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    19 repositories

    • TADbit

      Public
      TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify and compare the so-called Topologically Associating Domains (TADs), build 3D models f…
      mappingngshi-c3d-modelschromatinpython
      Python
      •
      GNU General Public License v3.0
      •61•100•66•1•Updated Jul 30, 2024Jul 30, 2024

    • METALoci

      Public
      METALoci: spatially auto-correlated signals in 3D genomes
      Python
      •
      GNU General Public License v3.0
      •0•2•0•0•Updated Jul 19, 2024Jul 19, 2024

    • IMP_BioSystem_Domain_Fly_Genome

      Public
      Example of using IMP to model a region of the Fly genome https://integrativemodeling.org/systems/
      Python
      •3•0•0•0•Updated Jun 21, 2023Jun 21, 2023

    • Sox9_METALoci

      Public
      Code example of METALoci applied to H3K27ac for the Sox9 mouse locus during development (E13.5)
      Jupyter Notebook
      •0•4•2•0•Updated Feb 9, 2023Feb 9, 2023

    • TADkit

      Public archive
      3D Genome Browser
      javascriptgenome3d-models3d-genome-browserchromatin
      JavaScript
      •
      MIT License
      •10•31•31•0•Updated Jan 22, 2022Jan 22, 2022

    • OligoFISSEQ

      Public
      Example of the analysis workflow of one image produced by OligoFISSEQ. All the files needed are contained in this repository
      Jupyter Notebook
      •3•4•0•0•Updated Jul 15, 2021Jul 15, 2021

    • 3DAROC

      Public
      list of notebooks for 4 days course on Hi-C data handling and 3D modeling of chromatin
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•8•0•0•Updated Jul 2, 2021Jul 2, 2021

    • SparseDataModelling

      Public
      Jupyter Notebook
      •2•0•0•0•Updated Apr 9, 2021Apr 9, 2021

    • loopbit

      Public
      Convolutional Neural Network to identify loops from 3C-based experiments
      Python
      •0•0•0•0•Updated Feb 27, 2021Feb 27, 2021

    • TADdyn

      Public
      TADdyn is a Python library that allows to model and explore single or time-series 3C-based data.
      Python
      •
      GNU General Public License v3.0
      •3•0•1•1•Updated Jan 27, 2021Jan 27, 2021

    • colvars

      Public archive
      Collective variables module for molecular simulation and analysis programs
      C++
      •
      GNU Lesser General Public License v3.0
      •59•0•0•0•Updated Jun 23, 2020Jun 23, 2020

    • metawaffle

      Public
      Python
      •1•0•0•0•Updated Apr 29, 2020Apr 29, 2020

    • TADpole

      Public
      TADpole is a computational tool designed to identify and analyze the entire hierarchy of topologically associated domains (TADs) in intra-chromosomal interaction matrices. This is the stable version of TADpole. You can find the development version at
      R
      •
      GNU Lesser General Public License v3.0
      •0•9•0•0•Updated Jan 28, 2020Jan 28, 2020

    • binless

      Public
      Resolution-independent normalization of Hi-C data
      rrcppcpp11hi-chigh-throughput-sequencingnormalizationgeneralized-additive-modelsfused-lassobinless
      C++
      •
      GNU Lesser General Public License v3.0
      •2•7•6•0•Updated Aug 28, 2019Aug 28, 2019

    • MethodsMolBiol

      Public
      bioinformaticshi-c3d-genometutorial-exerciseschromatin-interaction
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •1•5•0•0•Updated Mar 29, 2019Mar 29, 2019

    • angular-threejs

      Public archive
      Angular module implementing THREEjs
      JavaScript
      •5•8•0•1•Updated Mar 17, 2018Mar 17, 2018

    • TADkit-Viewer

      Public archive
      A 3D viewer for TADbit models
      JavaScript
      •
      MIT License
      •1•0•0•0•Updated Jun 19, 2017Jun 19, 2017

    • 3DViewerComponent

      Public archive
      A ThreeJS 3D Viewer Web Component composed with (Google's) Polymer
      JavaScript
      •
      MIT License
      •15•0•0•0•Updated Apr 5, 2017Apr 5, 2017

    • angular-d3js

      Public archive
      Angular module implementing D3
      JavaScript
      •1•1•0•0•Updated Nov 19, 2015Nov 19, 2015