/software/repository/github/pysal/pysal", + "content": "PySAL: Python Spatial Analysis Library Meta-Package" }, - "github/akashdhruv/BoxKit": { - "id": "github/akashdhruv/BoxKit", - "title": "github/akashdhruv/BoxKit", - "url": " https://rseng.github.io/software/repository/github/akashdhruv/BoxKit", - "content": "A Python library to manage analysis of block-structured simulation datasets." + "github/pysal/spaghetti": { + "id": "github/pysal/spaghetti", + "title": "github/pysal/spaghetti", + "url": " https://rseng.github.io/software/repository/github/pysal/spaghetti", + "content": "SPAtial GrapHs: nETworks, Topology, & Inference" }, - "github/elkebir-group/Jumper": { - "id": "github/elkebir-group/Jumper", - "title": "github/elkebir-group/Jumper", - 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"github/biobakery/halla": { - "id": "github/biobakery/halla", - "title": "github/biobakery/halla", - "url": " https://rseng.github.io/software/repository/github/biobakery/halla", - "content": "None" + "github/mariakotouza/TRIP-Tool": { + "id": "github/mariakotouza/TRIP-Tool", + "title": "github/mariakotouza/TRIP-Tool", + "url": " https://rseng.github.io/software/repository/github/mariakotouza/TRIP-Tool", + "content": "Antigen receptor gene profiler: A software framework that provides analytics services on NGS Data" }, - "github/martibosch/detectree": { - "id": "github/martibosch/detectree", - "title": "github/martibosch/detectree", - "url": " https://rseng.github.io/software/repository/github/martibosch/detectree", - "content": "Tree detection from aerial imagery in Python" + "github/awsteiner/o2scl": { + "id": "github/awsteiner/o2scl", + "title": "github/awsteiner/o2scl", + "url": " https://rseng.github.io/software/repository/github/awsteiner/o2scl", + "content": "Object-oriented Scientific Computing Library" }, - 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Currently targeting REST APIs." }, - "github/montilab/nf-gwas-pipeline": { - "id": "github/montilab/nf-gwas-pipeline", - "title": "github/montilab/nf-gwas-pipeline", - "url": " https://rseng.github.io/software/repository/github/montilab/nf-gwas-pipeline", - "content": "A Nextflow Genome-Wide Association Study (GWAS) Pipeline" + "github/cwieder/py-ssPA": { + "id": "github/cwieder/py-ssPA", + "title": "github/cwieder/py-ssPA", + "url": " https://rseng.github.io/software/repository/github/cwieder/py-ssPA", + "content": "Single sample pathway analysis tools for omics data" }, - "github/ABard0/MDGF-MCEC": { - "id": "github/ABard0/MDGF-MCEC", - "title": "github/ABard0/MDGF-MCEC", - "url": " https://rseng.github.io/software/repository/github/ABard0/MDGF-MCEC", - "content": "None" + "github/Autostronomy/AstroPhot": { + "id": "github/Autostronomy/AstroPhot", + "title": "github/Autostronomy/AstroPhot", + "url": " https://rseng.github.io/software/repository/github/Autostronomy/AstroPhot", + "content": "A fast, flexible, automated, and differentiable astronomical image modelling tool for precise parallel multi-wavelength photometry" }, - 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For information on the method see Schmidt et al. 2013, Menard et al. 2013, and Rahman et al. 2015, 2016b. Details on this implementation can be found in Morrison et al. 2017" }, - "github/NLESC-JCER/EigenCuda": { - "id": "github/NLESC-JCER/EigenCuda", - "title": "github/NLESC-JCER/EigenCuda", - "url": " https://rseng.github.io/software/repository/github/NLESC-JCER/EigenCuda", - "content": "Offload Eigen operations to GPUs" + "github/e-koch/FilFinder": { + "id": "github/e-koch/FilFinder", + "title": "github/e-koch/FilFinder", + "url": " https://rseng.github.io/software/repository/github/e-koch/FilFinder", + "content": "Detection of filamentary structure in molecular clouds" }, - "github/NLESC-JCER/QMCblip": { - "id": "github/NLESC-JCER/QMCblip", - "title": "github/NLESC-JCER/QMCblip", - "url": " https://rseng.github.io/software/repository/github/NLESC-JCER/QMCblip", - "content": "None" + "github/egpbos/barcode": { + "id": "github/egpbos/barcode", + "title": "github/egpbos/barcode", + "url": " https://rseng.github.io/software/repository/github/egpbos/barcode", + "content": "Bayesian reconstruction of cosmic density fields" }, - 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Following Curran (2014)" + "github/astrosupriyo/pyTANSPEC": { + "id": "github/astrosupriyo/pyTANSPEC", + "title": "github/astrosupriyo/pyTANSPEC", + "url": " https://rseng.github.io/software/repository/github/astrosupriyo/pyTANSPEC", + "content": "Python tool for extracting 1D TANSPEC spectra from 2D image" }, - "github/imcgreer/simqso": { - "id": "github/imcgreer/simqso", - "title": "github/imcgreer/simqso", - "url": " https://rseng.github.io/software/repository/github/imcgreer/simqso", - "content": "Module for generating simulated quasar spectra" + "github/conda/conda-package-handling": { + "id": "github/conda/conda-package-handling", + "title": "github/conda/conda-package-handling", + "url": " https://rseng.github.io/software/repository/github/conda/conda-package-handling", + "content": "Create and extract conda packages of various formats" }, - "github/bretthandrews/flexCE": { - "id": "github/bretthandrews/flexCE", - "title": "github/bretthandrews/flexCE", - "url": " https://rseng.github.io/software/repository/github/bretthandrews/flexCE", - "content": "A flexible Chemical Evolution model in python" + "github/conda/pycosat": { + "id": "github/conda/pycosat", + "title": "github/conda/pycosat", + "url": " https://rseng.github.io/software/repository/github/conda/pycosat", + "content": "Python bindings to picosat (a SAT solver)" }, - "github/MRCIEU/PHESANT": { - "id": "github/MRCIEU/PHESANT", - "title": "github/MRCIEU/PHESANT", - "url": " https://rseng.github.io/software/repository/github/MRCIEU/PHESANT", - "content": "PHESANT - PHEnome Scan ANalysis Tool (pheWAS, Mendelian randomisation (MR)-pheWAS etc.) in UK Biobank" + "github/conda/conda": { + "id": "github/conda/conda", + "title": "github/conda/conda", + "url": " https://rseng.github.io/software/repository/github/conda/conda", + "content": "OS-agnostic, system-level binary package manager and ecosystem" }, - "github/MRCIEU/metaboprep": { - "id": "github/MRCIEU/metaboprep", - "title": "github/MRCIEU/metaboprep", - "url": " https://rseng.github.io/software/repository/github/MRCIEU/metaboprep", - "content": "a pipeline of metabolomics data processing and quality control" + "github/vavrines/Kinetic.jl": { + "id": "github/vavrines/Kinetic.jl", + "title": "github/vavrines/Kinetic.jl", + "url": " https://rseng.github.io/software/repository/github/vavrines/Kinetic.jl", + "content": "Universal modeling and simulation of fluid dynamics upon machine learning" }, - "github/jfowkes/pycutest": { - "id": "github/jfowkes/pycutest", - "title": "github/jfowkes/pycutest", - "url": " https://rseng.github.io/software/repository/github/jfowkes/pycutest", - "content": "Python interface to CUTEst" + "github/alejostark/phase_space_cosmo_fisher": { + "id": "github/alejostark/phase_space_cosmo_fisher", + "title": "github/alejostark/phase_space_cosmo_fisher", + "url": " https://rseng.github.io/software/repository/github/alejostark/phase_space_cosmo_fisher", + "content": "Code used to produce Fisher matrix contours in Stark, Miller Huterer 2016" }, - "github/SteveMacenski/slam_toolbox": { - "id": "github/SteveMacenski/slam_toolbox", - "title": "github/SteveMacenski/slam_toolbox", - "url": " https://rseng.github.io/software/repository/github/SteveMacenski/slam_toolbox", - "content": "Slam Toolbox for lifelong mapping and localization in potentially massive maps with ROS" + "github/jadexter/grtrans": { + "id": "github/jadexter/grtrans", + "title": "github/jadexter/grtrans", + "url": " https://rseng.github.io/software/repository/github/jadexter/grtrans", + "content": "Public Kerr metric polarized ray tracing radiative transfer code" }, "github/federicomarulli/CosmoBolognaLib": { "id": "github/federicomarulli/CosmoBolognaLib", @@ -27627,887 +27765,899 @@ "url": " https://rseng.github.io/software/repository/github/federicomarulli/CosmoBolognaLib", "content": "free software C++ libraries for cosmological calculations" }, - "github/ImproPhoto/pymicmac": { - "id": "github/ImproPhoto/pymicmac", - "title": "github/ImproPhoto/pymicmac", - "url": " https://rseng.github.io/software/repository/github/ImproPhoto/pymicmac", - "content": "Python tools for the MicMac FOSS photogrammetric "suite"" - }, - "github/nand1155/CausNet": { - "id": "github/nand1155/CausNet", - "title": "github/nand1155/CausNet", - "url": " https://rseng.github.io/software/repository/github/nand1155/CausNet", - "content": "Generational orderings based search for optimal Bayesian networks via dynamic programming with parent set constraints" - }, - "github/dynamics-of-stellar-systems/dynamite_release": { - "id": "github/dynamics-of-stellar-systems/dynamite_release", - "title": "github/dynamics-of-stellar-systems/dynamite_release", - "url": " https://rseng.github.io/software/repository/github/dynamics-of-stellar-systems/dynamite_release", - "content": "dynamics, age and metallicity indicators tracing evolution" - }, - "github/ProfessorBrunner/rc3-pipeline": { - "id": "github/ProfessorBrunner/rc3-pipeline", - "title": "github/ProfessorBrunner/rc3-pipeline", - "url": " https://rseng.github.io/software/repository/github/ProfessorBrunner/rc3-pipeline", - "content": "Make digital images of RC3 galaxies by using final, calibrated SDSS images" + "github/jorisparet/partycls": { + "id": "github/jorisparet/partycls", + "title": "github/jorisparet/partycls", + "url": " https://rseng.github.io/software/repository/github/jorisparet/partycls", + "content": "Unsupervised learning of structure in systems of interacting particles." }, - 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Code repository associated with the papers https://arxiv.org/abs/2002.05165 and https://arxiv.org/abs/2004.06733." + "github/champsproject/ldds": { + "id": "github/champsproject/ldds", + "title": "github/champsproject/ldds", + "url": " https://rseng.github.io/software/repository/github/champsproject/ldds", + "content": "Python package for computing and visualizing Lagrangian Descriptors in Dynamical Systems" }, - "github/smsharma/mining-for-substructure-lens": { - "id": "github/smsharma/mining-for-substructure-lens", - "title": "github/smsharma/mining-for-substructure-lens", - "url": " https://rseng.github.io/software/repository/github/smsharma/mining-for-substructure-lens", - "content": "Inference of substructure properties in strong lensing systems with machine learning. 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(2007) J. Opt. Soc. Amer. 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For all countries supported, this includes a daily time-series of cases. Wherever available we also provide data on deaths, hospitalisations, and tests. 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This method is a further development of J-plots (https://github.com/SJaffa/Jplots)" }, - "github/zgazak/TAP": { - "id": "github/zgazak/TAP", - "title": "github/zgazak/TAP", - "url": " https://rseng.github.io/software/repository/github/zgazak/TAP", - "content": "Transit Analysis Package for IDL" + "github/prdm0/ropenblas": { + "id": "github/prdm0/ropenblas", + "title": "github/prdm0/ropenblas", + "url": " https://rseng.github.io/software/repository/github/prdm0/ropenblas", + "content": "Package to link R language to OpenBLAS library" }, - "github/JuliaQX/QXTools.jl": { - "id": "github/JuliaQX/QXTools.jl", - "title": "github/JuliaQX/QXTools.jl", - "url": " https://rseng.github.io/software/repository/github/JuliaQX/QXTools.jl", - "content": "Julia package for quantum circuit simulation using tensor networks" + "github/radiocosmology/driftscan": { + "id": "github/radiocosmology/driftscan", + "title": "github/radiocosmology/driftscan", + "url": " https://rseng.github.io/software/repository/github/radiocosmology/driftscan", + "content": "Data analysis of transit radio interferometers, particularly for 21cm cosmology." }, - "github/cameron314/concurrentqueue": { - "id": "github/cameron314/concurrentqueue", - "title": "github/cameron314/concurrentqueue", - "url": " https://rseng.github.io/software/repository/github/cameron314/concurrentqueue", - "content": "A fast multi-producer, multi-consumer lock-free concurrent queue for C++11" + "github/radiocosmology/draco": { + "id": "github/radiocosmology/draco", + "title": "github/radiocosmology/draco", + "url": " https://rseng.github.io/software/repository/github/radiocosmology/draco", + "content": "A pipeline for the analysis and simulation of drift scan radio data" }, - "github/bic-nirrh/precocity": { - "id": "github/bic-nirrh/precocity", - "title": "github/bic-nirrh/precocity", - "url": " https://rseng.github.io/software/repository/github/bic-nirrh/precocity", - "content": "Database and enrichment analysis of genes associated with precocious puberty" + "github/radiocosmology/caput": { + "id": "github/radiocosmology/caput", + "title": "github/radiocosmology/caput", + "url": " https://rseng.github.io/software/repository/github/radiocosmology/caput", + "content": "Cluster Astronomical Python Utilities" }, - "github/Stuermer/EchelleSimulator": { - "id": "github/Stuermer/EchelleSimulator", - "title": "github/Stuermer/EchelleSimulator", - "url": " https://rseng.github.io/software/repository/github/Stuermer/EchelleSimulator", - "content": "None" + "github/nkallima/sim-universal-construction": { + "id": "github/nkallima/sim-universal-construction", + "title": "github/nkallima/sim-universal-construction", + "url": " https://rseng.github.io/software/repository/github/nkallima/sim-universal-construction", + "content": "An open-source framework for concurrent data-structures and benchmarks. 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"url": " https://rseng.github.io/software/repository/github/rinikerlab/Ensembler", - "content": "None" + "github/CosmoStat/score": { + "id": "github/CosmoStat/score", + "title": "github/CosmoStat/score", + "url": " https://rseng.github.io/software/repository/github/CosmoStat/score", + "content": "Shape COnstraint REstoration" }, - "github/FraunhoferIWES/foxes": { - "id": "github/FraunhoferIWES/foxes", - "title": "github/FraunhoferIWES/foxes", - "url": " https://rseng.github.io/software/repository/github/FraunhoferIWES/foxes", - "content": "Farm Optimization and eXtended yield Evaluation Software" + "github/CosmoStat/shapepipe": { + "id": "github/CosmoStat/shapepipe", + "title": "github/CosmoStat/shapepipe", + "url": " https://rseng.github.io/software/repository/github/CosmoStat/shapepipe", + "content": "Shape Measurement Pipeline" }, - "github/trygvrad/DF-XRM_viz": { - "id": "github/trygvrad/DF-XRM_viz", - "title": "github/trygvrad/DF-XRM_viz", - "url": " https://rseng.github.io/software/repository/github/trygvrad/DF-XRM_viz", - 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"content": "biopeaks: a graphical user interface for feature extraction from heart- and breathing biosignals" + "github/caseyjlaw/rtpipe": { + "id": "github/caseyjlaw/rtpipe", + "title": "github/caseyjlaw/rtpipe", + "url": " https://rseng.github.io/software/repository/github/caseyjlaw/rtpipe", + "content": "Pipeline for real-time fast transient detection in radio interferometric data (see also https://github.com/realfastvla/rfpipe)" }, - "github/radis/radis": { - "id": "github/radis/radis", - "title": "github/radis/radis", - "url": " https://rseng.github.io/software/repository/github/radis/radis", - "content": "🌱 A fast line-by-line code for high-resolution infrared molecular spectra" + "github/caseyjlaw/tpipe": { + "id": "github/caseyjlaw/tpipe", + "title": "github/caseyjlaw/tpipe", + "url": " https://rseng.github.io/software/repository/github/caseyjlaw/tpipe", + "content": "Python library to search radio interferometry data for dispersed (fast) transients **superseded by caseyjlaw/rtpipe**" }, - 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Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae Kyung Im, Jonathan K. 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"title": "github/captain-exoplanet/misttborn", - "url": " https://rseng.github.io/software/repository/github/captain-exoplanet/misttborn", - "content": "MISTTBORN exoplanet fitting code, and various associated codes" + "github/jeremysanders/dsdeproj": { + "id": "github/jeremysanders/dsdeproj", + "title": "github/jeremysanders/dsdeproj", + "url": " https://rseng.github.io/software/repository/github/jeremysanders/dsdeproj", + "content": "Direct Spectral Deprojection code" }, - "github/dputhier/pygtftk": { - "id": "github/dputhier/pygtftk", - "title": "github/dputhier/pygtftk", - "url": " https://rseng.github.io/software/repository/github/dputhier/pygtftk", - "content": "A python package and a set of shell commands to handle GTF files" + "github/r3w0p/bobocep": { + "id": "github/r3w0p/bobocep", + "title": "github/r3w0p/bobocep", + "url": " https://rseng.github.io/software/repository/github/r3w0p/bobocep", + "content": "A fault-tolerant Complex Event Processing engine designed for edge computing in Internet of Things systems." }, - 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It can also be used as a local assembly tool." }, - "github/pfaucon/PBSIM-PacBio-Simulator": { - "id": "github/pfaucon/PBSIM-PacBio-Simulator", - "title": "github/pfaucon/PBSIM-PacBio-Simulator", - "url": " https://rseng.github.io/software/repository/github/pfaucon/PBSIM-PacBio-Simulator", - "content": "This is an updated mirror of the original PacBio Read Simulator" + "github/GATB/bcalm": { + "id": "github/GATB/bcalm", + "title": "github/GATB/bcalm", + "url": " https://rseng.github.io/software/repository/github/GATB/bcalm", + "content": "compacted de Bruijn graph construction in low memory" + }, + "github/su2code/SU2": { + "id": "github/su2code/SU2", + "title": "github/su2code/SU2", + "url": " https://rseng.github.io/software/repository/github/su2code/SU2", + "content": "SU2: An Open-Source Suite for Multiphysics Simulation and Design" }, "github/magnuspalmblad/shic": { "id": "github/magnuspalmblad/shic", @@ -28791,215 +28827,293 @@ "url": " https://rseng.github.io/software/repository/github/magnuspalmblad/shic", "content": "shic is a collection of shims for use in automated workflow composition" }, - "github/joshuakt/Oxygen-False-Positives": { - "id": "github/joshuakt/Oxygen-False-Positives", - "title": "github/joshuakt/Oxygen-False-Positives", - "url": " https://rseng.github.io/software/repository/github/joshuakt/Oxygen-False-Positives", - "content": "Python source code for planetary evolution model described in Krissansen-Totton et al. 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"content": "AMPtk: Amplicon ToolKit for NGS data (formally UFITS)" + "github/HillLab/SomaticSiMu": { + "id": "github/HillLab/SomaticSiMu", + "title": "github/HillLab/SomaticSiMu", + "url": " https://rseng.github.io/software/repository/github/HillLab/SomaticSiMu", + "content": "SomaticSiMu generates single and double base pair substitutions, and single base pair insertions and deletions of biologically representative mutation signature probabilities and combinations." }, - "github/nextgenusfs/funannotate": { - "id": "github/nextgenusfs/funannotate", - "title": "github/nextgenusfs/funannotate", - "url": " https://rseng.github.io/software/repository/github/nextgenusfs/funannotate", - "content": "Eukaryotic Genome Annotation Pipeline" + "github/dwkim78/ASTRiDE": { + "id": "github/dwkim78/ASTRiDE", + "title": "github/dwkim78/ASTRiDE", + "url": " https://rseng.github.io/software/repository/github/dwkim78/ASTRiDE", + "content": "AUTOMATED STREAK DETECTION FOR ASTRONOMICAL IMAGES" }, - "github/wadpac/GGIR": { - "id": "github/wadpac/GGIR", - "title": "github/wadpac/GGIR", - "url": " https://rseng.github.io/software/repository/github/wadpac/GGIR", - "content": "Code corresponding to R package GGIR" + "github/dwkim78/upsilon": { + "id": "github/dwkim78/upsilon", + "title": "github/dwkim78/upsilon", + "url": " https://rseng.github.io/software/repository/github/dwkim78/upsilon", + "content": "Automated Classification of Periodic Variable Stars Using Machine Learning" + }, + "github/dwkim78/pdtrend": { + "id": "github/dwkim78/pdtrend", + "title": "github/dwkim78/pdtrend", + "url": " https://rseng.github.io/software/repository/github/dwkim78/pdtrend", + "content": "Photometric Detrending Algorithm" + }, + "github/sbailey/empca": { + "id": "github/sbailey/empca", + "title": "github/sbailey/empca", + "url": " https://rseng.github.io/software/repository/github/sbailey/empca", + "content": "Principal Component Analysis (PCA) for Missing and/or Noisy Data" + }, + "github/tnakazato/priism": { + "id": "github/tnakazato/priism", + "title": "github/tnakazato/priism", + "url": " https://rseng.github.io/software/repository/github/tnakazato/priism", + "content": "PRIISM: Python Module for Radio Interferometry Imaging with Sparse Modeling" + }, + "github/mdshw5/pyfaidx": { + "id": "github/mdshw5/pyfaidx", + "title": "github/mdshw5/pyfaidx", + "url": " https://rseng.github.io/software/repository/github/mdshw5/pyfaidx", + "content": "Efficient pythonic random access to fasta subsequences" + }, + "github/PyPO-dev/PyPO": { + "id": "github/PyPO-dev/PyPO", + "title": "github/PyPO-dev/PyPO", + "url": " https://rseng.github.io/software/repository/github/PyPO-dev/PyPO", + "content": "📡 Open-source physical optics simulation package." + }, + "github/jordanlab/STing": { + "id": "github/jordanlab/STing", + "title": "github/jordanlab/STing", + "url": " https://rseng.github.io/software/repository/github/jordanlab/STing", + "content": "Ultrafast sequence typing and gene detection from NGS raw reads" + }, + "github/theosanderson/chronumental": { + "id": "github/theosanderson/chronumental", + "title": "github/theosanderson/chronumental", + "url": " https://rseng.github.io/software/repository/github/theosanderson/chronumental", + "content": "Estimating time trees from very large phylogenies" + }, + "github/FePhyFoFum/phyx": { + "id": "github/FePhyFoFum/phyx", + "title": "github/FePhyFoFum/phyx", + "url": " https://rseng.github.io/software/repository/github/FePhyFoFum/phyx", + "content": "phylogenetics tools for linux (and other mostly posix compliant) computers" + }, + "github/abatten/fruitbat": { + "id": "github/abatten/fruitbat", + "title": "github/abatten/fruitbat", + "url": " https://rseng.github.io/software/repository/github/abatten/fruitbat", + "content": "A fast radio burst (FRB) redshift estimation package written in Python." + }, + "github/dipangwvu/SPEGID": { + "id": "github/dipangwvu/SPEGID", + "title": "github/dipangwvu/SPEGID", + "url": " https://rseng.github.io/software/repository/github/dipangwvu/SPEGID", + "content": "Single-pulse Search Approach" }, - 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" + "github/adithirgis/pollucheck": { + "id": "github/adithirgis/pollucheck", + "title": "github/adithirgis/pollucheck", + "url": " https://rseng.github.io/software/repository/github/adithirgis/pollucheck", + "content": "This application helps exploring the open source air quality data." }, - "github/big-data-lab-team/spot": { - "id": "github/big-data-lab-team/spot", - "title": "github/big-data-lab-team/spot", - "url": " https://rseng.github.io/software/repository/github/big-data-lab-team/spot", - "content": "A set of tools to evaluate the reproducibility of computations" + "github/mrbell/fsclean": { + "id": "github/mrbell/fsclean", + "title": "github/mrbell/fsclean", + "url": " https://rseng.github.io/software/repository/github/mrbell/fsclean", + "content": "A Faraday synthesis application that performs 3D CLEAN deconvolution of multi-frequency, polarized radio interferometric data following Bell & Enßlin (2012)." }, - "github/bcbio/bcbio.variation.recall": { - "id": "github/bcbio/bcbio.variation.recall", - "title": "github/bcbio/bcbio.variation.recall", - "url": " https://rseng.github.io/software/repository/github/bcbio/bcbio.variation.recall", - "content": "Parallel merging, squaring off and ensemble calling for genomic variants" + "github/lucabaldini/ixpeobssim": { + "id": "github/lucabaldini/ixpeobssim", + "title": "github/lucabaldini/ixpeobssim", + "url": " https://rseng.github.io/software/repository/github/lucabaldini/ixpeobssim", + "content": "Simulation and analysis framework for the Imaging X-ray Polarimetry