Repositories list

• activelearning

  Public
  Active learning tools for fine-tuning ML models

  Python

  •

  MIT License

  •0•2•2•1•Updated Nov 22, 2024Nov 22, 2024

• intro_cellprofiler_workshop

  Public
  Introduction slides for an Intro to CellProfiler workshop

  0•0•0•0•Updated Nov 22, 2024Nov 22, 2024

• rit-imageanalysis-containers

  Public
  Making it easier for users to spin up a Singularity container with image analysis tools from a slurm-based cluster

  imaging-solutions

  Shell

  •

  MIT License

  •3•3•2•2•Updated Nov 21, 2024Nov 21, 2024

• STQ

  Public
  Spatial Transcriptomics Quantification pipeline for 10x Visium and H&E-stained whole slide images

  spatial-transcriptomicsrna-velocityvisium+ 4xenomehe-stained-wsixengsortspecies-deconvolution

  Python

  •

  MIT License

  •0•14•2•0•Updated Nov 20, 2024Nov 20, 2024

• geneweaver-api

  Public
  A system for the integration and analysis of heterogeneous functional genomics data.

  genomicsanalysisfunctional-genomics+ 1genomic-data-science

  Python

  •

  Apache License 2.0

  •0•5•0•0•Updated Nov 20, 2024Nov 20, 2024

• haplotype_reconstruction_qtl-nf

  Public
  R

  •0•0•0•0•Updated Nov 19, 2024Nov 19, 2024

• singularity-workshop-2023

  Public
  Other

  •0•0•0•0•Updated Nov 19, 2024Nov 19, 2024

• intro-napari-workshop

  Public
  Intro to napari Workshop

  visualizationpythonnapari

  BSD 3-Clause "New" or "Revised" License

  •2•1•0•0•Updated Nov 18, 2024Nov 18, 2024

• quilt-nf

  Public
  R

  •0•1•0•0•Updated Nov 14, 2024Nov 14, 2024

• geneweaver-legacy

  Public
  JavaScript

  •0•1•1•0•Updated Nov 11, 2024Nov 11, 2024

• meta_mapper

  Public
  Map fields in existing metadata documents to those in new, standardized templates.

  Python

  •0•0•0•0•Updated Nov 8, 2024Nov 8, 2024

• geneweaver-db

  Public
  The GeneWeaver database interaction code.

  sqlgenomicsfunctional-genomics+ 2genomic-data-sciencegeneweaver

  Python

  •

  Apache License 2.0

  •0•2•0•0•Updated Nov 6, 2024Nov 6, 2024

• fiji_workshops

  Public
  Repository for Fiji workshop materials

  JavaScript

  •

  MIT License

  •5•0•0•0•Updated Nov 6, 2024Nov 6, 2024

• Galaxy_Tools_CBA

  Public
  This is the Python and config files for the CBA tools deployed in Galaxy

  Python

  •0•0•0•0•Updated Nov 1, 2024Nov 1, 2024

• DccXmlGenerator

  Public
  This is the Python version of the DCC XML file generator.

  Python

  •0•0•0•0•Updated Oct 31, 2024Oct 31, 2024

• ezomero

  Public
  A module with convenience functions for writing Python code that interacts with OMERO.

  omeroomero-serverimaging-solutions+ 2omero-apipython

  Python

  •

  GNU General Public License v2.0

  •13•39•3•1•Updated Oct 30, 2024Oct 30, 2024

• hpo-web

  Public
  a web application to search and navigate the Human Phenotype Ontology (HPO)

  groovyhpograils3+ 1angular

  HTML

  •

  Other

  •12•13•7•9•Updated Oct 28, 2024Oct 28, 2024

• ontology-service

  Public
  A generic ontology term microservice

  Java

  •1•3•8•0•Updated Oct 25, 2024Oct 25, 2024

• ontology-annotation-network

  Public
  A rest-api to serve a neo4j database of supported ontology annotations.

  Java

  •

  Other

  •0•2•0•0•Updated Oct 25, 2024Oct 25, 2024

• nf-tenx

  Public
  All 10x Genomics processing pipelines rolled into one containerized pipelines

  bioinformaticspipeline

  Groovy

  •

  MIT License

  •1•7•3•1•Updated Oct 24, 2024Oct 24, 2024

• omero-k8s-templates

  Public
  omeroimaging-solutions

  Dockerfile

  •

  GNU General Public License v2.0

  •1•1•0•0•Updated Oct 18, 2024Oct 18, 2024

• imaging_applications

  Public
  repository for Imaging Applications Github Page

  Lua

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Oct 9, 2024Oct 9, 2024

• cs-nf-pipelines

  Public
  The Jackson Laboratory Computational Sciences Nextflow based analysis pipelines

  Nextflow

  •

  MIT License

  •10•20•0•0•Updated Oct 8, 2024Oct 8, 2024

• jax-omeroutils

  Public
  A module and scripts for working with OMERO

  omeroomero-importimaging-solutions

  Python

  •

  GNU General Public License v2.0

  •3•6•4•1•Updated Oct 8, 2024Oct 8, 2024

• omero_for_developers

  Public
  material for the "OMERO for developers" workshop.

  omeroimaging-solutions

  Jupyter Notebook

  •

  MIT License

  •4•5•0•0•Updated Oct 7, 2024Oct 7, 2024

• jax-ngff-challenge-2024

  Public
  1•0•0•1•Updated Oct 3, 2024Oct 3, 2024

• 2024-10-13-machine-learning-quant-behavior

  Public
  HTML

  •

  Other

  •0•0•0•0•Updated Oct 1, 2024Oct 1, 2024

• ro-crate-isa-context

  Public
  0•1•0•1•Updated Oct 1, 2024Oct 1, 2024

• dask_relabeling

  Public
  A relabeling tool for tiled segmentation with Dask

  imaging-solutions

  Python

  •

  MIT License

  •1•12•2•1•Updated Sep 24, 2024Sep 24, 2024

• splicing-pipelines-nf

  Public
  Repository for the Anczukow-Lab splicing pipeline

  Nextflow

  •10•14•31•6•Updated Sep 24, 2024Sep 24, 2024