Explorer" }, - "github/bcbio/bcbio-nextgen": { - "id": "github/bcbio/bcbio-nextgen", - "title": "github/bcbio/bcbio-nextgen", - "url": " https://rseng.github.io/software/repository/github/bcbio/bcbio-nextgen", - "content": "Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis" + "github/chrisaberson/BetterReg": { + "id": "github/chrisaberson/BetterReg", + "title": "github/chrisaberson/BetterReg", + "url": " https://rseng.github.io/software/repository/github/chrisaberson/BetterReg", + "content": "Better statistics for regression (OLS and logistic)" }, - 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It comes with a variety of integration schemes and some infrastructure of reading and writing data files." }, - "github/MaayanLab/signature-commons-ui": { - "id": "github/MaayanLab/signature-commons-ui", - "title": "github/MaayanLab/signature-commons-ui", - "url": " https://rseng.github.io/software/repository/github/MaayanLab/signature-commons-ui", - "content": "A front-end UI for demoing API integration" + "github/stammler/dustpylib": { + "id": "github/stammler/dustpylib", + "title": "github/stammler/dustpylib", + "url": " https://rseng.github.io/software/repository/github/stammler/dustpylib", + "content": "Library with auxiliary modules for DustPy" }, - "github/DReichLab/EIG": { - "id": "github/DReichLab/EIG", - "title": "github/DReichLab/EIG", - "url": " https://rseng.github.io/software/repository/github/DReichLab/EIG", - "content": "The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification correction method (Price et al. 2006)." + "github/stammler/dustpy": { + "id": "github/stammler/dustpy", + "title": "github/stammler/dustpy", + "url": " https://rseng.github.io/software/repository/github/stammler/dustpy", + "content": "Python package for the simulation of dust evolution in protoplanetary disks." }, - "github/biocore-ntnu/pyranges": { - "id": "github/biocore-ntnu/pyranges", - "title": "github/biocore-ntnu/pyranges", - "url": " https://rseng.github.io/software/repository/github/biocore-ntnu/pyranges", - "content": "Performant Pythonic GenomicRanges" + "github/gwastro/pycbc": { + "id": "github/gwastro/pycbc", + "title": "github/gwastro/pycbc", + "url": " https://rseng.github.io/software/repository/github/gwastro/pycbc", + "content": "Core package to analyze gravitational-wave data, find signals, and study their parameters. This package was used in the first direct detection of gravitational waves (GW150914), and is used in the ongoing analysis of LIGO/Virgo data. " }, - "github/biocore-ntnu/epic2": { - "id": "github/biocore-ntnu/epic2", - "title": "github/biocore-ntnu/epic2", - "url": " https://rseng.github.io/software/repository/github/biocore-ntnu/epic2", - "content": "Ultraperformant reimplementation of SICER" + "github/jonathanHuwP/CrystalGrowthTracker": { + "id": "github/jonathanHuwP/CrystalGrowthTracker", + "title": "github/jonathanHuwP/CrystalGrowthTracker", + "url": " https://rseng.github.io/software/repository/github/jonathanHuwP/CrystalGrowthTracker", + "content": "Extract face growth rate data from x-ray video of growing crystals." }, - "github/biocore-ntnu/ncls": { - "id": "github/biocore-ntnu/ncls", - "title": "github/biocore-ntnu/ncls", - "url": " https://rseng.github.io/software/repository/github/biocore-ntnu/ncls", - "content": "The Nested Containment List for Python. Basically a static interval-tree that is silly fast for both construction and lookups." + "github/HKU-BAL/Clair3": { + "id": "github/HKU-BAL/Clair3", + "title": "github/HKU-BAL/Clair3", + "url": " https://rseng.github.io/software/repository/github/HKU-BAL/Clair3", + "content": "Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling" }, - "github/GenomicParisCentre/toulligQC": { - "id": "github/GenomicParisCentre/toulligQC", - "title": "github/GenomicParisCentre/toulligQC", - "url": " https://rseng.github.io/software/repository/github/GenomicParisCentre/toulligQC", - "content": "A post sequencing QC tool for Oxford Nanopore sequencers" + "github/eleniadam/npgreat": { + "id": "github/eleniadam/npgreat", + "title": "github/eleniadam/npgreat", + "url": " https://rseng.github.io/software/repository/github/eleniadam/npgreat", + "content": "A hybrid assembly method that utilizes Nanopore and Linked-Reads datasets for the assembly of the human subtelomere regions." }, - "github/Balaje/iceFem": { - "id": "github/Balaje/iceFem", - "title": "github/Balaje/iceFem", - "url": " https://rseng.github.io/software/repository/github/Balaje/iceFem", - "content": "Contains FreeFem source codes for modelling wave induced ice-shelf vibrations" + "github/fakedrtom/oncogemini": { + "id": "github/fakedrtom/oncogemini", + "title": "github/fakedrtom/oncogemini", + "url": " https://rseng.github.io/software/repository/github/fakedrtom/oncogemini", + "content": "None" }, - "github/FitSNAP/FitSNAP": { - "id": "github/FitSNAP/FitSNAP", - "title": "github/FitSNAP/FitSNAP", - "url": " https://rseng.github.io/software/repository/github/FitSNAP/FitSNAP", - "content": "Software for generating SNAP machine-learning interatomic potentials" + "github/ferdymercury/amide": { + "id": "github/ferdymercury/amide", + "title": "github/ferdymercury/amide", + "url": " https://rseng.github.io/software/repository/github/ferdymercury/amide", + "content": "AMIDE: a Medical Imaging Data Examiner" }, - 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"github/christopher-vollmers/C3POa": { - "id": "github/christopher-vollmers/C3POa", - "title": "github/christopher-vollmers/C3POa", - "url": " https://rseng.github.io/software/repository/github/christopher-vollmers/C3POa", - "content": "(Concatemeric Consensus Caller with Partial Order alignments) is a computational pipeline for calling consensi on R2C2 nanopore data." + "github/jfowkes/pycutest": { + "id": "github/jfowkes/pycutest", + "title": "github/jfowkes/pycutest", + "url": " https://rseng.github.io/software/repository/github/jfowkes/pycutest", + "content": "Python interface to CUTEst" + }, + "github/DOnghiaGroup/MGwave": { + "id": "github/DOnghiaGroup/MGwave", + "title": "github/DOnghiaGroup/MGwave", + "url": " https://rseng.github.io/software/repository/github/DOnghiaGroup/MGwave", + "content": "Wavelet transformation code to enable detection of kinematic moving groups in astronomical data." + }, + "github/nlesc-ave/ave-rest-service": { + "id": "github/nlesc-ave/ave-rest-service", + "title": "github/nlesc-ave/ave-rest-service", + "url": " https://rseng.github.io/software/repository/github/nlesc-ave/ave-rest-service", + "content": "visualize (clustered) single-nucleotide variants across genomes" }, - "github/markheckmann/OpenRepGrid.ic": { - "id": "github/markheckmann/OpenRepGrid.ic", - "title": "github/markheckmann/OpenRepGrid.ic", - "url": " https://rseng.github.io/software/repository/github/markheckmann/OpenRepGrid.ic", - "content": "shiny app for interpretive clustering of repgrids:" + "github/czbiohub/cerebra": { + "id": "github/czbiohub/cerebra", + "title": "github/czbiohub/cerebra", + "url": " https://rseng.github.io/software/repository/github/czbiohub/cerebra", + "content": "A tool for fast and accurate summarizing of variant calling format (VCF) files" }, - "github/chocoteam/choco-solver": { - "id": "github/chocoteam/choco-solver", - "title": "github/chocoteam/choco-solver", - "url": " https://rseng.github.io/software/repository/github/chocoteam/choco-solver", - "content": "An open-source Java library for Constraint Programming" + "github/njcuk9999/apero-drs": { + "id": "github/njcuk9999/apero-drs", + "title": "github/njcuk9999/apero-drs", + "url": " https://rseng.github.io/software/repository/github/njcuk9999/apero-drs", + "content": "A PipelinE to Reduce Observations - The DRS for SPIRou (CFHT)" }, - "github/kernsuite-debian/parseltongue": { - "id": "github/kernsuite-debian/parseltongue", - "title": "github/kernsuite-debian/parseltongue", - "url": " https://rseng.github.io/software/repository/github/kernsuite-debian/parseltongue", - "content": "None" + "github/jrenaud90/TidalPy": { + "id": "github/jrenaud90/TidalPy", + "title": "github/jrenaud90/TidalPy", + "url": " https://rseng.github.io/software/repository/github/jrenaud90/TidalPy", + "content": "Software suite to perform solid-body tidal dissipation calculations for rocky and icy worlds" }, - "github/ELeeAstro/gCMCRT": { - "id": "github/ELeeAstro/gCMCRT", - "title": "github/ELeeAstro/gCMCRT", - "url": " https://rseng.github.io/software/repository/github/ELeeAstro/gCMCRT", - "content": "3D Monte Carlo Radiative Transfer for exoplanet atmospheres using GPUs." + "github/asgr/celestial": { + "id": "github/asgr/celestial", + "title": "github/asgr/celestial", + "url": " https://rseng.github.io/software/repository/github/asgr/celestial", + "content": "celestial R package" }, - "github/asgr/ProFuse": { - "id": "github/asgr/ProFuse", - "title": "github/asgr/ProFuse", - "url": " https://rseng.github.io/software/repository/github/asgr/ProFuse", - "content": "ProFound + ProFit + ProSpect = ProFuse" + "github/asgr/NFWdist": { + "id": "github/asgr/NFWdist", + "title": "github/asgr/NFWdist", + "url": " https://rseng.github.io/software/repository/github/asgr/NFWdist", + "content": "Density, distribution function, quantile function and random generation for the 3D NFW profile" }, "github/asgr/ProPane": { "id": "github/asgr/ProPane", @@ -29007,3821 +29121,3809 @@ "url": " https://rseng.github.io/software/repository/github/asgr/ProPane", "content": "Package of stacking related functions, replacing older Rwcs and ProFound related functions." }, + "github/asgr/ProFound": { + "id": "github/asgr/ProFound", + "title": "github/asgr/ProFound", + "url": " https://rseng.github.io/software/repository/github/asgr/ProFound", + "content": "ProFound source finding and extraction" + }, "github/asgr/ProSpect": { "id": "github/asgr/ProSpect", "title": "github/asgr/ProSpect", "url": " https://rseng.github.io/software/repository/github/asgr/ProSpect", "content": "Spectral Generation Package" }, + "github/asgr/ProFuse": { + "id": "github/asgr/ProFuse", + "title": "github/asgr/ProFuse", + "url": " https://rseng.github.io/software/repository/github/asgr/ProFuse", + "content": "ProFound + ProFit + ProSpect = ProFuse" + }, "github/asgr/Rfits": { "id": "github/asgr/Rfits", "title": "github/asgr/Rfits", "url": " https://rseng.github.io/software/repository/github/asgr/Rfits", "content": "Rfits stuff" }, - "github/asgr/ProFound": { - "id": "github/asgr/ProFound", - "title": "github/asgr/ProFound", - "url": " https://rseng.github.io/software/repository/github/asgr/ProFound", - "content": "ProFound source finding and extraction" - }, - "github/asgr/celestial": { - "id": "github/asgr/celestial", - "title": "github/asgr/celestial", - "url": " https://rseng.github.io/software/repository/github/asgr/celestial", - "content": "celestial R package" - }, "github/asgr/hyper.fit": { "id": "github/asgr/hyper.fit", "title": "github/asgr/hyper.fit", "url": " https://rseng.github.io/software/repository/github/asgr/hyper.fit", "content": "The hyper.fit hyperplane fitting package." }, - "github/asgr/NFWdist": { - "id": "github/asgr/NFWdist", - "title": "github/asgr/NFWdist", - "url": " https://rseng.github.io/software/repository/github/asgr/NFWdist", - "content": "Density, distribution function, quantile function and random generation for the 3D NFW profile" - }, "github/asgr/Rwcs": { "id": "github/asgr/Rwcs", "title": "github/asgr/Rwcs", "url": " https://rseng.github.io/software/repository/github/asgr/Rwcs", "content": "Interface to C wcslib" }, - "github/fast-data-transfer/fdt": { - "id": "github/fast-data-transfer/fdt", - "title": "github/fast-data-transfer/fdt", - "url": " https://rseng.github.io/software/repository/github/fast-data-transfer/fdt", - "content": "FDT is an Application for Efficient Data Transfers which is capable of reading and writing at disk speed over wide area networks (with standard TCP). It is written in Java, runs an all major platforms and it is easy to use. FDT is based on an asynchronous, flexible multithreaded system and is using the capabilities of the Java NIO libraries." - }, - "github/pierrehoudayer/RUBIS": { - "id": "github/pierrehoudayer/RUBIS", - "title": "github/pierrehoudayer/RUBIS", - "url": " https://rseng.github.io/software/repository/github/pierrehoudayer/RUBIS", - "content": "Rotation code Using Barotropy conservation over Isopotential Surfaces (RUBIS)" - }, - "github/max0x7ba/atomic_queue": { - "id": "github/max0x7ba/atomic_queue", - "title": "github/max0x7ba/atomic_queue", - "url": " https://rseng.github.io/software/repository/github/max0x7ba/atomic_queue", - "content": "C++ lockless queue." - }, - "github/nabeelre/BTSbot": { - "id": "github/nabeelre/BTSbot", - "title": "github/nabeelre/BTSbot", - "url": " https://rseng.github.io/software/repository/github/nabeelre/BTSbot", - "content": "Automated identification of supernovae with multi-modal deep learning" - }, - "github/nabeelre/NIMBLE": { - "id": "github/nabeelre/NIMBLE", - "title": "github/nabeelre/NIMBLE", - "url": " https://rseng.github.io/software/repository/github/nabeelre/NIMBLE", - "content": "A spherical Jeans modeling tool to compute a system's cumulative mass distribution from (observationally biased) 6D phase space coordinates" - }, - "github/arcaldwell49/SimplyAgree": { - "id": "github/arcaldwell49/SimplyAgree", - "title": "github/arcaldwell49/SimplyAgree", - "url": " https://rseng.github.io/software/repository/github/arcaldwell49/SimplyAgree", - "content": "A simple R package for calculating absolute agreement and estimating required sample sizes for studies of absolute agreement" - }, - "github/sanjibs/bmcmc": { - "id": "github/sanjibs/bmcmc", - "title": "github/sanjibs/bmcmc", - "url": " https://rseng.github.io/software/repository/github/sanjibs/bmcmc", - "content": "MCMC package for Bayesian data analysis" - }, - "github/surhudm/savitzky_golay_with_errors": { - "id": "github/surhudm/savitzky_golay_with_errors", - "title": "github/surhudm/savitzky_golay_with_errors", - "url": " https://rseng.github.io/software/repository/github/surhudm/savitzky_golay_with_errors", - "content": "Improving the Savitzky-Golay filtering in the presence of noisy data" - }, - "github/surhudm/aum": { - "id": "github/surhudm/aum", - "title": "github/surhudm/aum", - "url": " https://rseng.github.io/software/repository/github/surhudm/aum", - "content": "aum" - }, - "github/axgoujon/convex_ridge_regularizers": { - "id": "github/axgoujon/convex_ridge_regularizers", - "title": "github/axgoujon/convex_ridge_regularizers", - "url": " https://rseng.github.io/software/repository/github/axgoujon/convex_ridge_regularizers", - "content": "None" - }, - "github/FarnazFouladi/HashSeq_Manuscript": { - "id": "github/FarnazFouladi/HashSeq_Manuscript", - "title": "github/FarnazFouladi/HashSeq_Manuscript", - "url": " https://rseng.github.io/software/repository/github/FarnazFouladi/HashSeq_Manuscript", - "content": "None" - }, - "github/auctus-team/pycapacity": { - "id": "github/auctus-team/pycapacity", - "title": "github/auctus-team/pycapacity", - "url": " https://rseng.github.io/software/repository/github/auctus-team/pycapacity", - "content": "An efficient task-space capacity calculation package for robotics and biomechanics" - }, - "github/RuiningZHAO/wcpy": { - "id": "github/RuiningZHAO/wcpy", - "title": "github/RuiningZHAO/wcpy", - "url": " https://rseng.github.io/software/repository/github/RuiningZHAO/wcpy", - "content": "A UI for wavelength calibration." - }, - "github/Electrostatics/apbs": { - "id": "github/Electrostatics/apbs", - "title": "github/Electrostatics/apbs", - "url": " https://rseng.github.io/software/repository/github/Electrostatics/apbs", - "content": "Software for biomolecular electrostatics and solvation calculations" - }, - "github/econ-ark/HARK": { - "id": "github/econ-ark/HARK", - "title": "github/econ-ark/HARK", - "url": " https://rseng.github.io/software/repository/github/econ-ark/HARK", - "content": "Heterogenous Agents Resources & toolKit" - }, - "github/lsncibb/microbiomeGWAS": { - "id": "github/lsncibb/microbiomeGWAS", - "title": "github/lsncibb/microbiomeGWAS", - "url": " https://rseng.github.io/software/repository/github/lsncibb/microbiomeGWAS", - "content": "None" - }, - "github/nliulab/HRnV-Calc": { - "id": "github/nliulab/HRnV-Calc", - "title": "github/nliulab/HRnV-Calc", - "url": " https://rseng.github.io/software/repository/github/nliulab/HRnV-Calc", - "content": "HRnV-Calc software for heart rate n-variability and heart rate variability analysis" - }, - "github/Sulstice/cocktail-shaker": { - "id": "github/Sulstice/cocktail-shaker", - "title": "github/Sulstice/cocktail-shaker", - "url": " https://rseng.github.io/software/repository/github/Sulstice/cocktail-shaker", - "content": "None" - }, - "github/galizia-lab/pyview": { - "id": "github/galizia-lab/pyview", - "title": "github/galizia-lab/pyview", - "url": " https://rseng.github.io/software/repository/github/galizia-lab/pyview", - "content": "GUI + API for processing and visualizing Calcium imaging data. Largely based on the IDL software "VIEW" developed by Giovanni Galizia. Implemented in Python by Ajayrama Kumaraswamy" - }, - "github/jbattat/pep_core": { - "id": "github/jbattat/pep_core", - "title": "github/jbattat/pep_core", - "url": " https://rseng.github.io/software/repository/github/jbattat/pep_core", - "content": "PEP: Planetary Ephemeris Program core files" - }, - "github/ugovaretto/molekel": { - "id": "github/ugovaretto/molekel", - "title": "github/ugovaretto/molekel", - "url": " https://rseng.github.io/software/repository/github/ugovaretto/molekel", - "content": "molekel" - }, - "github/duetosymmetry/qnm": { - "id": "github/duetosymmetry/qnm", - "title": "github/duetosymmetry/qnm", - "url": " https://rseng.github.io/software/repository/github/duetosymmetry/qnm", - "content": "Python package for computing Kerr quasinormal mode frequencies, separation constants, and spherical-spheroidal mixing coefficients" + "github/smog-server/OpenSMOG": { + "id": "github/smog-server/OpenSMOG", + "title": "github/smog-server/OpenSMOG", + "url": " https://rseng.github.io/software/repository/github/smog-server/OpenSMOG", + "content": "OpenSMOG is a Python library for performing molecular dynamics simulations using Structure-Based Models. 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"github/ropensci/hunspell": { - "id": "github/ropensci/hunspell", - "title": "github/ropensci/hunspell", - "url": " https://rseng.github.io/software/repository/github/ropensci/hunspell", - "content": "High-Performance Stemmer, Tokenizer, and Spell Checker for R" + "github/konradhoeffner/hdt": { + "id": "github/konradhoeffner/hdt", + "title": "github/konradhoeffner/hdt", + "url": " https://rseng.github.io/software/repository/github/konradhoeffner/hdt", + "content": "Library for the Header Dictionary Triples (HDT) compression file format for RDF data." }, - "github/ropensci/BaseSet": { - "id": "github/ropensci/BaseSet", - "title": "github/ropensci/BaseSet", - "url": " https://rseng.github.io/software/repository/github/ropensci/BaseSet", - "content": "Provides classes for working with sets" + "github/Jesper-Karsten/MBASC": { + "id": "github/Jesper-Karsten/MBASC", + "title": "github/Jesper-Karsten/MBASC", + "url": " https://rseng.github.io/software/repository/github/Jesper-Karsten/MBASC", + "content": "None" }, - "github/ropensci/bikedata": { - "id": "github/ropensci/bikedata", - "title": "github/ropensci/bikedata", - "url": " https://rseng.github.io/software/repository/github/ropensci/bikedata", - "content": ":bike: Extract data from public hire bicycle systems" + "github/jsh58/Genrich": { + "id": "github/jsh58/Genrich", + "title": "github/jsh58/Genrich", + "url": " https://rseng.github.io/software/repository/github/jsh58/Genrich", + "content": "Detecting sites of genomic enrichment" }, - "github/ropensci/rdryad": { - "id": "github/ropensci/rdryad", - "title": "github/ropensci/rdryad", - "url": " https://rseng.github.io/software/repository/github/ropensci/rdryad", - "content": "R client for Dryad web services" + "github/pmkruyen/dearscholar": { + "id": "github/pmkruyen/dearscholar", + "title": "github/pmkruyen/dearscholar", + "url": " https://rseng.github.io/software/repository/github/pmkruyen/dearscholar", + "content": "DearScholar: An open-source smartphone app for longitudinal scientific qualitative and quantitative (self-report) diary, log and survey research" }, - "github/ropensci/virtuoso": { - "id": "github/ropensci/virtuoso", - "title": "github/ropensci/virtuoso", - "url": " https://rseng.github.io/software/repository/github/ropensci/virtuoso", - "content": ":package: Interact with Virtuoso Open Source database instances from R" + "github/JDabringhausen/BiPoS1": { + "id": "github/JDabringhausen/BiPoS1", + "title": "github/JDabringhausen/BiPoS1", + "url": " https://rseng.github.io/software/repository/github/JDabringhausen/BiPoS1", + "content": "This is the first version of the Binary Population Synthesizer (BiPoS1)" }, - "github/ropensci/refsplitr": { - "id": "github/ropensci/refsplitr", - "title": "github/ropensci/refsplitr", - "url": " https://rseng.github.io/software/repository/github/ropensci/refsplitr", - "content": "R package for processing, organizing, and visualizing reference records downloaded from the Web of Science. " + "github/tlambert03/pycudadecon": { + "id": "github/tlambert03/pycudadecon", + "title": "github/tlambert03/pycudadecon", + "url": " https://rseng.github.io/software/repository/github/tlambert03/pycudadecon", + "content": "Python wrapper for cudaDecon - GPU accelerated 3D deconvolution for microscopy" }, - "github/ropensci/tic": { - "id": "github/ropensci/tic", - "title": "github/ropensci/tic", - "url": " https://rseng.github.io/software/repository/github/ropensci/tic", - "content": "Tasks Integrating Continuously: CI-Agnostic Workflow Definitions" + "github/ITA-Solar/rh": { + "id": "github/ITA-Solar/rh", + "title": "github/ITA-Solar/rh", + "url": " https://rseng.github.io/software/repository/github/ITA-Solar/rh", + "content": "RH 1.5D" }, - "github/ropensci/antanym": { - "id": "github/ropensci/antanym", - "title": "github/ropensci/antanym", - "url": " https://rseng.github.io/software/repository/github/ropensci/antanym", - "content": "R package for Antarctic geographic placenames" + "github/myfang2021/VIPPID": { + "id": "github/myfang2021/VIPPID", + "title": "github/myfang2021/VIPPID", + "url": " https://rseng.github.io/software/repository/github/myfang2021/VIPPID", + "content": "None" }, - "github/ropensci/rmangal": { - "id": "github/ropensci/rmangal", - "title": "github/ropensci/rmangal", - "url": " https://rseng.github.io/software/repository/github/ropensci/rmangal", - "content": "Retrieve and explore data from the ecological interactions database MANGAL" + "github/miniufo/xinvert": { + "id": "github/miniufo/xinvert", + "title": "github/miniufo/xinvert", + "url": " https://rseng.github.io/software/repository/github/miniufo/xinvert", + "content": "Invert geophysical fluid dynamic problems (elliptic partial differential equations) using SOR iteration method." }, - "github/ropensci/exoplanets": { - "id": "github/ropensci/exoplanets", - "title": "github/ropensci/exoplanets", - "url": " https://rseng.github.io/software/repository/github/ropensci/exoplanets", - "content": ":earth_americas: Provides access to NASA's Exoplanet Archive" + "github/wfondrie/mokapot": { + "id": "github/wfondrie/mokapot", + "title": "github/wfondrie/mokapot", + "url": " https://rseng.github.io/software/repository/github/wfondrie/mokapot", + "content": "Fast and flexible semi-supervised learning for peptide detection in Python" }, - "github/ropensci/babette": { - "id": "github/ropensci/babette", - "title": "github/ropensci/babette", - "url": " https://rseng.github.io/software/repository/github/ropensci/babette", - "content": "babette is an R package to work with BEAST2" + "github/bio-ontology-research-group/deepgoplus": { + "id": "github/bio-ontology-research-group/deepgoplus", + "title": "github/bio-ontology-research-group/deepgoplus", + "url": " https://rseng.github.io/software/repository/github/bio-ontology-research-group/deepgoplus", + "content": "DeepGO with GOPlus axioms" }, - "github/ropensci/paleobioDB": { - "id": "github/ropensci/paleobioDB", - "title": "github/ropensci/paleobioDB", - "url": " https://rseng.github.io/software/repository/github/ropensci/paleobioDB", - "content": "R interface to the Paleobiology Database" + "github/astroweaver/the_farmer": { + "id": "github/astroweaver/the_farmer", + "title": "github/astroweaver/the_farmer", + "url": " https://rseng.github.io/software/repository/github/astroweaver/the_farmer", + "content": "The Farmer" + }, + "github/rafaeleufrasio/lightning": { + "id": "github/rafaeleufrasio/lightning", + "title": "github/rafaeleufrasio/lightning", + "url": " https://rseng.github.io/software/repository/github/rafaeleufrasio/lightning", + "content": "Lightning SED Fitting Package" }, - "github/ropensci/stats19": { - "id": "github/ropensci/stats19", - "title": "github/ropensci/stats19", - "url": " https://rseng.github.io/software/repository/github/ropensci/stats19", - "content": "R package for working with open road traffic casualty data from Great Britain" + "github/yangyanli/DO-Conv": { + "id": "github/yangyanli/DO-Conv", + "title": "github/yangyanli/DO-Conv", + "url": " https://rseng.github.io/software/repository/github/yangyanli/DO-Conv", + "content": "Depthwise Over-parameterized Convolutional Layer" }, - "github/ropensci/rnaturalearth": { - "id": "github/ropensci/rnaturalearth", - "title": "github/ropensci/rnaturalearth", - "url": " https://rseng.github.io/software/repository/github/ropensci/rnaturalearth", - "content": "an R package to hold and facilitate interaction with natural earth map data :earth_africa:" + "github/rice-solar-physics/EBTEL": { + "id": "github/rice-solar-physics/EBTEL", + "title": "github/rice-solar-physics/EBTEL", + "url": " https://rseng.github.io/software/repository/github/rice-solar-physics/EBTEL", + "content": "Enthalpy-Based Thermal Evolution of Loops (EBTEL) model coded in the IDL language by J. A. Klimchuk, S. Patsourakos, and P.J. Cargill " }, - "github/ropensci/censo2017": { - "id": "github/ropensci/censo2017", - "title": "github/ropensci/censo2017", - "url": " https://rseng.github.io/software/repository/github/ropensci/censo2017", - "content": "Una Base de Datos de Alto Rendimiento del Censo 2017 de Chile." + "github/florpi/sunbird": { + "id": "github/florpi/sunbird", + "title": "github/florpi/sunbird", + "url": " https://rseng.github.io/software/repository/github/florpi/sunbird", + "content": "COsmOlogical inference with dEnsity Split cluStering" }, - "github/ropensci/ssh": { - "id": "github/ropensci/ssh", - "title": "github/ropensci/ssh", - "url": " https://rseng.github.io/software/repository/github/ropensci/ssh", - "content": "Native SSH client in R based on libssh" + "github/MASILab/pyPheWAS": { + "id": "github/MASILab/pyPheWAS", + "title": "github/MASILab/pyPheWAS", + "url": " https://rseng.github.io/software/repository/github/MASILab/pyPheWAS", + "content": "MASI Lab Implementation of PheWAS in Python" }, - "github/ropensci/vcr": { - "id": "github/ropensci/vcr", - "title": "github/ropensci/vcr", - "url": " https://rseng.github.io/software/repository/github/ropensci/vcr", - "content": "Record HTTP calls and replay them" + "github/dirmeier/surjectors": { + "id": "github/dirmeier/surjectors", + "title": "github/dirmeier/surjectors", + "url": " https://rseng.github.io/software/repository/github/dirmeier/surjectors", + "content": "Surjection layers for density estimation with normalizing flows" }, - "github/ropensci/gtfsr": { - "id": "github/ropensci/gtfsr", - "title": "github/ropensci/gtfsr", - "url": " https://rseng.github.io/software/repository/github/ropensci/gtfsr", - "content": "Package for obtaining, validating, viewing, and storing GTFS (transit) data" + "github/pcubillos/rate": { + "id": "github/pcubillos/rate", + "title": "github/pcubillos/rate", + "url": " https://rseng.github.io/software/repository/github/pcubillos/rate", + "content": "Reliable Analytic Thermochemical Equilibrium" }, - "github/ropensci/bib2df": { - "id": "github/ropensci/bib2df", - "title": "github/ropensci/bib2df", - "url": " https://rseng.github.io/software/repository/github/ropensci/bib2df", - "content": "Parse a BibTeX file to a tibble" + "github/pcubillos/repack": { + "id": "github/pcubillos/repack", + "title": "github/pcubillos/repack", + "url": " https://rseng.github.io/software/repository/github/pcubillos/repack", + "content": "Repack and compress line-transition data" }, - "github/ropensci/elastic": { - "id": "github/ropensci/elastic", - "title": "github/ropensci/elastic", - "url": " https://rseng.github.io/software/repository/github/ropensci/elastic", - "content": "R client for the Elasticsearch HTTP API" + "github/pcubillos/pyratbay": { + "id": "github/pcubillos/pyratbay", + "title": "github/pcubillos/pyratbay", + "url": " https://rseng.github.io/software/repository/github/pcubillos/pyratbay", + "content": "Python Radiative Transfer in a Bayesian Framework" }, - "github/ropensci/tidync": { - "id": "github/ropensci/tidync", - "title": "github/ropensci/tidync", - "url": " https://rseng.github.io/software/repository/github/ropensci/tidync", - "content": "NetCDF exploration and data extraction" + "github/pcubillos/mc3": { + "id": "github/pcubillos/mc3", + "title": "github/pcubillos/mc3", + "url": " https://rseng.github.io/software/repository/github/pcubillos/mc3", + "content": "Python MCMC Sampler" }, - "github/ropensci/rnoaa": { - "id": "github/ropensci/rnoaa", - "title": "github/ropensci/rnoaa", - "url": " https://rseng.github.io/software/repository/github/ropensci/rnoaa", - "content": "R interface to many NOAA data APIs" + "github/flemingtonlab/SpliceV": { + "id": "github/flemingtonlab/SpliceV", + "title": "github/flemingtonlab/SpliceV", + "url": " https://rseng.github.io/software/repository/github/flemingtonlab/SpliceV", + "content": "Visualize coverage, canonical, and backsplice junctions." }, - "github/ropensci/USAboundariesData": { - "id": "github/ropensci/USAboundariesData", - "title": "github/ropensci/USAboundariesData", - "url": " https://rseng.github.io/software/repository/github/ropensci/USAboundariesData", - "content": "Datasets for the 'USAboundaries' package" + "github/eScatter/pyelsepa": { + "id": "github/eScatter/pyelsepa", + "title": "github/eScatter/pyelsepa", + "url": " https://rseng.github.io/software/repository/github/eScatter/pyelsepa", + "content": "A Python wrapper for ELSEPA" }, - "github/ropensci/solrium": { - "id": "github/ropensci/solrium", - "title": "github/ropensci/solrium", - "url": " https://rseng.github.io/software/repository/github/ropensci/solrium", - "content": "A general purpose R interface to Solr" + "github/dgarrimar/sqtlseeker2-nf": { + "id": "github/dgarrimar/sqtlseeker2-nf", + "title": "github/dgarrimar/sqtlseeker2-nf", + "url": " https://rseng.github.io/software/repository/github/dgarrimar/sqtlseeker2-nf", + "content": "An automated sQTL mapping pipeline using Nextflow" }, - "github/ropensci/ots": { - "id": "github/ropensci/ots", - "title": "github/ropensci/ots", - "url": " https://rseng.github.io/software/repository/github/ropensci/ots", - "content": "ocean time series datasets" + "github/AndreNicolasChene/DRAGRACES": { + "id": "github/AndreNicolasChene/DRAGRACES", + "title": "github/AndreNicolasChene/DRAGRACES", + "url": " https://rseng.github.io/software/repository/github/AndreNicolasChene/DRAGRACES", + "content": "Reduction pipeline for GRACES spectra (Gemini spectrograph)" }, - "github/ropensci/rAvis": { - "id": "github/ropensci/rAvis", - "title": "github/ropensci/rAvis", - "url": " https://rseng.github.io/software/repository/github/ropensci/rAvis", - "content": "rAvis: an R-package to download the information stored in “proyectoavis”, a citizen science bird project. " + "github/kinnala/scikit-fem": { + "id": "github/kinnala/scikit-fem", + "title": "github/kinnala/scikit-fem", + "url": " https://rseng.github.io/software/repository/github/kinnala/scikit-fem", + "content": "Simple finite element assemblers for Python" }, - "github/ropensci/DataSpaceR": { - "id": "github/ropensci/DataSpaceR", - "title": "github/ropensci/DataSpaceR", - "url": " https://rseng.github.io/software/repository/github/ropensci/DataSpaceR", - "content": "R Interface to the CAVD DataSpace" + "github/pennucci/PulsePortraiture": { + "id": "github/pennucci/PulsePortraiture", + "title": "github/pennucci/PulsePortraiture", + "url": " https://rseng.github.io/software/repository/github/pennucci/PulsePortraiture", + "content": "PulsePortraiture (PP): a wideband pulsar timing code written in python. It uses an extension of Joe Taylor's FFTFIT algorithm (Taylor 1992) to simultaneously measure a phase (TOA) and dispersion measure (DM). PSRCHIVE, lmfit, and the latest vertsions of numpy and scipy are required." }, - "github/ropensci/rsnps": { - "id": "github/ropensci/rsnps", - "title": "github/ropensci/rsnps", - "url": " https://rseng.github.io/software/repository/github/ropensci/rsnps", - "content": "Wrapper to a number of SNP web APIs" + "github/pacificbiosciences/bam2fastx": { + "id": "github/pacificbiosciences/bam2fastx", + "title": "github/pacificbiosciences/bam2fastx", + "url": " https://rseng.github.io/software/repository/github/pacificbiosciences/bam2fastx", + "content": "Converting and demultiplexing of PacBio BAM files into gzipped fasta and fastq files." }, - "github/ropensci/treedata.table": { - "id": "github/ropensci/treedata.table", - "title": "github/ropensci/treedata.table", - "url": " https://rseng.github.io/software/repository/github/ropensci/treedata.table", - "content": "A wrapper for data.table that enables fast manipulation of phylogenetic trees matched to data." + "github/loneknightpy/idba": { + "id": "github/loneknightpy/idba", + "title": "github/loneknightpy/idba", + "url": " https://rseng.github.io/software/repository/github/loneknightpy/idba", + "content": "iterative De Bruijn Graph short read assemblers" }, - "github/ropensci/tacmagic": { - "id": "github/ropensci/tacmagic", - "title": "github/ropensci/tacmagic", - "url": " https://rseng.github.io/software/repository/github/ropensci/tacmagic", - "content": "tacmagic: PET Analysis in R" + "github/labsyspharm/minerva-story": { + "id": "github/labsyspharm/minerva-story", + "title": "github/labsyspharm/minerva-story", + "url": " https://rseng.github.io/software/repository/github/labsyspharm/minerva-story", + "content": "Minerva Story is an image viewer that is designed specifically to make it easy for non-expert users to interact with complex tissue images." }, - "github/ropensci/assertr": { - "id": "github/ropensci/assertr", - "title": "github/ropensci/assertr", - "url": " https://rseng.github.io/software/repository/github/ropensci/assertr", - "content": "Assertive programming for R analysis pipelines" + "github/octapps/octapps": { + "id": "github/octapps/octapps", + "title": "github/octapps/octapps", + "url": " https://rseng.github.io/software/repository/github/octapps/octapps", + "content": "Library of Octave functions for continuous gravitational-wave data analysis" }, - "github/ropensci/microdemic": { - "id": "github/ropensci/microdemic", - "title": "github/ropensci/microdemic", - "url": " https://rseng.github.io/software/repository/github/ropensci/microdemic", - "content": "microsoft academic client" + "github/acerbilab/pybads": { + "id": "github/acerbilab/pybads", + "title": "github/acerbilab/pybads", + "url": " https://rseng.github.io/software/repository/github/acerbilab/pybads", + "content": "PyBADS: Bayesian Adaptive Direct Search optimization algorithm for model fitting in Python" }, - "github/ropensci/rdataretriever": { - "id": "github/ropensci/rdataretriever", - "title": "github/ropensci/rdataretriever", - "url": " https://rseng.github.io/software/repository/github/ropensci/rdataretriever", - "content": "R interface to the Data Retriever" + "github/pennsignals/chime": { + "id": "github/pennsignals/chime", + "title": "github/pennsignals/chime", + "url": " https://rseng.github.io/software/repository/github/pennsignals/chime", + "content": "COVID-19 Hospital Impact Model for Epidemics" }, - "github/ropensci/rnpn": { - "id": "github/ropensci/rnpn", - "title": "github/ropensci/rnpn", - "url": " https://rseng.github.io/software/repository/github/ropensci/rnpn", - "content": "R client for the National Phenology Network database API" + "github/glenco/lensed": { + "id": "github/glenco/lensed", + "title": "github/glenco/lensed", + "url": " https://rseng.github.io/software/repository/github/glenco/lensed", + "content": "forward reconstruction of lenses and sources from strong lensing observations" }, - "github/ropensci/arkdb": { - "id": "github/ropensci/arkdb", - "title": "github/ropensci/arkdb", - "url": " https://rseng.github.io/software/repository/github/ropensci/arkdb", - "content": "Archive and unarchive databases as flat text files" + "github/mtholder/ncl": { + "id": "github/mtholder/ncl", + "title": "github/mtholder/ncl", + "url": " https://rseng.github.io/software/repository/github/mtholder/ncl", + "content": "Nexus Class Library " }, - "github/ropensci/mapscanner": { - "id": "github/ropensci/mapscanner", - 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Single Dish Radio Astronomy Data Reduction Package" }, - "github/ropensci/rgpdd": { - "id": "github/ropensci/rgpdd", - "title": "github/ropensci/rgpdd", - "url": " https://rseng.github.io/software/repository/github/ropensci/rgpdd", - "content": "Interface to the Global Population Dynamics Database, http://www3.imperial.ac.uk/cpb/databases/gpdd" + "github/tvwenger/wisp": { + "id": "github/tvwenger/wisp", + "title": "github/tvwenger/wisp", + "url": " https://rseng.github.io/software/repository/github/tvwenger/wisp", + "content": "WISP: Wenger Interferometry Software Package" + }, + "github/tvwenger/kd": { + "id": "github/tvwenger/kd", + "title": "github/tvwenger/kd", + "url": " https://rseng.github.io/software/repository/github/tvwenger/kd", + "content": "Utilities to calculate kinematic distances" }, - "github/ropensci/grainchanger": { - "id": "github/ropensci/grainchanger", - "title": "github/ropensci/grainchanger", - "url": " https://rseng.github.io/software/repository/github/ropensci/grainchanger", - 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programs that generate code on the fly, then execute it. And having built a piece of code, you can apply various transformations to it (such as loop interchange and tiling)." }, - "github/ropensci/rrlite": { - "id": "github/ropensci/rrlite", - "title": "github/ropensci/rrlite", - "url": " https://rseng.github.io/software/repository/github/ropensci/rrlite", - "content": "R interface to rlite https://github.com/seppo0010/rlite" + "github/xenon-middleware/pyxenon": { + "id": "github/xenon-middleware/pyxenon", + "title": "github/xenon-middleware/pyxenon", + "url": " https://rseng.github.io/software/repository/github/xenon-middleware/pyxenon", + "content": "Python bindings for the Xenon API" }, - "github/ropensci/rglobi": { - "id": "github/ropensci/rglobi", - "title": "github/ropensci/rglobi", - "url": " https://rseng.github.io/software/repository/github/ropensci/rglobi", - "content": "R library to access species interaction data of http://globalbioticinteractions.org" + "github/xenon-middleware/xenon": { + "id": "github/xenon-middleware/xenon", + "title": "github/xenon-middleware/xenon", + "url": " https://rseng.github.io/software/repository/github/xenon-middleware/xenon", + "content": "A middleware abstraction library that provides a simple programming interface to various compute and storage resources." }, - 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"content": "Document DBI connector for R" + "github/koszullab/pareidolia": { + "id": "github/koszullab/pareidolia", + "title": "github/koszullab/pareidolia", + "url": " https://rseng.github.io/software/repository/github/koszullab/pareidolia", + "content": "Multi-sample change detection in Hi-C patterns" }, - "github/ropensci/skynet": { - "id": "github/ropensci/skynet", - "title": "github/ropensci/skynet", - "url": " https://rseng.github.io/software/repository/github/ropensci/skynet", - "content": "Generates networks from BTS DB1B/T-100 data" + "github/GenomePathogenAnalysisService/read-it-and-keep": { + "id": "github/GenomePathogenAnalysisService/read-it-and-keep", + "title": "github/GenomePathogenAnalysisService/read-it-and-keep", + "url": " https://rseng.github.io/software/repository/github/GenomePathogenAnalysisService/read-it-and-keep", + "content": "Read contamination removal" }, - "github/ropensci/traits": { - "id": "github/ropensci/traits", - "title": "github/ropensci/traits", - "url": " https://rseng.github.io/software/repository/github/ropensci/traits", - "content": "Species traits data" + "github/riogroup/SORA": { + "id": "github/riogroup/SORA", + "title": "github/riogroup/SORA", + "url": " https://rseng.github.io/software/repository/github/riogroup/SORA", + "content": "None" }, - "github/ropensci/taxlist": { - "id": "github/ropensci/taxlist", - "title": "github/ropensci/taxlist", - "url": " https://rseng.github.io/software/repository/github/ropensci/taxlist", - "content": "Handling taxonomic lists" + "github/jdonnert/WVTICs": { + "id": "github/jdonnert/WVTICs", + "title": "github/jdonnert/WVTICs", + "url": " https://rseng.github.io/software/repository/github/jdonnert/WVTICs", + "content": "SPH initial conditions using Weighted Voronoi Tesselations" }, - "github/ropensci/rerddap": { - "id": "github/ropensci/rerddap", - "title": "github/ropensci/rerddap", - "url": " https://rseng.github.io/software/repository/github/ropensci/rerddap", - "content": "R client for working with ERDDAP servers" + "github/vprusso/toqito": { + "id": "github/vprusso/toqito", + "title": "github/vprusso/toqito", + "url": " https://rseng.github.io/software/repository/github/vprusso/toqito", + "content": "|toqito> (Theory of Quantum Information Toolkit) in Python :snake:" }, - 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"id": "github/ropensci/gitignore", - "title": "github/ropensci/gitignore", - "url": " https://rseng.github.io/software/repository/github/ropensci/gitignore", - "content": "A R interface to fetch gitignore templates form gitignore.io" + "github/ajohnson-uoregon/llvm-project": { + "id": "github/ajohnson-uoregon/llvm-project", + "title": "github/ajohnson-uoregon/llvm-project", + "url": " https://rseng.github.io/software/repository/github/ajohnson-uoregon/llvm-project", + "content": "The LLVM Project is a collection of modular and reusable compiler and toolchain technologies. Note: the repository does not accept github pull requests at this moment. Please submit your patches at http://reviews.llvm.org." }, - "github/ropensci/mapr": { - "id": "github/ropensci/mapr", - "title": "github/ropensci/mapr", - "url": " https://rseng.github.io/software/repository/github/ropensci/mapr", - "content": "Map species occurrence data" + "github/scrm/scrmhub.io": { + "id": "github/scrm/scrmhub.io", + "title": "github/scrm/scrmhub.io", + "url": " https://rseng.github.io/software/repository/github/scrm/scrmhub.io", + "content": "a coalescent simulator for biological sequences." }, - "github/ropensci/rebird": { - "id": "github/ropensci/rebird", - "title": "github/ropensci/rebird", - "url": " https://rseng.github.io/software/repository/github/ropensci/rebird", - "content": "Wrapper to the eBird API" + "github/Yingjie4Science/SDGdetector": { + "id": "github/Yingjie4Science/SDGdetector", + "title": "github/Yingjie4Science/SDGdetector", + "url": " https://rseng.github.io/software/repository/github/Yingjie4Science/SDGdetector", + "content": "A novel R package that can identify and visualize 17 Sustainable Development Goals and associated 169 Targets in text" }, - "github/ropensci/av": { - "id": "github/ropensci/av", - "title": "github/ropensci/av", - "url": " https://rseng.github.io/software/repository/github/ropensci/av", - "content": "Working with Video in R" + "github/mikessh/oncofuse": { + "id": "github/mikessh/oncofuse", + "title": "github/mikessh/oncofuse", + "url": " https://rseng.github.io/software/repository/github/mikessh/oncofuse", + "content": "Predicting oncogenic potential of gene fusions" }, - "github/ropensci/hddtools": { - "id": "github/ropensci/hddtools", - "title": "github/ropensci/hddtools", - "url": " https://rseng.github.io/software/repository/github/ropensci/hddtools", - "content": "Hydrological Data Discovery Tools (R package for hydrology and open data)" + "github/mikessh/vdjtools": { + "id": "github/mikessh/vdjtools", + "title": "github/mikessh/vdjtools", + "url": " https://rseng.github.io/software/repository/github/mikessh/vdjtools", + "content": "Post-analysis of immune repertoire sequencing data" }, - "github/ropensci/rrricanesdata": { - "id": "github/ropensci/rrricanesdata", - "title": "github/ropensci/rrricanesdata", - "url": " https://rseng.github.io/software/repository/github/ropensci/rrricanesdata", - "content": "Supporting dataset for R package rrricanes" + "github/ReSurfEMG/ReSurfEMG": { + "id": "github/ReSurfEMG/ReSurfEMG", + "title": "github/ReSurfEMG/ReSurfEMG", + "url": " https://rseng.github.io/software/repository/github/ReSurfEMG/ReSurfEMG", + "content": "An open source library for analysis of respiratory EMG" }, - "github/ropensci/outsider": { - "id": "github/ropensci/outsider", - "title": "github/ropensci/outsider", - "url": " https://rseng.github.io/software/repository/github/ropensci/outsider", - "content": ":black_square_button::registered: Install and run programs, outside of R, inside of R" + "github/Pas-Kapli/mptp": { + "id": "github/Pas-Kapli/mptp", + "title": "github/Pas-Kapli/mptp", + "url": " https://rseng.github.io/software/repository/github/Pas-Kapli/mptp", + "content": "mPTP - a tool for single-locus species delimitation" }, - "github/ropensci/rtika": { - "id": "github/ropensci/rtika", - "title": "github/ropensci/rtika", - "url": " https://rseng.github.io/software/repository/github/ropensci/rtika", - "content": "R Interface to Apache Tika" + "github/nekokoe/Plasmer": { + "id": "github/nekokoe/Plasmer", + "title": "github/nekokoe/Plasmer", + "url": " https://rseng.github.io/software/repository/github/nekokoe/Plasmer", + "content": "An accurate and sensitive bacterial plasmid identification tool based on deep machine-learning of shared k-mers and genomic features." }, - "github/ropensci/spocc": { - "id": "github/ropensci/spocc", - "title": "github/ropensci/spocc", - "url": " https://rseng.github.io/software/repository/github/ropensci/spocc", - "content": "Species occurrence data toolkit for R" + "github/iobio-zjut/IPTDFold": { + "id": "github/iobio-zjut/IPTDFold", + "title": "github/iobio-zjut/IPTDFold", + "url": " https://rseng.github.io/software/repository/github/iobio-zjut/IPTDFold", + "content": "A de novo protein structure prediction by iterative partition sampling, topology adjustment, and residue-level distance deviation optimization" }, - "github/ropensci/internetarchive": { - "id": "github/ropensci/internetarchive", - "title": "github/ropensci/internetarchive", - "url": " https://rseng.github.io/software/repository/github/ropensci/internetarchive", - "content": "Search the Internet Archive, retrieve metadata, and download files" + "github/user29A/fastrometry": { + "id": "github/user29A/fastrometry", + "title": "github/user29A/fastrometry", + "url": " https://rseng.github.io/software/repository/github/user29A/fastrometry", + "content": "Fast Automatic World Coordinate Solution Solver. See the github Wiki link below for more info." }, - "github/ropensci/opencv": { - "id": "github/ropensci/opencv", - "title": "github/ropensci/opencv", - "url": " https://rseng.github.io/software/repository/github/ropensci/opencv", - "content": "R bindings for OpenCV" + "github/user29A/CCDLAB": { + "id": "github/user29A/CCDLAB", + "title": "github/user29A/CCDLAB", + "url": " https://rseng.github.io/software/repository/github/user29A/CCDLAB", + "content": "FITS image interaction, world coordinate solving, point source extraction, photometry, etc. See the github Wiki link below for more info. If you require CCDLAB for UVIT, please ensure you have the UVIT Calibration Database which you can find at the CCDLAB Wiki link below." }, - "github/ropensci/tidyhydat": { - "id": "github/ropensci/tidyhydat", - "title": "github/ropensci/tidyhydat", - "url": " https://rseng.github.io/software/repository/github/ropensci/tidyhydat", - "content": "An R package to import Water Survey of Canada hydrometric data and make it tidy" + "github/user29A/JPFITS": { + "id": "github/user29A/JPFITS", + "title": "github/user29A/JPFITS", + "url": " https://rseng.github.io/software/repository/github/user29A/JPFITS", + "content": "FITS File interaction written in Visual Studio C# .Net, compatible across all .Net platforms. JPFITS is not based on any other implementations and is written from the ground-up, consistent with the FITS standard, designed to interact with FITS files as object-oriented structures. See the github Wiki link below for more info." }, - "github/ropensci/cffr": { - "id": "github/ropensci/cffr", - "title": "github/ropensci/cffr", - "url": " https://rseng.github.io/software/repository/github/ropensci/cffr", - "content": "Generate Citation File Format (cff) Metadata for R Packages" + "github/VincentAlcazer/StatAid": { + "id": "github/VincentAlcazer/StatAid", + "title": "github/VincentAlcazer/StatAid", + "url": " https://rseng.github.io/software/repository/github/VincentAlcazer/StatAid", + "content": "StatAid is a Shiny app built in an R package to guide researchers and clinicians through data analysis" }, - "github/ropensci/MtreeRing": { - "id": "github/ropensci/MtreeRing", - "title": "github/ropensci/MtreeRing", - "url": " https://rseng.github.io/software/repository/github/ropensci/MtreeRing", - "content": " A tool for measuring tree-ring width" + "github/ajwheeler/korg.jl": { + "id": "github/ajwheeler/korg.jl", + "title": "github/ajwheeler/korg.jl", + "url": " https://rseng.github.io/software/repository/github/ajwheeler/korg.jl", + "content": "1D LTE stellar spectral synthesis in pure Julia" }, - 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For general information, see" }, - "github/ropensci/rentrez": { - "id": "github/ropensci/rentrez", - "title": "github/ropensci/rentrez", - "url": " https://rseng.github.io/software/repository/github/ropensci/rentrez", - "content": "talk with NCBI entrez using R" + "github/siara-cc/Unishox2": { + "id": "github/siara-cc/Unishox2", + "title": "github/siara-cc/Unishox2", + "url": " https://rseng.github.io/software/repository/github/siara-cc/Unishox2", + "content": "Guaranteed compression for Unicode short strings" }, - "github/ropensci/mauricer": { - "id": "github/ropensci/mauricer", - "title": "github/ropensci/mauricer", - "url": " https://rseng.github.io/software/repository/github/ropensci/mauricer", - "content": "Install BEAST2 packages from R" + "github/bezuidenhoutmc/SeeKAT": { + "id": "github/bezuidenhoutmc/SeeKAT", + "title": "github/bezuidenhoutmc/SeeKAT", + "url": " https://rseng.github.io/software/repository/github/bezuidenhoutmc/SeeKAT", + "content": "A code for localising a single pulse detected in multiple interferometer beams." }, - 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Efficient identification of butterfly sparse matrix factorizations" }, - "github/ropensci/rvertnet": { - "id": "github/ropensci/rvertnet", - "title": "github/ropensci/rvertnet", - "url": " https://rseng.github.io/software/repository/github/ropensci/rvertnet", - "content": "Wrapper to the VertNet API" + "github/leonzheng2/butterfly": { + "id": "github/leonzheng2/butterfly", + "title": "github/leonzheng2/butterfly", + "url": " https://rseng.github.io/software/repository/github/leonzheng2/butterfly", + "content": "None" }, - "github/ropensci/outcomerate": { - "id": "github/ropensci/outcomerate", - "title": "github/ropensci/outcomerate", - "url": " https://rseng.github.io/software/repository/github/ropensci/outcomerate", - "content": "AAPOR Survey Outcome Rates" + "github/AIgnesti/PT-REX": { + "id": "github/AIgnesti/PT-REX", + "title": "github/AIgnesti/PT-REX", + "url": " https://rseng.github.io/software/repository/github/AIgnesti/PT-REX", + "content": "None" }, - "github/ropensci/trufflesniffer": { - "id": "github/ropensci/trufflesniffer", - "title": "github/ropensci/trufflesniffer", - "url": " https://rseng.github.io/software/repository/github/ropensci/trufflesniffer", - "content": "snif out truffles (secrets) [passwords, tokens, api keys]" + "github/takafumi291/ESSENCE": { + "id": "github/takafumi291/ESSENCE", + "title": "github/takafumi291/ESSENCE", + "url": " https://rseng.github.io/software/repository/github/takafumi291/ESSENCE", + "content": "A python package for evaluating the statistical significance of the image analysis and signal detection under correlated noise in the interferometric images (e.g., ALMA, NOEMA)." }, - "github/ropensci/taxadb": { - "id": "github/ropensci/taxadb", - "title": "github/ropensci/taxadb", - "url": " https://rseng.github.io/software/repository/github/ropensci/taxadb", - "content": ":package: Taxonomic Database" + "github/cheginit/HyRiver": { + "id": "github/cheginit/HyRiver", + "title": "github/cheginit/HyRiver", + "url": " https://rseng.github.io/software/repository/github/cheginit/HyRiver", + "content": "A Python software stack for retrieving hydroclimate data from web services." }, - 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The package provides a set of functions to easily navigate and access data from the National Flood Insurance Program along and FEMA's various disaster aid programs." + "github/Eventdisplay/Eventdisplay": { + "id": "github/Eventdisplay/Eventdisplay", + "title": "github/Eventdisplay/Eventdisplay", + "url": " https://rseng.github.io/software/repository/github/Eventdisplay/Eventdisplay", + "content": "A reconstruction and analysis pipeline for ground-based imaging atmospheric Cherenkov Telescopes" }, - "github/ropensci/pathviewr": { - "id": "github/ropensci/pathviewr", - "title": "github/ropensci/pathviewr", - "url": " https://rseng.github.io/software/repository/github/ropensci/pathviewr", - "content": "🐦 Tools to import, clean, and visualize animal movement data in R" + "github/ynop/audiomate": { + "id": "github/ynop/audiomate", + "title": "github/ynop/audiomate", + "url": " https://rseng.github.io/software/repository/github/ynop/audiomate", + "content": "Python library for handling audio datasets." }, - 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All functions are designed to take optional weights" }, - "github/ropensci/rsat": { - "id": "github/ropensci/rsat", - "title": "github/ropensci/rsat", - "url": " https://rseng.github.io/software/repository/github/ropensci/rsat", - "content": "Dealing with Multiplatform Satellite Images from Landsat, MODIS, and Sentinel " + "github/pjedge/longshot": { + "id": "github/pjedge/longshot", + "title": "github/pjedge/longshot", + "url": " https://rseng.github.io/software/repository/github/pjedge/longshot", + "content": "diploid SNV caller for error-prone reads" }, - "github/ropensci/crul": { - "id": "github/ropensci/crul", - "title": "github/ropensci/crul", - "url": " https://rseng.github.io/software/repository/github/ropensci/crul", - "content": "R6 based http client for R (made for developers)" + "github/shinichiroando/sashimi-c": { + "id": "github/shinichiroando/sashimi-c", + "title": "github/shinichiroando/sashimi-c", + "url": " https://rseng.github.io/software/repository/github/shinichiroando/sashimi-c", + "content": "None" }, - 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"url": " https://rseng.github.io/software/repository/github/ropensci/PostcodesioR", - "content": "API wrapper around postcodes.io - free UK postcode lookup and geocoder" + "github/supernnova/SuperNNova": { + "id": "github/supernnova/SuperNNova", + "title": "github/supernnova/SuperNNova", + "url": " https://rseng.github.io/software/repository/github/supernnova/SuperNNova", + "content": "Open Source Photometric classification https://supernnova.readthedocs.io" }, - "github/ropensci/geojsonlint": { - "id": "github/ropensci/geojsonlint", - "title": "github/ropensci/geojsonlint", - "url": " https://rseng.github.io/software/repository/github/ropensci/geojsonlint", - "content": "GeoJSON linting for R (THIS IS NOT THE SRC FOR geojsonlint.com)" + "github/pratheesh3780/grapesAgri1": { + "id": "github/pratheesh3780/grapesAgri1", + "title": "github/pratheesh3780/grapesAgri1", + "url": " https://rseng.github.io/software/repository/github/pratheesh3780/grapesAgri1", + "content": "Collection of shiny apps for Agricultural research Data Analysis. Allows user to have graphical user interface to perform analysis of Agricultural experimental data. On using the functions in this package a Graphical User Interface will pop up. Apps Works by simple upload of files in CSV format." }, - "github/ropensci/emld": { - "id": "github/ropensci/emld", - "title": "github/ropensci/emld", - "url": " https://rseng.github.io/software/repository/github/ropensci/emld", - "content": ":package: JSON-LD representation of EML" + "github/snystrom/memes": { + "id": "github/snystrom/memes", + "title": "github/snystrom/memes", + "url": " https://rseng.github.io/software/repository/github/snystrom/memes", + "content": "An R interface to the MEME Suite" }, - "github/ropensci/stplanr": { - "id": "github/ropensci/stplanr", - "title": "github/ropensci/stplanr", - "url": " https://rseng.github.io/software/repository/github/ropensci/stplanr", - "content": "Sustainable transport planning with R" + "github/smoh/kinesis": { + "id": "github/smoh/kinesis", + "title": "github/smoh/kinesis", + "url": " https://rseng.github.io/software/repository/github/smoh/kinesis", + "content": "kinematic modelling of clusters with gaia" }, - "github/ropensci/ramlegacy": { - 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"github/ropensci/robotstxt": { - "id": "github/ropensci/robotstxt", - "title": "github/ropensci/robotstxt", - "url": " https://rseng.github.io/software/repository/github/ropensci/robotstxt", - "content": "robots.txt file parsing and checking for R" + "github/rpetit3/fastq-scan": { + "id": "github/rpetit3/fastq-scan", + "title": "github/rpetit3/fastq-scan", + "url": " https://rseng.github.io/software/repository/github/rpetit3/fastq-scan", + "content": "Output FASTQ summary statistics in JSON format" }, - "github/ropensci/historydata": { - "id": "github/ropensci/historydata", - "title": "github/ropensci/historydata", - "url": " https://rseng.github.io/software/repository/github/ropensci/historydata", - "content": "Datasets for Historians" + "github/BioGearsEngine/core": { + "id": "github/BioGearsEngine/core", + "title": "github/BioGearsEngine/core", + "url": " https://rseng.github.io/software/repository/github/BioGearsEngine/core", + "content": "Repository for libbiogears and all core utilities" }, - "github/ropensci/restez": { - "id": "github/ropensci/restez", - "title": "github/ropensci/restez", - "url": " https://rseng.github.io/software/repository/github/ropensci/restez", - "content": ":sleeping: :open_file_folder: Create and Query a Local Copy of GenBank in R" + "github/ZacharyJia/opsdn": { + "id": "github/ZacharyJia/opsdn", + "title": "github/ZacharyJia/opsdn", + "url": " https://rseng.github.io/software/repository/github/ZacharyJia/opsdn", + "content": "None" }, - "github/ropensci/fauxpas": { - "id": "github/ropensci/fauxpas", - "title": "github/ropensci/fauxpas", - "url": " https://rseng.github.io/software/repository/github/ropensci/fauxpas", - "content": "fauxpas does http errors" + "github/RabadanLab/arcasHLA": { + "id": "github/RabadanLab/arcasHLA", + "title": "github/RabadanLab/arcasHLA", + "url": " https://rseng.github.io/software/repository/github/RabadanLab/arcasHLA", + "content": "Fast and accurate in silico inference of HLA genotypes from RNA-seq" }, - "github/ropensci/cld3": { - "id": "github/ropensci/cld3", - "title": "github/ropensci/cld3", - "url": " https://rseng.github.io/software/repository/github/ropensci/cld3", - "content": "Bindings to Google's Compact Language Detector 3 " + "github/jeffzhen/omnical": { + "id": "github/jeffzhen/omnical", + "title": "github/jeffzhen/omnical", + "url": " https://rseng.github.io/software/repository/github/jeffzhen/omnical", + "content": "Redundant calibration code for low frequency radio interferometers, managed by Jeff Zheng" }, - "github/ropensci/binman": { - "id": "github/ropensci/binman", - "title": "github/ropensci/binman", - "url": " https://rseng.github.io/software/repository/github/ropensci/binman", - "content": "A Binary Download Manager" + "github/AlgoLab/shark": { + "id": "github/AlgoLab/shark", + "title": "github/AlgoLab/shark", + "url": " https://rseng.github.io/software/repository/github/AlgoLab/shark", + "content": "Mapping-free filtering of irrelevant RNA-Seq reads" }, - "github/ropensci/bold": { - "id": "github/ropensci/bold", - "title": "github/ropensci/bold", - "url": " https://rseng.github.io/software/repository/github/ropensci/bold", - "content": "Interface to the Bold Systems barcode webservice" + "github/ManuelBehrendt/Mera.jl": { + "id": "github/ManuelBehrendt/Mera.jl", + "title": "github/ManuelBehrendt/Mera.jl", + "url": " https://rseng.github.io/software/repository/github/ManuelBehrendt/Mera.jl", + "content": " Analysis Tool for Astrophysical Simulation Data in the Julia Language" }, - "github/ropensci/finch": { - "id": "github/ropensci/finch", - "title": "github/ropensci/finch", - "url": " https://rseng.github.io/software/repository/github/ropensci/finch", - "content": "Read Darwin Core Archive files" + "github/MariaTsantaki/FASMA-synthesis": { + "id": "github/MariaTsantaki/FASMA-synthesis", + "title": "github/MariaTsantaki/FASMA-synthesis", + "url": " https://rseng.github.io/software/repository/github/MariaTsantaki/FASMA-synthesis", + "content": "Python code for stellar spectral analysis" }, - "github/ropensci/tiler": { - "id": "github/ropensci/tiler", - "title": "github/ropensci/tiler", - "url": " https://rseng.github.io/software/repository/github/ropensci/tiler", - "content": "Generate geographic and non-geographic map tiles from R" + "github/ihmwg/python-modelcif": { + "id": "github/ihmwg/python-modelcif", + "title": "github/ihmwg/python-modelcif", + "url": " https://rseng.github.io/software/repository/github/ihmwg/python-modelcif", + "content": " Python package for handling ModelCIF mmCIF and BinaryCIF files " }, - "github/ropensci/jagstargets": { - "id": "github/ropensci/jagstargets", - "title": "github/ropensci/jagstargets", - "url": " https://rseng.github.io/software/repository/github/ropensci/jagstargets", - "content": "Reproducible Bayesian data analysis pipelines with targets and JAGS" + "github/fhcrc/seqmagick": { + "id": "github/fhcrc/seqmagick", + "title": "github/fhcrc/seqmagick", + "url": " https://rseng.github.io/software/repository/github/fhcrc/seqmagick", + "content": "An imagemagick-like frontend to Biopython SeqIO" }, - 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It is written in C++ and depends on the GNU Scientific Library (GSL)." }, - "github/ropensci/rzmq": { - "id": "github/ropensci/rzmq", - "title": "github/ropensci/rzmq", - "url": " https://rseng.github.io/software/repository/github/ropensci/rzmq", - "content": "R package for ZMQ" + "github/jkluter/MLG": { + "id": "github/jkluter/MLG", + "title": "github/jkluter/MLG", + "url": " https://rseng.github.io/software/repository/github/jkluter/MLG", + "content": "Microlensing with Gaia" + }, + "github/pymc-devs/pymc3": { + "id": "github/pymc-devs/pymc3", + "title": "github/pymc-devs/pymc3", + "url": " https://rseng.github.io/software/repository/github/pymc-devs/pymc3", + "content": "Probabilistic Programming in Python: Bayesian Modeling and Probabilistic Machine Learning with Theano" }, - "github/ropensci/dataaimsr": { - "id": "github/ropensci/dataaimsr", - "title": "github/ropensci/dataaimsr", - "url": " https://rseng.github.io/software/repository/github/ropensci/dataaimsr", - "content": "Australian Institute of Marine Science (AIMS) Data Platform API Client which provides easy access to AIMS Data Platform scientific data and information." + "github/pydata/xarray": { + "id": "github/pydata/xarray", + "title": "github/pydata/xarray", + "url": " https://rseng.github.io/software/repository/github/pydata/xarray", + "content": "N-D labeled arrays and datasets in Python" }, - 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"title": "github/ropensci/jsonld", - "url": " https://rseng.github.io/software/repository/github/ropensci/jsonld", - "content": "R wrapper for jsonld.js JavaScript library" + "github/pyxnat/pyxnat": { + "id": "github/pyxnat/pyxnat", + "title": "github/pyxnat/pyxnat", + "url": " https://rseng.github.io/software/repository/github/pyxnat/pyxnat", + "content": "XNAT in Python" }, - "github/ropensci/rfishbase": { - "id": "github/ropensci/rfishbase", - "title": "github/ropensci/rfishbase", - "url": " https://rseng.github.io/software/repository/github/ropensci/rfishbase", - "content": "R interface to the fishbase.org database" + "github/Cosmoglobe/zodipy": { + "id": "github/Cosmoglobe/zodipy", + "title": "github/Cosmoglobe/zodipy", + "url": " https://rseng.github.io/software/repository/github/Cosmoglobe/zodipy", + "content": "Zodiacal emission simulations in timestreams or HEALPix for solar system observers." }, - "github/ropensci/writexl": { - "id": "github/ropensci/writexl", - "title": "github/ropensci/writexl", - "url": " https://rseng.github.io/software/repository/github/ropensci/writexl", - "content": "Portable, light-weight data frame to xlsx exporter for R" + "github/COINtoolbox/ActSNClass": { + "id": "github/COINtoolbox/ActSNClass", + "title": "github/COINtoolbox/ActSNClass", + "url": " https://rseng.github.io/software/repository/github/COINtoolbox/ActSNClass", + "content": "Active Learning for SN photometric classification" }, - "github/ericmandel/funtools": { - "id": "github/ericmandel/funtools", - "title": "github/ericmandel/funtools", - "url": " https://rseng.github.io/software/repository/github/ericmandel/funtools", - "content": "a "minimal buy-in" FITS library and utility package for astronomical data analysis" + "github/COINtoolbox/CosmoPhotoz": { + "id": "github/COINtoolbox/CosmoPhotoz", + "title": "github/COINtoolbox/CosmoPhotoz", + "url": " https://rseng.github.io/software/repository/github/COINtoolbox/CosmoPhotoz", + "content": "Photometric redshift estimator utilising Generalized Linear Models." }, - 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"github/TNEL-UCSD/autolfads-deploy": { - "id": "github/TNEL-UCSD/autolfads-deploy", - "title": "github/TNEL-UCSD/autolfads-deploy", - "url": " https://rseng.github.io/software/repository/github/TNEL-UCSD/autolfads-deploy", - "content": "Deployment strategies for AutoLFADS" + "github/mlr-org/mcboost": { + "id": "github/mlr-org/mcboost", + "title": "github/mlr-org/mcboost", + "url": " https://rseng.github.io/software/repository/github/mlr-org/mcboost", + "content": "Multi-Calibration & Multi-Accuracy Boosting for R" }, - "github/bluenote-1577/sylph": { - "id": "github/bluenote-1577/sylph", - "title": "github/bluenote-1577/sylph", - "url": " https://rseng.github.io/software/repository/github/bluenote-1577/sylph", - "content": "ultrafast ANI querying and taxonomic profiling for metagenomic shotgun samples by abundance-corrected minhash." + "github/tmux/tmux": { + "id": "github/tmux/tmux", + "title": "github/tmux/tmux", + "url": " https://rseng.github.io/software/repository/github/tmux/tmux", + "content": "tmux source code" }, - 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"title": "github/EdanRein/pyPplusS", - "url": " https://rseng.github.io/software/repository/github/EdanRein/pyPplusS", - "content": "pyPplusS code package for modeling exoplanets with rings" + "github/gmrandazzo/libscientific": { + "id": "github/gmrandazzo/libscientific", + "title": "github/gmrandazzo/libscientific", + "url": " https://rseng.github.io/software/repository/github/gmrandazzo/libscientific", + "content": "Libscientific is a C framework for multivariate and other statistical analysis" }, - "github/sanger-pathogens/iva": { - "id": "github/sanger-pathogens/iva", - "title": "github/sanger-pathogens/iva", - "url": " https://rseng.github.io/software/repository/github/sanger-pathogens/iva", - "content": "de novo virus assembler of Illumina paired reads" + "github/lwang-astro/SDAR": { + "id": "github/lwang-astro/SDAR", + "title": "github/lwang-astro/SDAR", + "url": " https://rseng.github.io/software/repository/github/lwang-astro/SDAR", + "content": "Slow-down Algorithmic regularization (SDAR) code for solving few-body problems" }, - "github/sanger-pathogens/snp-sites": { - "id": "github/sanger-pathogens/snp-sites", - "title": "github/sanger-pathogens/snp-sites", - "url": " https://rseng.github.io/software/repository/github/sanger-pathogens/snp-sites", - "content": "Finds SNP sites from a multi-FASTA alignment file" + "github/lwang-astro/PeTar": { + "id": "github/lwang-astro/PeTar", + "title": "github/lwang-astro/PeTar", + "url": " https://rseng.github.io/software/repository/github/lwang-astro/PeTar", + "content": "PeTar is a high-performance N-body code for modelling the evolution of star clusters and tidal streams, including the effect of galactic potential, dynamics of binary and hierarchical system, single and binary stellar evolution." }, - "github/sanger-pathogens/ariba": { - "id": "github/sanger-pathogens/ariba", - "title": "github/sanger-pathogens/ariba", - "url": " https://rseng.github.io/software/repository/github/sanger-pathogens/ariba", - "content": "Antimicrobial Resistance Identification By Assembly" + "github/lzx325/DeeReCT-APA-repo": { + "id": "github/lzx325/DeeReCT-APA-repo", + "title": "github/lzx325/DeeReCT-APA-repo", + "url": " https://rseng.github.io/software/repository/github/lzx325/DeeReCT-APA-repo", + "content": "None" }, - "github/sanger-pathogens/gubbins": { - "id": "github/sanger-pathogens/gubbins", - "title": "github/sanger-pathogens/gubbins", - "url": " https://rseng.github.io/software/repository/github/sanger-pathogens/gubbins", - "content": "Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins" + "github/brandon-rhodes/python-jplephem": { + "id": "github/brandon-rhodes/python-jplephem", + "title": "github/brandon-rhodes/python-jplephem", + "url": " https://rseng.github.io/software/repository/github/brandon-rhodes/python-jplephem", + "content": "Python version of NASA DE4xx ephemerides, the basis for the Astronomical Alamanac" }, - "github/sanger-pathogens/Bio-Tradis": { - "id": "github/sanger-pathogens/Bio-Tradis", - "title": "github/sanger-pathogens/Bio-Tradis", - "url": " https://rseng.github.io/software/repository/github/sanger-pathogens/Bio-Tradis", - "content": "A set of tools to analyse the output from TraDIS analyses" + "github/nialov/fractopo": { + "id": "github/nialov/fractopo", + "title": "github/nialov/fractopo", + "url": " https://rseng.github.io/software/repository/github/nialov/fractopo", + "content": "fractopo is a Python package with tools for validating and analyzing lineament and fracture trace maps" }, - "github/sanger-pathogens/assembly-stats": { - "id": "github/sanger-pathogens/assembly-stats", - "title": "github/sanger-pathogens/assembly-stats", - "url": " https://rseng.github.io/software/repository/github/sanger-pathogens/assembly-stats", - "content": "Get assembly statistics from FASTA and FASTQ files" + "github/OrchardLANL/DPFEHM.jl": { + "id": "github/OrchardLANL/DPFEHM.jl", + "title": "github/OrchardLANL/DPFEHM.jl", + "url": " https://rseng.github.io/software/repository/github/OrchardLANL/DPFEHM.jl", + "content": "DPFEHM: A Differentiable Subsurface Flow Simulator" }, - "github/sanger-pathogens/Artemis": { - "id": "github/sanger-pathogens/Artemis", - "title": "github/sanger-pathogens/Artemis", - "url": " https://rseng.github.io/software/repository/github/sanger-pathogens/Artemis", - "content": "Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation" + "github/coleygroup/pyscreener": { + "id": "github/coleygroup/pyscreener", + "title": "github/coleygroup/pyscreener", + "url": " https://rseng.github.io/software/repository/github/coleygroup/pyscreener", + "content": "pythonic interface to virtual screening software" + }, + "github/ml-evs/matador": { + "id": "github/ml-evs/matador", + "title": "github/ml-evs/matador", + "url": " https://rseng.github.io/software/repository/github/ml-evs/matador", + "content": "⚗️ matador is an aggregator, manipulator and runner of first-principles calculations, written with a bent towards battery 🔋 electrode materials." }, - "github/sanger-pathogens/circlator": { - "id": "github/sanger-pathogens/circlator", - "title": "github/sanger-pathogens/circlator", - "url": " https://rseng.github.io/software/repository/github/sanger-pathogens/circlator", - "content": "Circlator is a tool to circularize genome assemblies. The input is a genome assembly in FASTA format and corrected PacBio or nanopore reads in FASTA or FASTQ format. Circlator will attempt to identify each circular sequence and output a linearised version of it. It does this by assembling all reads that map to contig ends and comparing the resulting contigs with the input assembly." + "github/MedMaxLab/selfEEG": { + "id": "github/MedMaxLab/selfEEG", + "title": "github/MedMaxLab/selfEEG", + "url": " https://rseng.github.io/software/repository/github/MedMaxLab/selfEEG", + "content": "selfEEG: a Python library for Self-Supervised Learning on Electroencephalography (EEG) data" }, - "github/sanger-pathogens/Fastaq": { - "id": "github/sanger-pathogens/Fastaq", - "title": "github/sanger-pathogens/Fastaq", - "url": " https://rseng.github.io/software/repository/github/sanger-pathogens/Fastaq", - "content": "Python3 scripts to manipulate FASTA and FASTQ files" + "github/jfalconbarroso/BAYES-LOSVD": { + "id": "github/jfalconbarroso/BAYES-LOSVD", + "title": "github/jfalconbarroso/BAYES-LOSVD", + "url": " https://rseng.github.io/software/repository/github/jfalconbarroso/BAYES-LOSVD", + "content": "Non-parametric recovery of the LOSVD of galaxies" }, - "github/sanger-pathogens/pymummer": { - "id": "github/sanger-pathogens/pymummer", - "title": "github/sanger-pathogens/pymummer", - "url": " https://rseng.github.io/software/repository/github/sanger-pathogens/pymummer", - "content": "Python3 module for running MUMmer and reading the output" + "github/mishioo/tesliper": { + "id": "github/mishioo/tesliper", + "title": "github/mishioo/tesliper", + "url": " https://rseng.github.io/software/repository/github/mishioo/tesliper", + "content": "Theoretical Spectroscopist's Little Helper" }, - "github/sanger-pathogens/Roary": { - "id": "github/sanger-pathogens/Roary", - "title": "github/sanger-pathogens/Roary", - "url": " https://rseng.github.io/software/repository/github/sanger-pathogens/Roary", - "content": "Rapid large-scale prokaryote pan genome analysis" + "github/SciOmicsLab/PhenoComb": { + "id": "github/SciOmicsLab/PhenoComb", + "title": "github/SciOmicsLab/PhenoComb", + "url": " https://rseng.github.io/software/repository/github/SciOmicsLab/PhenoComb", + "content": "An R package for combinatorial analysis of phenotypes" }, - "github/Blosc/c-blosc": { - "id": "github/Blosc/c-blosc", - "title": "github/Blosc/c-blosc", - "url": " https://rseng.github.io/software/repository/github/Blosc/c-blosc", - "content": "A blocking, shuffling and loss-less compression library that can be faster than `memcpy()`." + "github/MICCoM/SSAGES-public": { + "id": "github/MICCoM/SSAGES-public", + "title": "github/MICCoM/SSAGES-public", + "url": " https://rseng.github.io/software/repository/github/MICCoM/SSAGES-public", + "content": "Software Suite for Advanced General Ensemble Simulations" }, - "github/CarlosCoba/XookSuut-code": { - "id": "github/CarlosCoba/XookSuut-code", - "title": "github/CarlosCoba/XookSuut-code", - "url": " https://rseng.github.io/software/repository/github/CarlosCoba/XookSuut-code", - "content": "XookSuut is a python tool for modeling non-circular flows in galaxies with resolved velocity maps." + "github/MikeSWang/Harmonia": { + "id": "github/MikeSWang/Harmonia", + "title": "github/MikeSWang/Harmonia", + "url": " https://rseng.github.io/software/repository/github/MikeSWang/Harmonia", + "content": "Hybrid-basis inference for large-scale galaxy clustering" }, - 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"github/muLAn-project/muLAn": { - "id": "github/muLAn-project/muLAn", - "title": "github/muLAn-project/muLAn", - "url": " https://rseng.github.io/software/repository/github/muLAn-project/muLAn", - "content": "muLAn: MICROlensing Analysis software" + "github/statOmics/tradeSeqPaper": { + "id": "github/statOmics/tradeSeqPaper", + "title": "github/statOmics/tradeSeqPaper", + "url": " https://rseng.github.io/software/repository/github/statOmics/tradeSeqPaper", + "content": "Scripts to reproduce analyses of tradeSeq paper." }, - "github/RTIInternational/gobbli": { - "id": "github/RTIInternational/gobbli", - "title": "github/RTIInternational/gobbli", - "url": " https://rseng.github.io/software/repository/github/RTIInternational/gobbli", - "content": "Deep learning with text doesn't have to be scary." + "github/statOmics/satuRnPaper": { + "id": "github/statOmics/satuRnPaper", + "title": "github/statOmics/satuRnPaper", + "url": " https://rseng.github.io/software/repository/github/statOmics/satuRnPaper", + "content": "Github repository associated with the publication of *satuRn: Scalable Analysis of Differential Transcript Usage for Bulk and Single-cell RNA-sequencing Applications*" }, - "github/wullm/zwindstroom": { - "id": "github/wullm/zwindstroom", - "title": "github/wullm/zwindstroom", - "url": " https://rseng.github.io/software/repository/github/wullm/zwindstroom", - "content": "Library for cosmic neutrino calculations" + "github/atakan/KeplerSolver": { + "id": "github/atakan/KeplerSolver", + "title": "github/atakan/KeplerSolver", + "url": " https://rseng.github.io/software/repository/github/atakan/KeplerSolver", + "content": "A code for solving Kepler's equation, with arbitrary epoch." }, - "github/wullm/fastdf": { - "id": "github/wullm/fastdf", - "title": "github/wullm/fastdf", - "url": " https://rseng.github.io/software/repository/github/wullm/fastdf", - "content": "Integrate neutrino geodesics in linear theory." + "github/Substra/substra": { + "id": "github/Substra/substra", + "title": "github/Substra/substra", + "url": " https://rseng.github.io/software/repository/github/Substra/substra", + "content": "Low-level Python library used to interact with a Substra network" }, - 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"github/HajimeKawahara/sot": { - "id": "github/HajimeKawahara/sot", - "title": "github/HajimeKawahara/sot", - "url": " https://rseng.github.io/software/repository/github/HajimeKawahara/sot", - "content": "Python package for taking a photo and movie of an exo Earth" + "github/frescigno/magpy_rv": { + "id": "github/frescigno/magpy_rv", + "title": "github/frescigno/magpy_rv", + "url": " https://rseng.github.io/software/repository/github/frescigno/magpy_rv", + "content": "Modelling Activity with Gaussian process regression in Python" }, - "github/UK-Digital-Heart-Project/4Dsurvival": { - "id": "github/UK-Digital-Heart-Project/4Dsurvival", - "title": "github/UK-Digital-Heart-Project/4Dsurvival", - "url": " https://rseng.github.io/software/repository/github/UK-Digital-Heart-Project/4Dsurvival", - "content": "Deep learning cardiac motion analysis for survival prediction" + "github/vmplacco/linemake": { + "id": "github/vmplacco/linemake", + "title": "github/vmplacco/linemake", + "url": " https://rseng.github.io/software/repository/github/vmplacco/linemake", + "content": "linelist generator" }, - "github/UK-Digital-Heart-Project/4Dsegment": { - "id": "github/UK-Digital-Heart-Project/4Dsegment", - "title": "github/UK-Digital-Heart-Project/4Dsegment", - "url": " https://rseng.github.io/software/repository/github/UK-Digital-Heart-Project/4Dsegment", - "content": "None" + "github/khyox/recentrifuge": { + "id": "github/khyox/recentrifuge", + "title": "github/khyox/recentrifuge", + "url": " https://rseng.github.io/software/repository/github/khyox/recentrifuge", + "content": "Recentrifuge: robust comparative analysis and contamination removal for metagenomics" }, - "github/jessecambon/tidygeocoder": { - "id": "github/jessecambon/tidygeocoder", - "title": "github/jessecambon/tidygeocoder", - "url": " https://rseng.github.io/software/repository/github/jessecambon/tidygeocoder", - "content": "Geocoding Made Easy" + "github/AlexanderLabWHOI/EUKulele": { + "id": "github/AlexanderLabWHOI/EUKulele", + "title": "github/AlexanderLabWHOI/EUKulele", + "url": " https://rseng.github.io/software/repository/github/AlexanderLabWHOI/EUKulele", + "content": "Automatic eukaryotic taxonomic classification" }, - 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Maintainers: @keflavich and @bsipocz and @ceb8" }, - "github/equib/equib": { - "id": "github/equib/equib", - "title": "github/equib/equib", - "url": " https://rseng.github.io/software/repository/github/equib/equib", - "content": "EQUIB - Fortran Program for Equilibrium Atomic Populations and Line Emissivities" + "github/astropy/ccdproc": { + "id": "github/astropy/ccdproc", + "title": "github/astropy/ccdproc", + "url": " https://rseng.github.io/software/repository/github/astropy/ccdproc", + "content": "Astropy affiliated package for reducing optical/IR CCD data" }, - "github/pyxnat/pyxnat": { - "id": "github/pyxnat/pyxnat", - "title": "github/pyxnat/pyxnat", - "url": " https://rseng.github.io/software/repository/github/pyxnat/pyxnat", - "content": "XNAT in Python" + "github/astropy/astroplan": { + "id": "github/astropy/astroplan", + "title": "github/astropy/astroplan", + "url": " https://rseng.github.io/software/repository/github/astropy/astroplan", + "content": "Observation planning package for astronomers" }, - "github/marziarivi/RadioLensfit2": { - "id": "github/marziarivi/RadioLensfit2", - "title": "github/marziarivi/RadioLensfit2", - "url": " https://rseng.github.io/software/repository/github/marziarivi/RadioLensfit2", - "content": "Radio Weak Lensing shear measurement in the Visibility Domain " + "github/astropy/SPISEA": { + "id": "github/astropy/SPISEA", + "title": "github/astropy/SPISEA", + "url": " https://rseng.github.io/software/repository/github/astropy/SPISEA", + "content": "Stellar Population Synthesis Modeling" }, - "github/nickhand/pyRSD": { - "id": "github/nickhand/pyRSD", - "title": "github/nickhand/pyRSD", - "url": " https://rseng.github.io/software/repository/github/nickhand/pyRSD", - "content": "Accurate predictions for the clustering of galaxies in redshift-space in Python" + "github/astropy/astroscrappy": { + "id": "github/astropy/astroscrappy", + "title": "github/astropy/astroscrappy", + "url": " https://rseng.github.io/software/repository/github/astropy/astroscrappy", + "content": "Speedy Cosmic Ray Annihilation Package in Python" + }, + "github/astropy/specutils": { + "id": "github/astropy/specutils", + "title": "github/astropy/specutils", + "url": " https://rseng.github.io/software/repository/github/astropy/specutils", + "content": "An Astropy coordinated package for astronomical spectroscopy. Maintainers: @nmearl @rosteen @keflavich @eteq" }, - "github/EGaraldi/ZInCo": { - "id": "github/EGaraldi/ZInCo", - "title": "github/EGaraldi/ZInCo", - "url": " https://rseng.github.io/software/repository/github/EGaraldi/ZInCo", - "content": "The ZInCo code for manipulating GADGET initial conditions" + "github/astropy/astropy": { + "id": "github/astropy/astropy", + "title": "github/astropy/astropy", + "url": " https://rseng.github.io/software/repository/github/astropy/astropy", + "content": "Repository for the Astropy core package" }, - "github/EGaraldi/corecon": { - "id": "github/EGaraldi/corecon", - "title": "github/EGaraldi/corecon", - "url": " https://rseng.github.io/software/repository/github/EGaraldi/corecon", - "content": "User-friendly collection of Reionization-related constraints" + "github/astropy/halotools": { + "id": "github/astropy/halotools", + "title": "github/astropy/halotools", + "url": " https://rseng.github.io/software/repository/github/astropy/halotools", + "content": "Python package for studying large scale structure, cosmology, and galaxy evolution using N-body simulations and halo models" }, - "github/singularityhub/sregistry": { - "id": "github/singularityhub/sregistry", - "title": "github/singularityhub/sregistry", - "url": " https://rseng.github.io/software/repository/github/singularityhub/sregistry", - "content": "server for storage and management of singularity images" + "github/andycasey/sick": { + "id": "github/andycasey/sick", + "title": "github/andycasey/sick", + "url": " https://rseng.github.io/software/repository/github/andycasey/sick", + "content": "sick, the spectroscopic inference crank" }, - "github/singularityhub/singularity-hpc": { - "id": "github/singularityhub/singularity-hpc", - "title": "github/singularityhub/singularity-hpc", - "url": " https://rseng.github.io/software/repository/github/singularityhub/singularity-hpc", - "content": "Local filesystem registry for containers (intended for HPC) using Lmod or Environement Modules. 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It decomposes a multi-objective optimization problem into a number of single-objective optimization sub-problems and then uses a search heuristic to optimize these sub-problems simultaneously and cooperatively." + "github/tomasstolker/pycrires": { + "id": "github/tomasstolker/pycrires", + "title": "github/tomasstolker/pycrires", + "url": " https://rseng.github.io/software/repository/github/tomasstolker/pycrires", + "content": "Data reduction pipeline for VLT/CRIRES+" }, - "github/tidyverse/glue": { - "id": "github/tidyverse/glue", - "title": "github/tidyverse/glue", - "url": " https://rseng.github.io/software/repository/github/tidyverse/glue", - "content": "Glue strings to data in R. Small, fast, dependency free interpreted string literals." + "github/tomasstolker/ARTES": { + "id": "github/tomasstolker/ARTES", + "title": "github/tomasstolker/ARTES", + "url": " https://rseng.github.io/software/repository/github/tomasstolker/ARTES", + "content": "Radiative transfer of polarized light in 3D exoplanet atmospheres" }, - "github/dhubber/seren": { - "id": "github/dhubber/seren", - "title": "github/dhubber/seren", - "url": " https://rseng.github.io/software/repository/github/dhubber/seren", - "content": "SEREN SPH code (Hubber et al. 2011) for astrophysical hydrodynamics simulations" + "github/ianvcaldas/smalldisco": { + "id": "github/ianvcaldas/smalldisco", + "title": "github/ianvcaldas/smalldisco", + "url": " https://rseng.github.io/software/repository/github/ianvcaldas/smalldisco", + "content": "Discovery of siRNA regions and small RNA tail quantification" }, - "github/vanheeringen-lab/gimmemotifs": { - "id": "github/vanheeringen-lab/gimmemotifs", - "title": "github/vanheeringen-lab/gimmemotifs", - "url": " https://rseng.github.io/software/repository/github/vanheeringen-lab/gimmemotifs", - "content": "Suite of motif tools, including a motif prediction pipeline for ChIP-seq experiments. See full GimmeMotifs documentation for detailed installation instructions and usage examples." + "github/masadcv/FastGeodis": { + "id": "github/masadcv/FastGeodis", + "title": "github/masadcv/FastGeodis", + "url": " https://rseng.github.io/software/repository/github/masadcv/FastGeodis", + "content": "Fast Implementation of Generalised Geodesic Distance Transform for CPU (OpenMP) and GPU (CUDA)" }, - "github/drphilmarshall/HumVI": { - "id": "github/drphilmarshall/HumVI", - "title": "github/drphilmarshall/HumVI", - "url": " https://rseng.github.io/software/repository/github/drphilmarshall/HumVI", - "content": "Color composite image creation, mostly following the Lupton, Wherry et al (2004) algorithm." + "github/garrelt/C2-Ray3Dm1D_Helium": { + "id": "github/garrelt/C2-Ray3Dm1D_Helium", + "title": "github/garrelt/C2-Ray3Dm1D_Helium", + "url": " https://rseng.github.io/software/repository/github/garrelt/C2-Ray3Dm1D_Helium", + "content": "C2-Ray radiative transfer / photo-ionziation code, version with helium, combining 1D and 3D" }, - "github/drphilmarshall/Pangloss": { - "id": "github/drphilmarshall/Pangloss", - "title": "github/drphilmarshall/Pangloss", - "url": " https://rseng.github.io/software/repository/github/drphilmarshall/Pangloss", - "content": "Line of sight mass reconstruction in the Universe" + "github/garrelt/C2-Ray1D": { + "id": "github/garrelt/C2-Ray1D", + "title": "github/garrelt/C2-Ray1D", + "url": " https://rseng.github.io/software/repository/github/garrelt/C2-Ray1D", + "content": "1D version of C2-Ray" }, - "github/snowformatics/macrobot": { - "id": "github/snowformatics/macrobot", - "title": "github/snowformatics/macrobot", - "url": " https://rseng.github.io/software/repository/github/snowformatics/macrobot", - "content": "Macrobot is an open source image analysis software for studying plant-pathogen interactions on macroscopic level." + "github/aothmane-control/Algebraic-differentiators": { + "id": "github/aothmane-control/Algebraic-differentiators", + "title": "github/aothmane-control/Algebraic-differentiators", + "url": " https://rseng.github.io/software/repository/github/aothmane-control/Algebraic-differentiators", + "content": "A Python class implementing all necessary tools for the design, analysis, and discretization of algebraic differentiators. 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This tool, intended for long read sequencing such as PacBio or ONT, filters and trims a fastq file." + "github/hall-lab/speedseq": { + "id": "github/hall-lab/speedseq", + "title": "github/hall-lab/speedseq", + "url": " https://rseng.github.io/software/repository/github/hall-lab/speedseq", + "content": "A flexible framework for rapid genome analysis and interpretation" }, - "github/wdecoster/nanolyse": { - "id": "github/wdecoster/nanolyse", - "title": "github/wdecoster/nanolyse", - "url": " https://rseng.github.io/software/repository/github/wdecoster/nanolyse", - "content": "Remove lambda phage reads from a fastq file" + "github/lnferris/ocean_data_tools": { + "id": "github/lnferris/ocean_data_tools", + "title": "github/lnferris/ocean_data_tools", + "url": " https://rseng.github.io/software/repository/github/lnferris/ocean_data_tools", + "content": "A MATLAB toolbox for interacting with bulk freely-available oceanographic data." }, - "github/wdecoster/nanoget": { - "id": "github/wdecoster/nanoget", - "title": "github/wdecoster/nanoget", - "url": " https://rseng.github.io/software/repository/github/wdecoster/nanoget", - "content": "Functions to extract information from Oxford Nanopore sequencing data and alignments" + "github/biocore-ntnu/epic2": { + "id": "github/biocore-ntnu/epic2", + "title": "github/biocore-ntnu/epic2", + "url": " https://rseng.github.io/software/repository/github/biocore-ntnu/epic2", + "content": "Ultraperformant reimplementation of SICER" }, - "github/wdecoster/nanoQC": { - "id": "github/wdecoster/nanoQC", - "title": "github/wdecoster/nanoQC", - "url": " https://rseng.github.io/software/repository/github/wdecoster/nanoQC", - "content": "Quality control tools for nanopore sequencing data" + "github/biocore-ntnu/pyranges": { + "id": "github/biocore-ntnu/pyranges", + "title": "github/biocore-ntnu/pyranges", + "url": " https://rseng.github.io/software/repository/github/biocore-ntnu/pyranges", + "content": "Performant Pythonic GenomicRanges" }, - "github/wdecoster/nanostat": { - "id": "github/wdecoster/nanostat", - "title": "github/wdecoster/nanostat", - "url": " https://rseng.github.io/software/repository/github/wdecoster/nanostat", - "content": "Create statistic summary of an Oxford Nanopore read dataset" + "github/biocore-ntnu/ncls": { + "id": "github/biocore-ntnu/ncls", + "title": "github/biocore-ntnu/ncls", + "url": " https://rseng.github.io/software/repository/github/biocore-ntnu/ncls", + "content": "The Nested Containment List for Python. 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"github/Astroua/SCIMES": { - "id": "github/Astroua/SCIMES", - "title": "github/Astroua/SCIMES", - "url": " https://rseng.github.io/software/repository/github/Astroua/SCIMES", - "content": "Spectral Clustering for Interstellar Molecular Emission Segmentation" + "github/afeinstein20/stella": { + "id": "github/afeinstein20/stella", + "title": "github/afeinstein20/stella", + "url": " https://rseng.github.io/software/repository/github/afeinstein20/stella", + "content": "For characterizing flares with convolutional neural networks" }, - "github/Astroua/TurbuStat": { - "id": "github/Astroua/TurbuStat", - "title": "github/Astroua/TurbuStat", - "url": " https://rseng.github.io/software/repository/github/Astroua/TurbuStat", - "content": "Statistics of Turbulence Python Package" + "github/EpiVec/TDLM": { + "id": "github/EpiVec/TDLM", + "title": "github/EpiVec/TDLM", + "url": " https://rseng.github.io/software/repository/github/EpiVec/TDLM", + "content": ":package: Systematic comparison of trip distribution laws and models" }, - "github/bd-j/sedpy": { - "id": "github/bd-j/sedpy", - "title": "github/bd-j/sedpy", - "url": " https://rseng.github.io/software/repository/github/bd-j/sedpy", - "content": "Utilities for astronomical spectral energy distributions" + "github/BioMedIA/MIRTK": { + "id": "github/BioMedIA/MIRTK", + "title": "github/BioMedIA/MIRTK", + "url": " https://rseng.github.io/software/repository/github/BioMedIA/MIRTK", + "content": "The Medical Image Registration ToolKit (MIRTK), the successor of the IRTK, contains common CMake build configuration files, core libraries, and basic command-line tools. Extension packages are hosted by the MIRTK GitHub group at" }, - "github/bd-j/prospector": { - "id": "github/bd-j/prospector", - "title": "github/bd-j/prospector", - "url": " https://rseng.github.io/software/repository/github/bd-j/prospector", - "content": "Python code for Stellar Population Inference from Spectra and SEDs" + "github/jiwoncpark/baobab": { + "id": "github/jiwoncpark/baobab", + "title": "github/jiwoncpark/baobab", + "url": " https://rseng.github.io/software/repository/github/jiwoncpark/baobab", + "content": "Generates the training data for hierarchical inference of strongly-lensed systems with Bayesian neural networks" }, - "github/cbirdferrer/collatrix": { - "id": "github/cbirdferrer/collatrix", - "title": "github/cbirdferrer/collatrix", - "url": " https://rseng.github.io/software/repository/github/cbirdferrer/collatrix", - "content": "this tool collates the outputs of the MorphoMetriX photogrammetry tool" + "github/ACTCollaboration/zCluster": { + "id": "github/ACTCollaboration/zCluster", + "title": "github/ACTCollaboration/zCluster", + "url": " https://rseng.github.io/software/repository/github/ACTCollaboration/zCluster", + "content": "A package for measuring galaxy cluster photometric redshifts using data from large public surveys." }, - "github/adamgayoso/totalVI_reproducibility": { - "id": "github/adamgayoso/totalVI_reproducibility", - "title": "github/adamgayoso/totalVI_reproducibility", - "url": " https://rseng.github.io/software/repository/github/adamgayoso/totalVI_reproducibility", - "content": "None" + "github/kundajelab/phantompeakqualtools": { + "id": "github/kundajelab/phantompeakqualtools", + "title": "github/kundajelab/phantompeakqualtools", + "url": " https://rseng.github.io/software/repository/github/kundajelab/phantompeakqualtools", + "content": "This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays." }, - "github/gerddie/maxflow": { - "id": "github/gerddie/maxflow", - "title": "github/gerddie/maxflow", - "url": " https://rseng.github.io/software/repository/github/gerddie/maxflow", - "content": "A library that implements the maxflow-mincut algorithm. " + "github/stefanradev93/BayesFlow": { + "id": "github/stefanradev93/BayesFlow", + "title": "github/stefanradev93/BayesFlow", + "url": " https://rseng.github.io/software/repository/github/stefanradev93/BayesFlow", + "content": "A Python library for amortized Bayesian workflows using generative neural networks." }, - "github/domenico-simone/rmlst_api": { - "id": "github/domenico-simone/rmlst_api", - "title": "github/domenico-simone/rmlst_api", - "url": " https://rseng.github.io/software/repository/github/domenico-simone/rmlst_api", - "content": "Run rmlst API through python script" + "github/rdpstaff/ReadSeq": { + "id": "github/rdpstaff/ReadSeq", + "title": "github/rdpstaff/ReadSeq", + "url": " https://rseng.github.io/software/repository/github/rdpstaff/ReadSeq", + "content": "Java based common sequence file format reader and sequence file manipulation. Most RDP projects require this package." }, - "github/damar-wicaksono/uqtestfuns": { - "id": "github/damar-wicaksono/uqtestfuns", - "title": "github/damar-wicaksono/uqtestfuns", - "url": " https://rseng.github.io/software/repository/github/damar-wicaksono/uqtestfuns", - "content": "A Python3 library of test functions from the uncertainty quantification community with a common interface for validation and benchmarking purposes." + "github/rdpstaff/classifier": { + "id": "github/rdpstaff/classifier", + "title": "github/rdpstaff/classifier", + "url": " https://rseng.github.io/software/repository/github/rdpstaff/classifier", + "content": "RDP extensible sequence classifier for fungal lsu, bacterial and archaeal 16s" }, - "github/sorenwacker/ProteomicsQC": { - "id": "github/sorenwacker/ProteomicsQC", - "title": "github/sorenwacker/ProteomicsQC", - "url": " https://rseng.github.io/software/repository/github/sorenwacker/ProteomicsQC", - "content": "Quality Control Pipeline Server for quantitative Proteomics" + "github/rdpstaff/TaxonomyTree": { + "id": "github/rdpstaff/TaxonomyTree", + "title": "github/rdpstaff/TaxonomyTree", + "url": " https://rseng.github.io/software/repository/github/rdpstaff/TaxonomyTree", + "content": "TaxonomyTree building and traversal utility classes." }, - "github/LucyMcGowan/tipr": { - "id": "github/LucyMcGowan/tipr", - "title": "github/LucyMcGowan/tipr", - "url": " https://rseng.github.io/software/repository/github/LucyMcGowan/tipr", - "content": "An R package for conducting sensitivity analyses for unmeasured confounders" + "github/rdpstaff/AlignmentTools": { + "id": "github/rdpstaff/AlignmentTools", + "title": "github/rdpstaff/AlignmentTools", + "url": " https://rseng.github.io/software/repository/github/rdpstaff/AlignmentTools", + "content": "Tools for pairwise sequence comparison, distance calculation, and hidden markov model sequence scoring (using HMMER3 models). Many RDP Projects require this package." }, - "github/JuliaDiff/ForwardDiff.jl": { - "id": "github/JuliaDiff/ForwardDiff.jl", - "title": "github/JuliaDiff/ForwardDiff.jl", - "url": " https://rseng.github.io/software/repository/github/JuliaDiff/ForwardDiff.jl", - "content": "Forward Mode Automatic Differentiation for Julia" + "github/shahmoradi/grb_world": { + "id": "github/shahmoradi/grb_world", + "title": "github/shahmoradi/grb_world", + "url": " https://rseng.github.io/software/repository/github/shahmoradi/grb_world", + "content": "Containing codes for the SGRB and LGRB world models" }, - "github/sibyllema/Fast-Multiscale-Diffusion-on-Graphs": { - "id": "github/sibyllema/Fast-Multiscale-Diffusion-on-Graphs", - "title": "github/sibyllema/Fast-Multiscale-Diffusion-on-Graphs", - "url": " https://rseng.github.io/software/repository/github/sibyllema/Fast-Multiscale-Diffusion-on-Graphs", - "content": "Standalone code to generate the figures for the paper "Fast Multiscale Diffusion on Graphs" accepted at ICASSP 2022." + "github/darioizzo/dcgp": { + "id": "github/darioizzo/dcgp", + "title": "github/darioizzo/dcgp", + "url": " https://rseng.github.io/software/repository/github/darioizzo/dcgp", + "content": "Implementation of a differentiable CGP (Cartesian Genetic Programming)" }, - "github/viash-io/viash": { - "id": "github/viash-io/viash", - "title": "github/viash-io/viash", - "url": " https://rseng.github.io/software/repository/github/viash-io/viash", - "content": "script + metadata = standalone component" + "github/Onogi/VIGoR": { + "id": "github/Onogi/VIGoR", + "title": "github/Onogi/VIGoR", + "url": " https://rseng.github.io/software/repository/github/Onogi/VIGoR", + "content": "Variational Bayesian Inference for Genome-Wide Regression" }, - "github/BogdanCiambur/PROFILER": { - "id": "github/BogdanCiambur/PROFILER", - "title": "github/BogdanCiambur/PROFILER", - "url": " https://rseng.github.io/software/repository/github/BogdanCiambur/PROFILER", - "content": "This repository contains the code Profiler, a Python program for decomposing galaxy light profiles in 1D" + "github/bramvandijk88/cacatoo": { + "id": "github/bramvandijk88/cacatoo", + "title": "github/bramvandijk88/cacatoo", + "url": " https://rseng.github.io/software/repository/github/bramvandijk88/cacatoo", + "content": "A javascript library for building, exploring, and sharing spatially structured models of biological systems" }, - "github/nithyanandan/PRISim": { - "id": "github/nithyanandan/PRISim", - "title": "github/nithyanandan/PRISim", - "url": " https://rseng.github.io/software/repository/github/nithyanandan/PRISim", - "content": "Precision Radio Interferometry Simulator (for radio astronomy applications)" + "github/yesint/EnCurv": { + "id": "github/yesint/EnCurv", + "title": "github/yesint/EnCurv", + "url": " https://rseng.github.io/software/repository/github/yesint/EnCurv", + "content": "Tools for maintaining predefined membrane curvature in MD simulations" }, - "github/mlhutchins/LWPC": { - "id": "github/mlhutchins/LWPC", - "title": "github/mlhutchins/LWPC", - "url": " https://rseng.github.io/software/repository/github/mlhutchins/LWPC", - "content": "Version 2.1 of the U.S. Navy Long Wave Propagation Capability code with alterations for running as a MATLAB function. The altered version has most warning and error reporting removed." + "github/rsnemmen/BCES": { + "id": "github/rsnemmen/BCES", + "title": "github/rsnemmen/BCES", + "url": " https://rseng.github.io/software/repository/github/rsnemmen/BCES", + "content": "Python module for performing linear regression for data with measurement errors and intrinsic scatter" }, - "github/stevengj/nlopt": { - "id": "github/stevengj/nlopt", - "title": "github/stevengj/nlopt", - "url": " https://rseng.github.io/software/repository/github/stevengj/nlopt", - "content": "library for nonlinear optimization, wrapping many algorithms for global and local, constrained or unconstrained, optimization" + "github/bwvdnbro/HydroCode1D": { + "id": "github/bwvdnbro/HydroCode1D", + "title": "github/bwvdnbro/HydroCode1D", + "url": " https://rseng.github.io/software/repository/github/bwvdnbro/HydroCode1D", + "content": "Basic 1D finite volume code that can handle pure 1D problems and problems with 2D and 3D spherical symmetry." }, - "github/deweylab/RSEM": { - "id": "github/deweylab/RSEM", - "title": "github/deweylab/RSEM", - "url": " https://rseng.github.io/software/repository/github/deweylab/RSEM", - "content": "RSEM: accurate quantification of gene and isoform expression from RNA-Seq data" + "github/bwvdnbro/CMacIonize": { + "id": "github/bwvdnbro/CMacIonize", + "title": "github/bwvdnbro/CMacIonize", + "url": " https://rseng.github.io/software/repository/github/bwvdnbro/CMacIonize", + "content": "C++ Monte Carlo photoionization and radiation hydrodynamics code." }, - "github/dcjones/quip": { - "id": "github/dcjones/quip", - "title": "github/dcjones/quip", - "url": " https://rseng.github.io/software/repository/github/dcjones/quip", - "content": "Compressing next-generation sequencing data with extreme prejudice." + "github/narunlifescience/runcircos-gui": { + "id": "github/narunlifescience/runcircos-gui", + "title": "github/narunlifescience/runcircos-gui", + "url": " https://rseng.github.io/software/repository/github/narunlifescience/runcircos-gui", + "content": ":radio_button: GUI tool to run circos" }, - "github/keflavich/HiGal_SEDfitter": { - "id": "github/keflavich/HiGal_SEDfitter", - "title": "github/keflavich/HiGal_SEDfitter", - "url": " https://rseng.github.io/software/repository/github/keflavich/HiGal_SEDfitter", - "content": "SED fitting tools for Herschel Hi-Gal data" + "github/cwentland0/perform": { + "id": "github/cwentland0/perform", + "title": "github/cwentland0/perform", + "url": " https://rseng.github.io/software/repository/github/cwentland0/perform", + "content": "One-dimensional unsteady compressible reacting flow simulation framework, designed for simple prototyping and testing of novel reduced-order model methods." }, - "github/miniufo/xinvert": { - "id": "github/miniufo/xinvert", - "title": "github/miniufo/xinvert", - "url": " https://rseng.github.io/software/repository/github/miniufo/xinvert", - "content": "Invert geophysical fluid dynamic problems (elliptic partial differential equations) using SOR iteration method." + "github/CatarinaMMarques/FisherCosmology": { + "id": "github/CatarinaMMarques/FisherCosmology", + "title": "github/CatarinaMMarques/FisherCosmology", + "url": " https://rseng.github.io/software/repository/github/CatarinaMMarques/FisherCosmology", + "content": "Forecasting Code for Redshift Drift and Alpha Measurements" }, - "github/etempel/Bisous": { - "id": "github/etempel/Bisous", - "title": "github/etempel/Bisous", - "url": " https://rseng.github.io/software/repository/github/etempel/Bisous", + "github/Sarc-Graph/sarcgraph": { + "id": "github/Sarc-Graph/sarcgraph", + "title": "github/Sarc-Graph/sarcgraph", + "url": " https://rseng.github.io/software/repository/github/Sarc-Graph/sarcgraph", "content": "None" }, - "github/martinlackner/abcvoting": { - "id": "github/martinlackner/abcvoting", - "title": "github/martinlackner/abcvoting", - "url": " https://rseng.github.io/software/repository/github/martinlackner/abcvoting", - "content": "Python implementations of approval-based committee (multi-winner) voting rules" - }, - "github/luntergroup/octopus": { - "id": "github/luntergroup/octopus", - "title": "github/luntergroup/octopus", - "url": " https://rseng.github.io/software/repository/github/luntergroup/octopus", - "content": "Bayesian haplotype-based mutation calling" + "github/PaulSt/NGSTrefftz": { + "id": "github/PaulSt/NGSTrefftz", + "title": "github/PaulSt/NGSTrefftz", + "url": " https://rseng.github.io/software/repository/github/PaulSt/NGSTrefftz", + "content": "Add-On to NGSolve for Trefftz methods" }, - "github/JulioHC00/PEPITA": { - "id": "github/JulioHC00/PEPITA", - "title": "github/JulioHC00/PEPITA", - "url": " https://rseng.github.io/software/repository/github/JulioHC00/PEPITA", - "content": "Prediction of Exoplanet Precisions using Information in Transit Analysis" + "github/volkamerlab/opencadd": { + "id": "github/volkamerlab/opencadd", + "title": "github/volkamerlab/opencadd", + "url": " https://rseng.github.io/software/repository/github/volkamerlab/opencadd", + "content": "A Python library for structural cheminformatics" }, - "github/sparks-baird/xtal2png": { - "id": "github/sparks-baird/xtal2png", - "title": "github/sparks-baird/xtal2png", - "url": " https://rseng.github.io/software/repository/github/sparks-baird/xtal2png", - "content": "Encode/decode a crystal structure to/from a grayscale PNG image for direct use with image-based machine learning models such as Palette." + "github/fruzsinaagocs/oscode": { + "id": "github/fruzsinaagocs/oscode", + "title": "github/fruzsinaagocs/oscode", + "url": " https://rseng.github.io/software/repository/github/fruzsinaagocs/oscode", + "content": "Code for efficient solution of oscillatory ordinary differential equations" }, - "github/MCTwo/MCMAC": { - "id": "github/MCTwo/MCMAC", - "title": "github/MCTwo/MCMAC", - "url": " https://rseng.github.io/software/repository/github/MCTwo/MCMAC", - "content": "Monte Carlo Merger Analysis Code (MCMAC)" + "github/jpahlers/LASR": { + "id": "github/jpahlers/LASR", + "title": "github/jpahlers/LASR", + "url": " https://rseng.github.io/software/repository/github/jpahlers/LASR", + "content": "Code and dependencies for the Linear Algorithm for Significance Reduction, developed by various members of the University of Idaho's Department of Physics." }, - "github/afarahi/PoPE": { - "id": "github/afarahi/PoPE", - "title": "github/afarahi/PoPE", - "url": " https://rseng.github.io/software/repository/github/afarahi/PoPE", - "content": "Population Profile Estimator" + "github/ntveem/sterile-dm": { + "id": "github/ntveem/sterile-dm", + "title": "github/ntveem/sterile-dm", + "url": " https://rseng.github.io/software/repository/github/ntveem/sterile-dm", + "content": "A program to follow the production of sterile neutrino dark matter" }, - "github/afarahi/tatter": { - "id": "github/afarahi/tatter", - "title": "github/afarahi/tatter", - "url": " https://rseng.github.io/software/repository/github/afarahi/tatter", - "content": "TATTER (Two-sAmple TesT EstimatoR) is a tool to perform two-sample hypothesis test." + "github/kazewong/flowMC": { + "id": "github/kazewong/flowMC", + "title": "github/kazewong/flowMC", + "url": " https://rseng.github.io/software/repository/github/kazewong/flowMC", + "content": "Normalizing-flow enhanced sampling package for probabilistic inference in Jax" }, - "github/afarahi/kllr": { - "id": "github/afarahi/kllr", - "title": "github/afarahi/kllr", - "url": " https://rseng.github.io/software/repository/github/afarahi/kllr", - "content": "Kernel Localized Linear Regression (KLLR)" + "github/liuhao-cn/fastSHT": { + "id": "github/liuhao-cn/fastSHT", + "title": "github/liuhao-cn/fastSHT", + "url": " https://rseng.github.io/software/repository/github/liuhao-cn/fastSHT", + "content": "Fast Spherical Harmonic Transforms for a large number of sky maps" }, - "github/vincentlab/PyFR": { - "id": "github/vincentlab/PyFR", - "title": "github/vincentlab/PyFR", - "url": " https://rseng.github.io/software/repository/github/vincentlab/PyFR", - "content": "PyFR" + "github/jeremiah-corrado/fem_2d": { + "id": "github/jeremiah-corrado/fem_2d", + "title": "github/jeremiah-corrado/fem_2d", + "url": " https://rseng.github.io/software/repository/github/jeremiah-corrado/fem_2d", + "content": "A rust library for 2D Finite Element Method computations" }, - "github/cnsetzer/kilopop": { - "id": "github/cnsetzer/kilopop", - "title": "github/cnsetzer/kilopop", - "url": " https://rseng.github.io/software/repository/github/cnsetzer/kilopop", - "content": "Binary neutron star (BNS) population of optical kilonovae (kNe)." + "github/philbull/RadioFisher": { + "id": "github/philbull/RadioFisher", + "title": "github/philbull/RadioFisher", + "url": " https://rseng.github.io/software/repository/github/philbull/RadioFisher", + "content": "Fisher forecasting for 21cm intensity mapping and spectroscopic galaxy surveys" }, - "github/jacobmerson/model-traits": { - "id": "github/jacobmerson/model-traits", - "title": "github/jacobmerson/model-traits", - "url": " https://rseng.github.io/software/repository/github/jacobmerson/model-traits", - "content": "simple library for dealing with simulation boundary conditions" + "github/cy-xu/cosmic-conn": { + "id": "github/cy-xu/cosmic-conn", + "title": "github/cy-xu/cosmic-conn", + "url": " https://rseng.github.io/software/repository/github/cy-xu/cosmic-conn", + "content": "Cosmic-CoNN: A Cosmic Ray Detection Deep-Learning Framework, Dataset, and Toolkit" }, - "github/danielenricocahall/elephas": { - "id": "github/danielenricocahall/elephas", - "title": "github/danielenricocahall/elephas", - "url": " https://rseng.github.io/software/repository/github/danielenricocahall/elephas", - "content": "Distributed Deep learning with Keras & Spark" + "github/spectralcode/OCTproZ": { + "id": "github/spectralcode/OCTproZ", + "title": "github/spectralcode/OCTproZ", + "url": " https://rseng.github.io/software/repository/github/spectralcode/OCTproZ", + "content": "OCTproZ is an open source software for optical coherence tomography processing and visualization." }, - "github/xfangcosmo/FFTLog-and-beyond": { - "id": "github/xfangcosmo/FFTLog-and-beyond", - "title": "github/xfangcosmo/FFTLog-and-beyond", - "url": " https://rseng.github.io/software/repository/github/xfangcosmo/FFTLog-and-beyond", - "content": "An FFTLog code for efficiently computing integrals containing 1 spherical Bessel function or Bessel function or its 1st/2nd derivative." + "github/domenico-simone/rmlst_api": { + "id": "github/domenico-simone/rmlst_api", + "title": "github/domenico-simone/rmlst_api", + "url": " https://rseng.github.io/software/repository/github/domenico-simone/rmlst_api", + "content": "Run rmlst API through python script" }, - "github/xfangcosmo/2DFFTLog": { - "id": "github/xfangcosmo/2DFFTLog", - "title": "github/xfangcosmo/2DFFTLog", - "url": " https://rseng.github.io/software/repository/github/xfangcosmo/2DFFTLog", - "content": "2DFFTLog for Covariances from Fourier Space to Real Space" + "github/rega-cev/virulign": { + "id": "github/rega-cev/virulign", + "title": "github/rega-cev/virulign", + "url": " https://rseng.github.io/software/repository/github/rega-cev/virulign", + "content": "VIRULIGN: fast codon-correct alignment and annotation of viral genomes" }, - "github/taranu/AllStarFit": { - "id": "github/taranu/AllStarFit", - "title": "github/taranu/AllStarFit", - "url": " https://rseng.github.io/software/repository/github/taranu/AllStarFit", - "content": "Experimental R package for source detection, PSF and multi-component galaxy fitting" + "github/AnantharamanLab/vRhyme": { + "id": "github/AnantharamanLab/vRhyme", + "title": "github/AnantharamanLab/vRhyme", + "url": " https://rseng.github.io/software/repository/github/AnantharamanLab/vRhyme", + "content": "Binning Virus Genomes from Metagenomes" }, - "github/dunhamlab/PacRAT": { - "id": "github/dunhamlab/PacRAT", - "title": "github/dunhamlab/PacRAT", - "url": " https://rseng.github.io/software/repository/github/dunhamlab/PacRAT", - "content": "Improving long-read barcode-variant mapping using multiple sequence alignment. " + "github/AstroChem/VISIBLE": { + "id": "github/AstroChem/VISIBLE", + "title": "github/AstroChem/VISIBLE", + "url": " https://rseng.github.io/software/repository/github/AstroChem/VISIBLE", + "content": "VISIbility Based Line Extraction" }, - "github/1313e/PRISM": { - "id": "github/1313e/PRISM", - "title": "github/1313e/PRISM", - "url": " https://rseng.github.io/software/repository/github/1313e/PRISM", - "content": "An alternative to MCMC for rapid analysis of models" + "github/sczesla/PyAstronomy": { + "id": "github/sczesla/PyAstronomy", + "title": "github/sczesla/PyAstronomy", + "url": " https://rseng.github.io/software/repository/github/sczesla/PyAstronomy", + "content": "A collection of astronomy-related routines in Python" }, - "github/1313e/CMasher": { - "id": "github/1313e/CMasher", - "title": "github/1313e/CMasher", - "url": " https://rseng.github.io/software/repository/github/1313e/CMasher", - "content": "Scientific colormaps for making accessible, informative and 'cmashing' plots" + "github/saltastro/pyhrs": { + "id": "github/saltastro/pyhrs", + "title": "github/saltastro/pyhrs", + "url": " https://rseng.github.io/software/repository/github/saltastro/pyhrs", + "content": "Software for reducing observations from the SALT High Resolution Spectrograph" }, - "github/BPSB/combine-p-values-discrete": { - "id": "github/BPSB/combine-p-values-discrete", - "title": "github/BPSB/combine-p-values-discrete", - "url": " https://rseng.github.io/software/repository/github/BPSB/combine-p-values-discrete", - "content": "None" + "github/revoltek/losoto": { + "id": "github/revoltek/losoto", + "title": "github/revoltek/losoto", + "url": " https://rseng.github.io/software/repository/github/revoltek/losoto", + "content": "LOFAR solutions tool" }, - "github/teuben/nemo": { - "id": "github/teuben/nemo", - "title": "github/teuben/nemo", - "url": " https://rseng.github.io/software/repository/github/teuben/nemo", - "content": "a Stellar Dynamics Toolbox (Not Everybody Must Observe)" + "github/WangLabTHU/DeSP": { + "id": "github/WangLabTHU/DeSP", + "title": "github/WangLabTHU/DeSP", + "url": " https://rseng.github.io/software/repository/github/WangLabTHU/DeSP", + "content": "DNA-D2S: a systematic error simulation Model for DNA Data Storage channel" }, - "github/teuben/DataComb": { - "id": "github/teuben/DataComb", - "title": "github/teuben/DataComb", - "url": " https://rseng.github.io/software/repository/github/teuben/DataComb", - "content": "Code for the DataComb paper" + "github/mindearth/mobilkit": { + "id": "github/mindearth/mobilkit", + "title": "github/mindearth/mobilkit", + "url": " https://rseng.github.io/software/repository/github/mindearth/mobilkit", + "content": "A Python Toolkit for Urban Resilience and Disaster Risk Management Analytics using High Frequency Human Mobility Data" }, - "github/teuben/QAC": { - "id": "github/teuben/QAC", - "title": "github/teuben/QAC", - "url": " https://rseng.github.io/software/repository/github/teuben/QAC", - "content": "Quick Array Combinations: front end to CASA to run tp2vis, feather and various array combination methods" + "github/ctSkennerton/crass": { + "id": "github/ctSkennerton/crass", + "title": "github/ctSkennerton/crass", + "url": " https://rseng.github.io/software/repository/github/ctSkennerton/crass", + "content": "Crass is designed to identify and reconstruct CRISPR loci from raw metagenomic data without the need for assembly or prior knowledge of CRISPR in the data set." }, - "github/FAU-LAP/NOMAD-CAMELS": { - "id": "github/FAU-LAP/NOMAD-CAMELS", - "title": "github/FAU-LAP/NOMAD-CAMELS", - "url": " https://rseng.github.io/software/repository/github/FAU-LAP/NOMAD-CAMELS", - "content": "We are developing a configurable measurement software (CAMELS), targeted towards the requirements of experimental solid-state physics. Here many experiments utilize a multitude of measurement devices used in dynamically changing setups." + "github/ctSkennerton/minced": { + "id": "github/ctSkennerton/minced", + "title": "github/ctSkennerton/minced", + "url": " https://rseng.github.io/software/repository/github/ctSkennerton/minced", + "content": "Mining CRISPRs in Environmental Datasets" }, - "github/he2016012996/CABnet": { - "id": "github/he2016012996/CABnet", - "title": "github/he2016012996/CABnet", - "url": " https://rseng.github.io/software/repository/github/he2016012996/CABnet", - "content": "None" + "github/connectomicslab/connectomemapper3": { + "id": "github/connectomicslab/connectomemapper3", + "title": "github/connectomicslab/connectomemapper3", + "url": " https://rseng.github.io/software/repository/github/connectomicslab/connectomemapper3", + "content": "Connectome Mapper 3 is a BIDS App that implements full anatomical, diffusion, resting/state functional MRI, and recently EEG processing pipelines, from raw T1 / DWI / BOLD data, and preprocessed EEG to multi-resolution brain parcellation with corresponding connection matrices." }, - "github/RWTH-EBC/AixCaliBuHA": { - "id": "github/RWTH-EBC/AixCaliBuHA", - "title": "github/RWTH-EBC/AixCaliBuHA", - "url": " https://rseng.github.io/software/repository/github/RWTH-EBC/AixCaliBuHA", - "content": "Wield this tool to be King Arthur of your models." + "github/SWE-UniStuttgart/Qlunc": { + "id": "github/SWE-UniStuttgart/Qlunc", + "title": "github/SWE-UniStuttgart/Qlunc", + "url": " https://rseng.github.io/software/repository/github/SWE-UniStuttgart/Qlunc", + "content": "A numerical framework to estimate hardware and data processing uncertainties of a lidar device" }, - "github/pawni/BayesByHypernet": { - "id": "github/pawni/BayesByHypernet", - "title": "github/pawni/BayesByHypernet", - "url": " https://rseng.github.io/software/repository/github/pawni/BayesByHypernet", - "content": "Code for the paper Implicit Weight Uncertainty in Neural Networks" + "github/bihealth/sodar_core": { + "id": "github/bihealth/sodar_core", + "title": "github/bihealth/sodar_core", + "url": " https://rseng.github.io/software/repository/github/bihealth/sodar_core", + "content": "Django-based framework for building scientific data management web apps." }, - "github/zhoulinumass/ML-wPBE": { - "id": "github/zhoulinumass/ML-wPBE", - "title": "github/zhoulinumass/ML-wPBE", - "url": " https://rseng.github.io/software/repository/github/zhoulinumass/ML-wPBE", + "github/SciML/GlobalSensitivity.jl": { + "id": "github/SciML/GlobalSensitivity.jl", + "title": "github/SciML/GlobalSensitivity.jl", + "url": " https://rseng.github.io/software/repository/github/SciML/GlobalSensitivity.jl", "content": "None" }, - "github/scipion-em/scipion-em-continuousflex": { - "id": "github/scipion-em/scipion-em-continuousflex", - "title": "github/scipion-em/scipion-em-continuousflex", - "url": " https://rseng.github.io/software/repository/github/scipion-em/scipion-em-continuousflex", - "content": "Plugin for continuous conformational flexibility analysis containing HEMNMA, StructMap, HEMNMA-3D and TomoFlow for in vitro and in situ cryo-EM/ET." + "github/jfoster17/extinction-distances": { + "id": "github/jfoster17/extinction-distances", + "title": "github/jfoster17/extinction-distances", + "url": " https://rseng.github.io/software/repository/github/jfoster17/extinction-distances", + "content": "Code to implement the blue star number count method from Foster et al. (2012) http://adsabs.harvard.edu/abs/2012ApJ...751..157F" }, - "github/bioturing/hera": { - "id": "github/bioturing/hera", - "title": "github/bioturing/hera", - "url": " https://rseng.github.io/software/repository/github/bioturing/hera", - "content": "a bioinformatics tool that helps analyze RNA-seq data, providing base-to-base alignment BAM files, transcript abundance estimation, and fusion gene detection." + "github/kokron/skyLine": { + "id": "github/kokron/skyLine", + "title": "github/kokron/skyLine", + "url": " https://rseng.github.io/software/repository/github/kokron/skyLine", + "content": "None" }, - "github/pkestene/ramsesGPU": { - "id": "github/pkestene/ramsesGPU", - "title": "github/pkestene/ramsesGPU", - "url": " https://rseng.github.io/software/repository/github/pkestene/ramsesGPU", - "content": "Astrophysics MHD simulation code optimized for large cluster of GPU" + "github/dpryan79/MethylDackel": { + "id": "github/dpryan79/MethylDackel", + "title": "github/dpryan79/MethylDackel", + "url": " https://rseng.github.io/software/repository/github/dpryan79/MethylDackel", + "content": "A (mostly) universal methylation extractor for BS-seq experiments." }, - "github/pkestene/xsmurf": { - "id": "github/pkestene/xsmurf", - "title": "github/pkestene/xsmurf", - "url": " https://rseng.github.io/software/repository/github/pkestene/xsmurf", - "content": "a wavelet-based multifractal image analysis tool implementing the WTMM (Wavelet Transform Modulus Maxima) method." + "github/dpryan79/pyBigWig": { + "id": "github/dpryan79/pyBigWig", + "title": "github/dpryan79/pyBigWig", + "url": " https://rseng.github.io/software/repository/github/dpryan79/pyBigWig", + "content": "A python extension for quick access to bigWig and bigBed files" }, - "github/stedolan/jq": { - "id": "github/stedolan/jq", - "title": "github/stedolan/jq", - "url": " https://rseng.github.io/software/repository/github/stedolan/jq", - "content": "Command-line JSON processor" + "github/dpryan79/libBigWig": { + "id": "github/dpryan79/libBigWig", + "title": "github/dpryan79/libBigWig", + "url": " https://rseng.github.io/software/repository/github/dpryan79/libBigWig", + "content": "A C library for handling bigWig files" }, - "github/torognes/vsearch": { - "id": "github/torognes/vsearch", - "title": "github/torognes/vsearch", - "url": " https://rseng.github.io/software/repository/github/torognes/vsearch", - "content": "Versatile open-source tool for microbiome analysis" + "github/dparks1134/RefineM": { + "id": "github/dparks1134/RefineM", + "title": "github/dparks1134/RefineM", + "url": " https://rseng.github.io/software/repository/github/dparks1134/RefineM", + "content": "A toolbox for improving metagenome-assembled genomes." }, - "github/torognes/swarm": { - "id": "github/torognes/swarm", - "title": "github/torognes/swarm", - "url": " https://rseng.github.io/software/repository/github/torognes/swarm", - "content": "A robust and fast clustering method for amplicon-based studies" + "github/morpheus-project/morpheus": { + "id": "github/morpheus-project/morpheus", + "title": "github/morpheus-project/morpheus", + "url": " https://rseng.github.io/software/repository/github/morpheus-project/morpheus", + "content": "A Library For Generating Morphological Semantic Segmentation Maps of Astronomical Images" }, - "github/kanaverse/kana": { - "id": "github/kanaverse/kana", - "title": "github/kanaverse/kana", - "url": " https://rseng.github.io/software/repository/github/kanaverse/kana", - "content": "Single cell analysis in the browser" + "github/eldariont/svim": { + "id": "github/eldariont/svim", + "title": "github/eldariont/svim", + "url": " https://rseng.github.io/software/repository/github/eldariont/svim", + "content": "Structural Variant Identification Method using Long Reads" }, - "github/tjlcbakx/redshift-search-graphs": { - "id": "github/tjlcbakx/redshift-search-graphs", - "title": "github/tjlcbakx/redshift-search-graphs", - "url": " https://rseng.github.io/software/repository/github/tjlcbakx/redshift-search-graphs", - "content": "Efficient analysis of bandwidth coverage and spectral lines for finding z-specs" + "github/SESMG/SESMG": { + "id": "github/SESMG/SESMG", + "title": "github/SESMG/SESMG", + "url": " https://rseng.github.io/software/repository/github/SESMG/SESMG", + "content": "Model generator for the optimization of energy systems, based on the modeling framework oemof. No programming skills are required to use it, as the parameters are entered using spreadsheets (e.g. Excel, LibreOffice)." }, - "github/e-koch/FilFinder": { - "id": "github/e-koch/FilFinder", - "title": "github/e-koch/FilFinder", - "url": " https://rseng.github.io/software/repository/github/e-koch/FilFinder", - "content": "Detection of filamentary structure in molecular clouds" + "github/astrostat/Automark": { + "id": "github/astrostat/Automark", + "title": "github/astrostat/Automark", + "url": " https://rseng.github.io/software/repository/github/astrostat/Automark", + "content": "Automatic marking of marked Poisson process in astronomical high-dimensional datasets" }, - "github/maxpumperla/hyperas": { - "id": "github/maxpumperla/hyperas", - "title": "github/maxpumperla/hyperas", - "url": " https://rseng.github.io/software/repository/github/maxpumperla/hyperas", - "content": "Keras + Hyperopt: A very simple wrapper for convenient hyperparameter optimization" + "github/astrostat/LIRA": { + "id": "github/astrostat/LIRA", + "title": "github/astrostat/LIRA", + "url": " https://rseng.github.io/software/repository/github/astrostat/LIRA", + "content": "Low-counts Image Reconstruction and Analysis" }, - "github/neuralgraphs/diman": { - "id": "github/neuralgraphs/diman", - "title": "github/neuralgraphs/diman", - "url": " https://rseng.github.io/software/repository/github/neuralgraphs/diman", - "content": "A Clojure library for applying dimensional analysis." + "github/astrostat/BASCS": { + "id": "github/astrostat/BASCS", + "title": "github/astrostat/BASCS", + "url": " https://rseng.github.io/software/repository/github/astrostat/BASCS", + "content": "Bayesian Separation of Close Sources" }, - "github/H-E-L-P/XID_plus": { - "id": "github/H-E-L-P/XID_plus", - "title": "github/H-E-L-P/XID_plus", - "url": " https://rseng.github.io/software/repository/github/H-E-L-P/XID_plus", - "content": "Next generation XID development" + "github/nikhilroxtomar/FANet": { + "id": "github/nikhilroxtomar/FANet", + "title": "github/nikhilroxtomar/FANet", + "url": " https://rseng.github.io/software/repository/github/nikhilroxtomar/FANet", + "content": "FANet: A Feedback Attention Network for Improved Biomedical Image Segmentation [IEEE Transactions on Neural Networks and Learning Systems]" }, - "github/vgl-hub/gfastats": { - "id": "github/vgl-hub/gfastats", - "title": "github/vgl-hub/gfastats", - "url": " https://rseng.github.io/software/repository/github/vgl-hub/gfastats", - "content": "A single fast and exhaustive tool for summary statistics and simultaneous *fa* (fasta, fastq, gfa [.gz]) genome assembly file manipulation." + "github/michaelhb/superplot": { + "id": "github/michaelhb/superplot", + "title": "github/michaelhb/superplot", + "url": " https://rseng.github.io/software/repository/github/michaelhb/superplot", + "content": "GUI for making high-quality plots from data from MultiNest or BAYES-X" }, - "github/r-spatialecology/shar": { - "id": "github/r-spatialecology/shar", - "title": "github/r-spatialecology/shar", - "url": " https://rseng.github.io/software/repository/github/r-spatialecology/shar", - "content": ":package: Analyse species-habitat associations in R" + "github/ericmandel/funtools": { + "id": "github/ericmandel/funtools", + "title": "github/ericmandel/funtools", + "url": " https://rseng.github.io/software/repository/github/ericmandel/funtools", + "content": "a "minimal buy-in" FITS library and utility package for astronomical data analysis" }, - "github/saopicc/DDFacet": { - "id": "github/saopicc/DDFacet", - "title": "github/saopicc/DDFacet", - "url": " https://rseng.github.io/software/repository/github/saopicc/DDFacet", - "content": "DDFacet Imaging Project" + "github/CajoterBraak/demc2": { + "id": "github/CajoterBraak/demc2", + "title": "github/CajoterBraak/demc2", + "url": " https://rseng.github.io/software/repository/github/CajoterBraak/demc2", + "content": "Differential Evolution Markov Chain parameter estimation" }, - "github/saopicc/killMS": { - "id": "github/saopicc/killMS", - "title": "github/saopicc/killMS", - "url": " https://rseng.github.io/software/repository/github/saopicc/killMS", - "content": "Package for direction dependent calibration" + "github/AstarVienna/AnisoCADO": { + "id": "github/AstarVienna/AnisoCADO", + "title": "github/AstarVienna/AnisoCADO", + "url": " https://rseng.github.io/software/repository/github/AstarVienna/AnisoCADO", + "content": "A package to generate off-axis PSFs for the SCAO mode for MICADO at the ELT" }, - "github/tramarobin/fctSPM": { - "id": "github/tramarobin/fctSPM", - "title": "github/tramarobin/fctSPM", - "url": " https://rseng.github.io/software/repository/github/tramarobin/fctSPM", - "content": "Using spm1d package (v.0.4.3), compute anova and post-hoc tests from anova1 to anova3rm, with a non-parametric approach (permutation tests)" + "github/AstarVienna/ScopeSim_Templates": { + "id": "github/AstarVienna/ScopeSim_Templates", + "title": "github/AstarVienna/ScopeSim_Templates", + "url": " https://rseng.github.io/software/repository/github/AstarVienna/ScopeSim_Templates", + "content": "None" }, - "github/Singh-Lab/DeMaSk": { - "id": "github/Singh-Lab/DeMaSk", - "title": "github/Singh-Lab/DeMaSk", - "url": " https://rseng.github.io/software/repository/github/Singh-Lab/DeMaSk", - "content": "Prediction of protein substitution impact using a directional substitution matrix and homolog alignments" + "github/AstarVienna/Pyckles": { + "id": "github/AstarVienna/Pyckles", + "title": "github/AstarVienna/Pyckles", + "url": " https://rseng.github.io/software/repository/github/AstarVienna/Pyckles", + "content": "A super lightweight interface to load spectra from the Pickles 1998 catalogue" }, - "github/Singh-Lab/uKIN": { - "id": "github/Singh-Lab/uKIN", - "title": "github/Singh-Lab/uKIN", - "url": " https://rseng.github.io/software/repository/github/Singh-Lab/uKIN", - "content": "Using Knowledge In Networks" + "github/AstarVienna/irdb": { + "id": "github/AstarVienna/irdb", + "title": "github/AstarVienna/irdb", + "url": " https://rseng.github.io/software/repository/github/AstarVienna/irdb", + "content": "A database containing instrument data for infrared telescopes" }, - "github/jkbonfield/crumble": { - "id": "github/jkbonfield/crumble", - "title": "github/jkbonfield/crumble", - "url": " https://rseng.github.io/software/repository/github/jkbonfield/crumble", - "content": "controllable lossy compression of BAM/CRAM files." + "github/AstarVienna/skycalc_ipy": { + "id": "github/AstarVienna/skycalc_ipy", + "title": "github/AstarVienna/skycalc_ipy", + "url": " https://rseng.github.io/software/repository/github/AstarVienna/skycalc_ipy", + "content": "iPython version of skycalc_cli" }, - 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This contains code for reading and writing a variety of Bioinformatics / DNA Sequence formats." + "github/BitSeq/BitSeq": { + "id": "github/BitSeq/BitSeq", + "title": "github/BitSeq/BitSeq", + "url": " https://rseng.github.io/software/repository/github/BitSeq/BitSeq", + "content": "BitSeq code" }, - "github/jkbonfield/htscodecs": { - "id": "github/jkbonfield/htscodecs", - "title": "github/jkbonfield/htscodecs", - "url": " https://rseng.github.io/software/repository/github/jkbonfield/htscodecs", - "content": "Custom compression for CRAM and others." + "github/skendrew/midIR_sensitivity": { + "id": "github/skendrew/midIR_sensitivity", + "title": "github/skendrew/midIR_sensitivity", + "url": " https://rseng.github.io/software/repository/github/skendrew/midIR_sensitivity", + "content": "Code to calculate the sensitivity of a ground-based instrument for astronomy at mid-infrared wavelengths (3-15 micron). Written for the METIS instrument for the E-ELT but easily customisable." }, - "github/EESI/Complet-Plus": { - "id": "github/EESI/Complet-Plus", - "title": "github/EESI/Complet-Plus", - "url": " https://rseng.github.io/software/repository/github/EESI/Complet-Plus", - "content": "Complet-Plus by Rachel Nguyen and Drexel EESI Lab" + "github/skendrew/milkywayproject_triggering": { + "id": "github/skendrew/milkywayproject_triggering", + "title": "github/skendrew/milkywayproject_triggering", + "url": " https://rseng.github.io/software/repository/github/skendrew/milkywayproject_triggering", + "content": "Code to calculate correlation functions for two (astrophysical) catalogue datasets" }, - "github/WGLab/InterVar": { - "id": "github/WGLab/InterVar", - "title": "github/WGLab/InterVar", - "url": " https://rseng.github.io/software/repository/github/WGLab/InterVar", - "content": "A bioinformatics software tool for clinical interpretation of genetic variants by the 2015 ACMG-AMP guideline" + "github/ethankruse/koi3278": { + "id": "github/ethankruse/koi3278", + "title": "github/ethankruse/koi3278", + "url": " https://rseng.github.io/software/repository/github/ethankruse/koi3278", + "content": "Analysis files for the KOI-3278 system" }, - "github/WGLab/LongGF": { - "id": "github/WGLab/LongGF", - "title": "github/WGLab/LongGF", - "url": " https://rseng.github.io/software/repository/github/WGLab/LongGF", - "content": "A computational algorithm and software tool for fast and accurate detection of gene fusion by long-read transcriptome sequencing" + "github/henry2004y/Vlasiator.jl": { + "id": "github/henry2004y/Vlasiator.jl", + "title": "github/henry2004y/Vlasiator.jl", + "url": " https://rseng.github.io/software/repository/github/henry2004y/Vlasiator.jl", + "content": "Data processor for Vlasiator" }, - "github/ratt-ru/eidos": { - "id": "github/ratt-ru/eidos", - "title": "github/ratt-ru/eidos", - "url": " https://rseng.github.io/software/repository/github/ratt-ru/eidos", - "content": "Modelling primary beams of radio astronomy antennas" + "github/piernik-dev/piernik": { + "id": "github/piernik-dev/piernik", + "title": "github/piernik-dev/piernik", + "url": " https://rseng.github.io/software/repository/github/piernik-dev/piernik", + "content": "Piernik MHD Code" }, - "github/ratt-ru/QuartiCal": { - "id": "github/ratt-ru/QuartiCal", - "title": "github/ratt-ru/QuartiCal", - "url": " https://rseng.github.io/software/repository/github/ratt-ru/QuartiCal", - "content": "CubiCal, but with greater power." + "github/tp2vis/distribute": { + "id": "github/tp2vis/distribute", + "title": "github/tp2vis/distribute", + "url": " https://rseng.github.io/software/repository/github/tp2vis/distribute", + "content": "None" }, - "github/ratt-ru/solarkat": { - "id": "github/ratt-ru/solarkat", - "title": "github/ratt-ru/solarkat", - "url": " https://rseng.github.io/software/repository/github/ratt-ru/solarkat", - "content": "MeerKAT as a solar telescope" + "github/AngusWright/LAMBDAR": { + "id": "github/AngusWright/LAMBDAR", + "title": "github/AngusWright/LAMBDAR", + "url": " https://rseng.github.io/software/repository/github/AngusWright/LAMBDAR", + "content": "LAMBDAR: Lambda Adaptive Multi-Band Deblending Algorithm in R" }, - "github/ratt-ru/CubiCal": { - "id": "github/ratt-ru/CubiCal", - "title": "github/ratt-ru/CubiCal", - "url": " https://rseng.github.io/software/repository/github/ratt-ru/CubiCal", - "content": "A fast radio interferometric calibration suite." + "github/sybila/biodivine-aeon-py": { + "id": "github/sybila/biodivine-aeon-py", + "title": "github/sybila/biodivine-aeon-py", + "url": " https://rseng.github.io/software/repository/github/sybila/biodivine-aeon-py", + "content": "None" }, - "github/ratt-ru/montblanc": { - "id": "github/ratt-ru/montblanc", - "title": "github/ratt-ru/montblanc", - "url": " https://rseng.github.io/software/repository/github/ratt-ru/montblanc", - "content": "GPU-accelerated RIME implementations. An offshoot of the BIRO projects, and one of the foothills of Mt Exaflop." + "github/markusbonse/applefy": { + "id": "github/markusbonse/applefy", + "title": "github/markusbonse/applefy", + "url": " https://rseng.github.io/software/repository/github/markusbonse/applefy", + "content": "A Python package for calculating detection limits for exoplanet high contrast imaging (HCI) datasets." }, - "github/ratt-ru/PyMORESANE": { - "id": "github/ratt-ru/PyMORESANE", - "title": "github/ratt-ru/PyMORESANE", - "url": " https://rseng.github.io/software/repository/github/ratt-ru/PyMORESANE", - "content": "Repository for the Python version of the MORESANE deconvolution algorithm" + "github/haoharryfeng/NeuCA": { + "id": "github/haoharryfeng/NeuCA", + "title": "github/haoharryfeng/NeuCA", + "url": " https://rseng.github.io/software/repository/github/haoharryfeng/NeuCA", + "content": "Neural-network based Cell Annotation tool" }, - "github/ratt-ru/rodrigues": { - "id": "github/ratt-ru/rodrigues", - "title": "github/ratt-ru/rodrigues", - "url": " https://rseng.github.io/software/repository/github/ratt-ru/rodrigues", - "content": "web based radio telescope calibration simulation" + "github/scottleedavis/googleearthtoolbox": { + "id": "github/scottleedavis/googleearthtoolbox", + "title": "github/scottleedavis/googleearthtoolbox", + "url": " https://rseng.github.io/software/repository/github/scottleedavis/googleearthtoolbox", + "content": "Leverages the intuitive interactive virtual globe interface provided by Google Earth, providing programatic tools useful in spatio-temporal analysis." }, - "github/ratt-ru/Stimela-classic": { - "id": "github/ratt-ru/Stimela-classic", - "title": "github/ratt-ru/Stimela-classic", - "url": " https://rseng.github.io/software/repository/github/ratt-ru/Stimela-classic", - "content": "Containerized radio interferometry scripting framework -- NB: Classic version is no longer in active development, use stimela 2! See README for details." + "github/yuansh3354/CaSee": { + "id": "github/yuansh3354/CaSee", + "title": "github/yuansh3354/CaSee", + "url": " https://rseng.github.io/software/repository/github/yuansh3354/CaSee", + "content": "None" }, - "github/ratt-ru/breizorro": { - "id": "github/ratt-ru/breizorro", - "title": "github/ratt-ru/breizorro", - "url": " https://rseng.github.io/software/repository/github/ratt-ru/breizorro", - "content": "Image masking tool(s) possibly of Breton spiritual origin" + "github/ChenYangyao/hipp": { + "id": "github/ChenYangyao/hipp", + "title": "github/ChenYangyao/hipp", + "url": " https://rseng.github.io/software/repository/github/ChenYangyao/hipp", + "content": "HIPP: Modern C++ Toolkit for HPC" }, - "github/ratt-ru/Stimela": { - "id": "github/ratt-ru/Stimela", - "title": "github/ratt-ru/Stimela", - "url": " https://rseng.github.io/software/repository/github/ratt-ru/Stimela", - "content": "A containerized radio interferometry scripting framework" + "github/combine-lab/salmon": { + "id": "github/combine-lab/salmon", + "title": "github/combine-lab/salmon", + "url": " https://rseng.github.io/software/repository/github/combine-lab/salmon", + "content": "🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment" }, - "github/farhanferoz/MultiNest": { - "id": "github/farhanferoz/MultiNest", - "title": "github/farhanferoz/MultiNest", - "url": " https://rseng.github.io/software/repository/github/farhanferoz/MultiNest", - "content": "MultiNest is a Bayesian inference tool which calculates the evidence and explores the parameter space which may contain multiple posterior modes and pronounced (curving) degeneracies in moderately high dimensions. " + "github/mofanv/darknetz": { + "id": "github/mofanv/darknetz", + "title": "github/mofanv/darknetz", + "url": " https://rseng.github.io/software/repository/github/mofanv/darknetz", + "content": "runs several layers of a deep learning model in TrustZone" }, - "github/farhanferoz/SkyNet": { - "id": "github/farhanferoz/SkyNet", - "title": "github/farhanferoz/SkyNet", - "url": " https://rseng.github.io/software/repository/github/farhanferoz/SkyNet", - "content": "SkyNet is an efficient and robust neural network training code for machine learning." + "github/denglab/SeqSero": { + "id": "github/denglab/SeqSero", + "title": "github/denglab/SeqSero", + "url": " https://rseng.github.io/software/repository/github/denglab/SeqSero", + "content": "Salmonella serotyping from genome sequencing data" }, - "github/farhanferoz/BAMBI": { - "id": "github/farhanferoz/BAMBI", - "title": "github/farhanferoz/BAMBI", - "url": " https://rseng.github.io/software/repository/github/farhanferoz/BAMBI", - "content": "None" + "github/wadpac/GGIR": { + "id": "github/wadpac/GGIR", + "title": "github/wadpac/GGIR", + "url": " https://rseng.github.io/software/repository/github/wadpac/GGIR", + "content": "Code corresponding to R package GGIR" }, - "github/dmilakovic/QSOSIM10": { - "id": "github/dmilakovic/QSOSIM10", - "title": "github/dmilakovic/QSOSIM10", - "url": " https://rseng.github.io/software/repository/github/dmilakovic/QSOSIM10", - "content": "Fortran code to generate artificial QSO spectra" + "github/timstaley/voevent-parse": { + "id": "github/timstaley/voevent-parse", + "title": "github/timstaley/voevent-parse", + "url": " https://rseng.github.io/software/repository/github/timstaley/voevent-parse", + "content": "VOEvent parsing and manipulation routines built on lxml.objectify." }, - "github/JiangFangzhou/SIDM": { - "id": "github/JiangFangzhou/SIDM", - "title": "github/JiangFangzhou/SIDM", - "url": " https://rseng.github.io/software/repository/github/JiangFangzhou/SIDM", - "content": "analytical model for the density profiles of self-interacting dark-matter halos with inhabitant galaxies" + "github/timstaley/amisurvey": { + "id": "github/timstaley/amisurvey", + "title": "github/timstaley/amisurvey", + "url": " https://rseng.github.io/software/repository/github/timstaley/amisurvey", + "content": "End-to-end calibration and imaging of AMI-LA data." }, - "github/khowe/quick": { - "id": "github/khowe/quick", - "title": "github/khowe/quick", - "url": " https://rseng.github.io/software/repository/github/khowe/quick", - "content": "an efficient implementation of the Neighbor-Joining algorithm." + "github/timstaley/chimenea": { + "id": "github/timstaley/chimenea", + "title": "github/timstaley/chimenea", + "url": " https://rseng.github.io/software/repository/github/timstaley/chimenea", + "content": "Automated image-synthesis of multi-epoch radio-telescope data." }, - "github/STEllAR-GROUP/octotiger": { - "id": "github/STEllAR-GROUP/octotiger", - "title": "github/STEllAR-GROUP/octotiger", - "url": " https://rseng.github.io/software/repository/github/STEllAR-GROUP/octotiger", - "content": "Astrophysics program simulating the evolution of star systems based on the fast multipole method on adaptive Octrees" + "github/mlujnie/simple": { + "id": "github/mlujnie/simple", + "title": "github/mlujnie/simple", + "url": " https://rseng.github.io/software/repository/github/mlujnie/simple", + "content": "Simple Intensity Map Producer for Line Emission (public code)" + }, + "github/NMBU-Data-Science/RENT": { + "id": "github/NMBU-Data-Science/RENT", + "title": "github/NMBU-Data-Science/RENT", + "url": " https://rseng.github.io/software/repository/github/NMBU-Data-Science/RENT", + "content": "Feature selection method based on repeated elastic net." }, - "github/STEllAR-GROUP/hpx": { - "id": "github/STEllAR-GROUP/hpx", - "title": "github/STEllAR-GROUP/hpx", - "url": " https://rseng.github.io/software/repository/github/STEllAR-GROUP/hpx", - "content": "The C++ Standard Library for Parallelism and Concurrency" + "github/max-little/GRAPL": { + "id": "github/max-little/GRAPL", + "title": "github/max-little/GRAPL", + "url": " https://rseng.github.io/software/repository/github/max-little/GRAPL", + "content": "GRAPL: A computational library for nonparametric structural causal modelling, analysis and inference" }, - "github/simoncasassus/ConeRot": { - "id": "github/simoncasassus/ConeRot", - "title": "github/simoncasassus/ConeRot", - "url": " https://rseng.github.io/software/repository/github/simoncasassus/ConeRot", + "github/mikaelLEROY/AxionNS_RayTracing": { + "id": "github/mikaelLEROY/AxionNS_RayTracing", + "title": "github/mikaelLEROY/AxionNS_RayTracing", + "url": " https://rseng.github.io/software/repository/github/mikaelLEROY/AxionNS_RayTracing", "content": "None" }, - "github/rdpstaff/classifier": { - "id": "github/rdpstaff/classifier", - "title": "github/rdpstaff/classifier", - "url": " https://rseng.github.io/software/repository/github/rdpstaff/classifier", - "content": "RDP extensible sequence classifier for fungal lsu, bacterial and archaeal 16s" + "github/cire-thk/BifacialSimu": { + "id": "github/cire-thk/BifacialSimu", + "title": "github/cire-thk/BifacialSimu", + "url": " https://rseng.github.io/software/repository/github/cire-thk/BifacialSimu", + "content": "Simulation of bifacial PV" }, - "github/rdpstaff/TaxonomyTree": { - "id": "github/rdpstaff/TaxonomyTree", - "title": "github/rdpstaff/TaxonomyTree", - "url": " https://rseng.github.io/software/repository/github/rdpstaff/TaxonomyTree", - "content": "TaxonomyTree building and traversal utility classes." + "github/andersen-lab/ivar": { + "id": "github/andersen-lab/ivar", + "title": "github/andersen-lab/ivar", + "url": " https://rseng.github.io/software/repository/github/andersen-lab/ivar", + "content": "iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing." }, - "github/rdpstaff/AlignmentTools": { - "id": "github/rdpstaff/AlignmentTools", - "title": "github/rdpstaff/AlignmentTools", - "url": " https://rseng.github.io/software/repository/github/rdpstaff/AlignmentTools", - "content": "Tools for pairwise sequence comparison, distance calculation, and hidden markov model sequence scoring (using HMMER3 models). Many RDP Projects require this package." + "github/andersen-lab/html": { + "id": "github/andersen-lab/html", + "title": "github/andersen-lab/html", + "url": " https://rseng.github.io/software/repository/github/andersen-lab/html", + "content": "is a computational package that contains functions broadly useful for viral amplicon-based sequencing." }, - "github/rdpstaff/ReadSeq": { - "id": "github/rdpstaff/ReadSeq", - "title": "github/rdpstaff/ReadSeq", - "url": " https://rseng.github.io/software/repository/github/rdpstaff/ReadSeq", - "content": "Java based common sequence file format reader and sequence file manipulation. Most RDP projects require this package." + "github/sourmash-bio/sourmash": { + "id": "github/sourmash-bio/sourmash", + "title": "github/sourmash-bio/sourmash", + "url": " https://rseng.github.io/software/repository/github/sourmash-bio/sourmash", + "content": "Quickly search, compare, and analyze genomic and metagenomic data sets." }, - "github/caseyjlaw/tpipe": { - "id": "github/caseyjlaw/tpipe", - "title": "github/caseyjlaw/tpipe", - "url": " https://rseng.github.io/software/repository/github/caseyjlaw/tpipe", - "content": "Python library to search radio interferometry data for dispersed (fast) transients **superseded by caseyjlaw/rtpipe**" + "github/andizq/sf3dmodels": { + "id": "github/andizq/sf3dmodels", + "title": "github/andizq/sf3dmodels", + "url": " https://rseng.github.io/software/repository/github/andizq/sf3dmodels", + "content": "sf3dmodels: star-forming regions 3D modelling package in Python :partly_sunny:" }, - "github/caseyjlaw/rtpipe": { - "id": "github/caseyjlaw/rtpipe", - "title": "github/caseyjlaw/rtpipe", - "url": " https://rseng.github.io/software/repository/github/caseyjlaw/rtpipe", - "content": "Pipeline for real-time fast transient detection in radio interferometric data (see also https://github.com/realfastvla/rfpipe)" + "github/cole-trapnell-lab/cufflinks": { + "id": "github/cole-trapnell-lab/cufflinks", + "title": "github/cole-trapnell-lab/cufflinks", + "url": " https://rseng.github.io/software/repository/github/cole-trapnell-lab/cufflinks", + "content": "a reference-guided assembler that assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples." }, - "github/Valcin/BE_HaPPy": { - "id": "github/Valcin/BE_HaPPy", - "title": "github/Valcin/BE_HaPPy", - "url": " https://rseng.github.io/software/repository/github/Valcin/BE_HaPPy", - "content": "Bias Emulator for Halo Power Spectrum " + "github/HHTpy/HHTpywrapper": { + "id": "github/HHTpy/HHTpywrapper", + "title": "github/HHTpy/HHTpywrapper", + "url": " https://rseng.github.io/software/repository/github/HHTpy/HHTpywrapper", + "content": "Python Wrapper for Hilbert–Huang Transform MATLAB Package" }, - "github/ExoSim/ExoSimPublic": { - "id": "github/ExoSim/ExoSimPublic", - "title": "github/ExoSim/ExoSimPublic", - "url": " https://rseng.github.io/software/repository/github/ExoSim/ExoSimPublic", - "content": "None" + "github/csj607/STaRS": { + "id": "github/csj607/STaRS", + "title": "github/csj607/STaRS", + "url": " https://rseng.github.io/software/repository/github/csj607/STaRS", + "content": "Sejong Radiative Transfer through Raman and Rayleigh Scattering with atomic hydrogen" }, - "github/herrsalmi/FConverter": { - "id": "github/herrsalmi/FConverter", - "title": "github/herrsalmi/FConverter", - "url": " https://rseng.github.io/software/repository/github/herrsalmi/FConverter", - "content": "File format converter for FImpute2" + "github/micahvista/MAMnet": { + "id": "github/micahvista/MAMnet", + "title": "github/micahvista/MAMnet", + "url": " https://rseng.github.io/software/repository/github/micahvista/MAMnet", + "content": "MAMnet uses a deep learning network to call genetic variants from third generation DNA sequencing data." }, - "github/kutaslab/fitgrid": { - "id": "github/kutaslab/fitgrid", - "title": "github/kutaslab/fitgrid", - "url": " https://rseng.github.io/software/repository/github/kutaslab/fitgrid", - "content": "Multichannel event-related time-series regression modeling for EEG, MEG, and sensor array data" + "github/mattpitkin/lintegrate": { + "id": "github/mattpitkin/lintegrate", + "title": "github/mattpitkin/lintegrate", + "url": " https://rseng.github.io/software/repository/github/mattpitkin/lintegrate", + "content": "A numerical integration routine that works for the natural logarithm of functions " }, - "github/TRIQS/solid_dmft": { - "id": "github/TRIQS/solid_dmft", - "title": "github/TRIQS/solid_dmft", - "url": " https://rseng.github.io/software/repository/github/TRIQS/solid_dmft", - "content": "solid_dmft is a versatile python wrapper to perform DFT+DMFT calculations utilizing the TRIQS software library." + "github/mattpitkin/psrqpy": { + "id": "github/mattpitkin/psrqpy", + "title": "github/mattpitkin/psrqpy", + "url": " https://rseng.github.io/software/repository/github/mattpitkin/psrqpy", + "content": "A python module to query the ATNF pulsar catalogue" }, - "github/lzkelley/kalepy": { - "id": "github/lzkelley/kalepy", - "title": "github/lzkelley/kalepy", - "url": " https://rseng.github.io/software/repository/github/lzkelley/kalepy", - "content": "Kernel Density Estimation and (re)sampling" + "github/online-behaviour/find-journalists": { + "id": "github/online-behaviour/find-journalists", + "title": "github/online-behaviour/find-journalists", + "url": " https://rseng.github.io/software/repository/github/online-behaviour/find-journalists", + "content": "None" }, - "github/jmhuie/Slicer-SegmentGeometry": { - "id": "github/jmhuie/Slicer-SegmentGeometry", - "title": "github/jmhuie/Slicer-SegmentGeometry", - "url": " https://rseng.github.io/software/repository/github/jmhuie/Slicer-SegmentGeometry", - "content": "Extension to calculate second moment of area and other cross-sectional properties in 3D Slicer" + "github/online-behaviour/machine-learning": { + "id": "github/online-behaviour/machine-learning", + "title": "github/online-behaviour/machine-learning", + "url": " https://rseng.github.io/software/repository/github/online-behaviour/machine-learning", + "content": "Python scripts for tweet retrieval and machine learning in the eScience project Automated Analysis of Online Behaviour on Social Media" }, - "github/CPM-project/MCPM": { - "id": "github/CPM-project/MCPM", - "title": "github/CPM-project/MCPM", - "url": " https://rseng.github.io/software/repository/github/CPM-project/MCPM", - "content": "Modified CPM method" + "github/basp-group/SARA-dimensionality-reduction": { + "id": "github/basp-group/SARA-dimensionality-reduction", + "title": "github/basp-group/SARA-dimensionality-reduction", + "url": " https://rseng.github.io/software/repository/github/basp-group/SARA-dimensionality-reduction", + "content": "SARA-dimensionality-reduction: Fourier Dimensionality Reduction for radio-interferometric imaging with SARA" }, - "github/dianna-ai/dianna": { - "id": "github/dianna-ai/dianna", - "title": "github/dianna-ai/dianna", - "url": " https://rseng.github.io/software/repository/github/dianna-ai/dianna", - "content": "Deep Insight And Neural Network Analysis" + "github/basp-group/purify": { + "id": "github/basp-group/purify", + "title": "github/basp-group/purify", + "url": " https://rseng.github.io/software/repository/github/basp-group/purify", + "content": "Software for radio-interferometric imaging 1.0" }, - 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Check out also version 2.0 at https://github.com/CrowdTruth/CrowdTruth-core. Data collected with CrowdTruth methodology: http://data.crowdtruth.org/. 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"title": "github/enthought/vpsearch", - "url": " https://rseng.github.io/software/repository/github/enthought/vpsearch", - "content": "Fast similarity search for genomic sequences via vantage-point trees" + "github/ACEnglish/truvari": { + "id": "github/ACEnglish/truvari", + "title": "github/ACEnglish/truvari", + "url": " https://rseng.github.io/software/repository/github/ACEnglish/truvari", + "content": "Structural variant toolkit for VCFs" }, - "github/enthought/mayavi": { - "id": "github/enthought/mayavi", - "title": "github/enthought/mayavi", - "url": " https://rseng.github.io/software/repository/github/enthought/mayavi", - "content": "3D visualization of scientific data in Python" + "github/JuliaOpt/JuMP.jl": { + "id": "github/JuliaOpt/JuMP.jl", + "title": "github/JuliaOpt/JuMP.jl", + "url": " https://rseng.github.io/software/repository/github/JuliaOpt/JuMP.jl", + "content": "Modeling language for Mathematical Optimization (linear, mixed-integer, conic, semidefinite, nonlinear)" }, - 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"title": "github/el2718/FastQSL", - "url": " https://rseng.github.io/software/repository/github/el2718/FastQSL", + "github/LalResearchGroup/CNV-clinviewer": { + "id": "github/LalResearchGroup/CNV-clinviewer", + "title": "github/LalResearchGroup/CNV-clinviewer", + "url": " https://rseng.github.io/software/repository/github/LalResearchGroup/CNV-clinviewer", "content": "None" }, - "github/carnotresearch/cr-sparse": { - "id": "github/carnotresearch/cr-sparse", - "title": "github/carnotresearch/cr-sparse", - "url": " https://rseng.github.io/software/repository/github/carnotresearch/cr-sparse", - "content": "Functional models and algorithms for sparse signal processing" + "github/Libensemble/libensemble": { + "id": "github/Libensemble/libensemble", + "title": "github/Libensemble/libensemble", + "url": " https://rseng.github.io/software/repository/github/Libensemble/libensemble", + "content": "A Python toolkit for coordinating asynchronous and dynamic ensembles of calculations." }, - "github/iancze/DiskJockey": { - 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Pronounced "soap."" + "github/caselawanalytics/CaseLawAnalytics": { + "id": "github/caselawanalytics/CaseLawAnalytics", + "title": "github/caselawanalytics/CaseLawAnalytics", + "url": " https://rseng.github.io/software/repository/github/caselawanalytics/CaseLawAnalytics", + "content": "None" }, - "github/amusecode/TRES": { - "id": "github/amusecode/TRES", - "title": "github/amusecode/TRES", - "url": " https://rseng.github.io/software/repository/github/amusecode/TRES", - "content": "TRiple Evolution Simulation package" + "github/hongli-ma/RNANetMotif": { + "id": "github/hongli-ma/RNANetMotif", + "title": "github/hongli-ma/RNANetMotif", + "url": " https://rseng.github.io/software/repository/github/hongli-ma/RNANetMotif", + "content": "RNA structural motif finder" }, - "github/amusecode/amuse": { - "id": "github/amusecode/amuse", - "title": "github/amusecode/amuse", - "url": " https://rseng.github.io/software/repository/github/amusecode/amuse", - "content": "Astrophysical Multipurpose Software Environment. 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Initially designed to produce maps of observing condition related sources of systematics for the Dark Energy Survey, but will work with any multi-epoch survey and collection of images with valid WCS information." + "github/JetBrains-Research/spbla": { + "id": "github/JetBrains-Research/spbla", + "title": "github/JetBrains-Research/spbla", + "url": " https://rseng.github.io/software/repository/github/JetBrains-Research/spbla", + "content": "Sparse Boolean linear algebra for Nvidia Cuda, OpenCL and CPU computations" }, - "github/ixkael/Delight": { - "id": "github/ixkael/Delight", - "title": "github/ixkael/Delight", - "url": " https://rseng.github.io/software/repository/github/ixkael/Delight", - "content": "Photometric redshift via Gaussian processes with physical kernels" + "github/tbep-tech/tbeptools": { + "id": "github/tbep-tech/tbeptools", + "title": "github/tbep-tech/tbeptools", + "url": " https://rseng.github.io/software/repository/github/tbep-tech/tbeptools", + "content": "R package for Tampa Bay Estuary Program functions" }, - "github/ixkael/3DEX": { - "id": "github/ixkael/3DEX", - "title": "github/ixkael/3DEX", - "url": " https://rseng.github.io/software/repository/github/ixkael/3DEX", - "content": "3D expansions" + "github/stan-dev/stan": { + "id": "github/stan-dev/stan", + "title": "github/stan-dev/stan", + "url": " https://rseng.github.io/software/repository/github/stan-dev/stan", + "content": "Stan development repository. 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"id": "github/rbturnbull/ausdex", - "title": "github/rbturnbull/ausdex", - "url": " https://rseng.github.io/software/repository/github/rbturnbull/ausdex", - "content": "A Python package for adjusting Australian dollars for inflation" + "github/Yu-Group/veridical-flow": { + "id": "github/Yu-Group/veridical-flow", + "title": "github/Yu-Group/veridical-flow", + "url": " https://rseng.github.io/software/repository/github/Yu-Group/veridical-flow", + "content": "Making it easier to build stable, trustworthy data-science pipelines." }, - "github/bonsai-team/Porechop_ABI": { - "id": "github/bonsai-team/Porechop_ABI", - "title": "github/bonsai-team/Porechop_ABI", - "url": " https://rseng.github.io/software/repository/github/bonsai-team/Porechop_ABI", - "content": "Adapter trimmer for Oxford Nanopore reads using ab initio method" + "github/linqs/psl": { + "id": "github/linqs/psl", + "title": "github/linqs/psl", + "url": " https://rseng.github.io/software/repository/github/linqs/psl", + "content": "The PSL software from the University of Maryland and the University of California Santa Cruz" }, - 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"github/CEMeNT-PSAAP/MCDC": { - "id": "github/CEMeNT-PSAAP/MCDC", - "title": "github/CEMeNT-PSAAP/MCDC", - "url": " https://rseng.github.io/software/repository/github/CEMeNT-PSAAP/MCDC", - "content": "MC/DC: Monte Carlo Dynamic Code" + "github/fjdu/rac-2d": { + "id": "github/fjdu/rac-2d", + "title": "github/fjdu/rac-2d", + "url": " https://rseng.github.io/software/repository/github/fjdu/rac-2d", + "content": "Radiative transfer and chemistry" }, - "github/jiujiezz/tsnad": { - "id": "github/jiujiezz/tsnad", - "title": "github/jiujiezz/tsnad", - "url": " https://rseng.github.io/software/repository/github/jiujiezz/tsnad", - "content": "Detecting somatic mutations and predicting tumor-specific neo-antigens" + "github/fjdu/myRadex": { + "id": "github/fjdu/myRadex", + "title": "github/fjdu/myRadex", + "url": " https://rseng.github.io/software/repository/github/fjdu/myRadex", + "content": "Similar to radex, with a different way to solve the statistical equilibrium problem" }, - "github/arvados/arvados": { - "id": "github/arvados/arvados", - "title": "github/arvados/arvados", - "url": " https://rseng.github.io/software/repository/github/arvados/arvados", - "content": "An open source platform for managing and analyzing biomedical big data" + "github/streamlit/streamlit": { + "id": "github/streamlit/streamlit", + "title": "github/streamlit/streamlit", + "url": " https://rseng.github.io/software/repository/github/streamlit/streamlit", + "content": "Streamlit — The fastest way to build data apps in Python" }, - "github/SJaffa/Jplots": { - "id": "github/SJaffa/Jplots", - "title": "github/SJaffa/Jplots", - "url": " https://rseng.github.io/software/repository/github/SJaffa/Jplots", - "content": "Astrophysical data analysis tool: quantifying the shape of pixelated structures using moments" + "github/SJLeo/FFSD": { + "id": "github/SJLeo/FFSD", + "title": "github/SJLeo/FFSD", + "url": " https://rseng.github.io/software/repository/github/SJLeo/FFSD", + "content": "Pytorch implementation of our paper accepted by IEEE TNNLS, 2022 -- Distilling a Powerful Student Model via Online Knowledge Distillation" }, - 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"url": " https://rseng.github.io/software/repository/github/fabiopardo/qmap", - "content": "Scaling All-Goals Updates in Reinforcement Learning Using Convolutional Neural Networks" + "github/theonefromnowhere/FitCov": { + "id": "github/theonefromnowhere/FitCov", + "title": "github/theonefromnowhere/FitCov", + "url": " https://rseng.github.io/software/repository/github/theonefromnowhere/FitCov", + "content": "The code for the Fitted Covariance generation based on %paper link%" }, - "github/4pisky/fourpisky-core": { - "id": "github/4pisky/fourpisky-core", - "title": "github/4pisky/fourpisky-core", - "url": " https://rseng.github.io/software/repository/github/4pisky/fourpisky-core", - "content": "Core code defining alert handling, etc for the 4PiSky voevent hub." + "github/MetaCell/scicrunch-antibody-registry": { + "id": "github/MetaCell/scicrunch-antibody-registry", + "title": "github/MetaCell/scicrunch-antibody-registry", + "url": " https://rseng.github.io/software/repository/github/MetaCell/scicrunch-antibody-registry", + "content": "A repo for the SciCrunch antibody registry portal " }, - 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" }, - "github/nf-core/mag": { - "id": "github/nf-core/mag", - "title": "github/nf-core/mag", - "url": " https://rseng.github.io/software/repository/github/nf-core/mag", - "content": "Assembly and binning of metagenomes" + "github/CouncilDataProject/speakerbox": { + "id": "github/CouncilDataProject/speakerbox", + "title": "github/CouncilDataProject/speakerbox", + "url": " https://rseng.github.io/software/repository/github/CouncilDataProject/speakerbox", + "content": "Speakerbox: Fine-tune Audio Transformers for speaker identification." }, - "github/hnikaein/stark": { - "id": "github/hnikaein/stark", - "title": "github/hnikaein/stark", - "url": " https://rseng.github.io/software/repository/github/hnikaein/stark", - "content": "A tool for bluntifying a bidirected de bruijn graph by removing overlaps." + "github/CouncilDataProject/cookiecutter-cdp-deployment": { + "id": "github/CouncilDataProject/cookiecutter-cdp-deployment", + "title": "github/CouncilDataProject/cookiecutter-cdp-deployment", + "url": " https://rseng.github.io/software/repository/github/CouncilDataProject/cookiecutter-cdp-deployment", + "content": "Cookiecutter template for creating new CDP instances." }, - "github/takfung/ResDisMapper": { - "id": "github/takfung/ResDisMapper", - "title": "github/takfung/ResDisMapper", - "url": " https://rseng.github.io/software/repository/github/takfung/ResDisMapper", - "content": "None" + "github/RECeSS-EU-Project/stanscofi": { + "id": "github/RECeSS-EU-Project/stanscofi", + "title": "github/RECeSS-EU-Project/stanscofi", + "url": " https://rseng.github.io/software/repository/github/RECeSS-EU-Project/stanscofi", + "content": "Package for STANdard drug Screening by COllaborative FIltering. Performs benchmarks against datasets and SotA algorithms, and implements training, validation and testing procedures." }, - "github/mjuric/galfast": { - "id": "github/mjuric/galfast", - "title": "github/mjuric/galfast", - "url": " https://rseng.github.io/software/repository/github/mjuric/galfast", - "content": "Milky Way Mock Catalog Generator" + "github/pybamm-team/PyBaMM": { + "id": "github/pybamm-team/PyBaMM", + "title": "github/pybamm-team/PyBaMM", + "url": " https://rseng.github.io/software/repository/github/pybamm-team/PyBaMM", + "content": "Fast and flexible physics-based battery models in Python" }, - "github/bootphon/phonemizer": { - "id": "github/bootphon/phonemizer", - "title": "github/bootphon/phonemizer", - "url": " https://rseng.github.io/software/repository/github/bootphon/phonemizer", - "content": "Simple text to phones converter for multiple languages" + "github/pybamm-team/liionpack": { + "id": "github/pybamm-team/liionpack", + "title": "github/pybamm-team/liionpack", + "url": " https://rseng.github.io/software/repository/github/pybamm-team/liionpack", + "content": "A battery pack simulation tool that uses the PyBaMM framework" }, - "github/PaulRitsche/DLTrack": { - "id": "github/PaulRitsche/DLTrack", - "title": "github/PaulRitsche/DLTrack", - "url": " https://rseng.github.io/software/repository/github/PaulRitsche/DLTrack", - "content": "This repositories contains code for automatic analysis of human lower limb ultrasonography images." + "github/jgducoin/galclaim": { + "id": "github/jgducoin/galclaim", + "title": "github/jgducoin/galclaim", + "url": " https://rseng.github.io/software/repository/github/jgducoin/galclaim", + "content": "GALaxy Chance of Local Alignment algorIthM" }, - "github/yiwenstat/MCPCA_PopGen": { - "id": "github/yiwenstat/MCPCA_PopGen", - "title": "github/yiwenstat/MCPCA_PopGen", - "url": " https://rseng.github.io/software/repository/github/yiwenstat/MCPCA_PopGen", + "github/ot483/NetCom": { + "id": "github/ot483/NetCom", + "title": "github/ot483/NetCom", + "url": " https://rseng.github.io/software/repository/github/ot483/NetCom", "content": "None" }, - "github/Oftatkofta/cellocity": { - "id": "github/Oftatkofta/cellocity", - "title": "github/Oftatkofta/cellocity", - "url": " https://rseng.github.io/software/repository/github/Oftatkofta/cellocity", - "content": "Scientific software for analysis of confluent cell dynamics." - }, - "github/miguelzuma/hi_class_public": { - "id": "github/miguelzuma/hi_class_public", - "title": "github/miguelzuma/hi_class_public", - "url": " https://rseng.github.io/software/repository/github/miguelzuma/hi_class_public", - "content": "Public version of Horndeski in the Cosmic Linear Anisotropy Solving System" + "github/vembrane/vembrane": { + "id": "github/vembrane/vembrane", + "title": "github/vembrane/vembrane", + "url": " https://rseng.github.io/software/repository/github/vembrane/vembrane", + "content": "vembrane filters VCF records using python expressions" }, - "github/pennucci/PulsePortraiture": { - "id": "github/pennucci/PulsePortraiture", - "title": "github/pennucci/PulsePortraiture", - "url": " https://rseng.github.io/software/repository/github/pennucci/PulsePortraiture", - "content": "PulsePortraiture (PP): a wideband pulsar timing code written in python. It uses an extension of Joe Taylor's FFTFIT algorithm (Taylor 1992) to simultaneously measure a phase (TOA) and dispersion measure (DM). PSRCHIVE, lmfit, and the latest vertsions of numpy and scipy are required." + "github/johannesulf/dsigma": { + "id": "github/johannesulf/dsigma", + "title": "github/johannesulf/dsigma", + "url": " https://rseng.github.io/software/repository/github/johannesulf/dsigma", + "content": "A Galaxy-Galaxy Lensing Python Package" }, - "github/GEUS-Glaciology-and-Climate/pypromice": { - "id": "github/GEUS-Glaciology-and-Climate/pypromice", - "title": "github/GEUS-Glaciology-and-Climate/pypromice", - "url": " https://rseng.github.io/software/repository/github/GEUS-Glaciology-and-Climate/pypromice", - "content": "Process AWS data from L0 (raw logger) through Lx (end user)" + "github/andymummeryastro/tidalspin": { + "id": "github/andymummeryastro/tidalspin", + "title": "github/andymummeryastro/tidalspin", + "url": " https://rseng.github.io/software/repository/github/andymummeryastro/tidalspin", + "content": "Python package for constraining black hole spins using the properties of relativistic tidal forces" }, - "github/hsocasnavarro/NICOLE": { - "id": "github/hsocasnavarro/NICOLE", - "title": "github/hsocasnavarro/NICOLE", - "url": " https://rseng.github.io/software/repository/github/hsocasnavarro/NICOLE", - "content": "NLTE Stokes Synthesis/Inversion Code" + "github/jodyphelan/tb-ml": { + "id": "github/jodyphelan/tb-ml", + "title": "github/jodyphelan/tb-ml", + "url": " https://rseng.github.io/software/repository/github/jodyphelan/tb-ml", + "content": "A simple tool for creating machine learning antimicrobial resistance prediction pipelines using Docker containers for M. tuberculosis" }, - "github/alastair-droop/fqtools": { - "id": "github/alastair-droop/fqtools", - "title": "github/alastair-droop/fqtools", - "url": " https://rseng.github.io/software/repository/github/alastair-droop/fqtools", - "content": "An efficient FASTQ manipulation suite" + "github/jodyphelan/TBProfiler": { + "id": "github/jodyphelan/TBProfiler", + "title": "github/jodyphelan/TBProfiler", + "url": " https://rseng.github.io/software/repository/github/jodyphelan/TBProfiler", + "content": "Profiling tool for Mycobacterium tuberculosis to detect ressistance and strain type from WGS data" } };