Repositories list

• hpo-web

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

  groovyangularhpo+ 1grails3

  TypeScript

  •

  Other

  •12•14•8•4•Updated Dec 24, 2025Dec 24, 2025

• jds-nf-test

  Public
  Repository for hosting test data for cs-nf-pipelines

  MIT License

  •0•0•0•0•Updated Dec 23, 2025Dec 23, 2025

• image-processing-ia

  Public
  Image Processing with Python

  HTML

  •

  Other

  •125•0•0•0•Updated Dec 23, 2025Dec 23, 2025

• HeartSeneDataAnalysis

  Public
  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Dec 22, 2025Dec 22, 2025

• imaging-applications-documentation

  Public
  Creative Commons Attribution 4.0 International

  •0•1•0•0•Updated Dec 11, 2025Dec 11, 2025

• 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

  •3•22•2•0•Updated Dec 8, 2025Dec 8, 2025

• ezomero

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

  pythonomeroomero-server+ 2imaging-solutionsomero-api

  Python

  •

  GNU General Public License v2.0

  •18•46•4•1•Updated Dec 4, 2025Dec 4, 2025

• deeplearning-image-analysis-workshop

  Public
  Notebooks for the workshop Advanced Machine learning with Python

  imaging-solutions

  CSS

  •

  MIT License

  •0•1•0•0•Updated Nov 21, 2025Nov 21, 2025

• 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 21, 2025Nov 21, 2025

• geneweaver-legacy

  Public
  JavaScript

  •0•1•28•1•Updated Nov 21, 2025Nov 21, 2025

• NBL1

  Public
  This is a repository for code used in the manuscript titled "NBL1 Correlates with Renal Phenotypes in Mouse Models of Kidney Disease, but Is Not Causal"

  R

  •

  MIT License

  •0•0•0•0•Updated Nov 20, 2025Nov 20, 2025

• LIRICAL

  Public
  LIkelihood Ratio Interpretation of Clinical AbnormaLities

  Java

  •

  Other

  •13•32•9•2•Updated Nov 19, 2025Nov 19, 2025

• jds-nf-workflows

  Public
  The Jackson Laboratory Data Science Nextflow based analysis workflows

  Nextflow

  •

  MIT License

  •11•25•0•0•Updated Nov 14, 2025Nov 14, 2025

• bestpractices_workshop

  Public
  Best Practices in Python Workshop

  Python

  •

  MIT License

  •8•2•0•0•Updated Nov 12, 2025Nov 12, 2025

• ontology-annotation-network

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

  Java

  •

  Other

  •1•3•0•0•Updated Nov 5, 2025Nov 5, 2025

• bioimaging-tasks-to-tools

  Public
  Quick reference for selecting the right open source tool for a bioimage analysis task.

  CSS

  •

  Creative Commons Attribution 4.0 International

  •0•2•4•0•Updated Oct 17, 2025Oct 17, 2025

• 2025-10-12-machine-learning-quant-behavior

  Public
  HTML

  •

  Other

  •0•0•0•0•Updated Oct 17, 2025Oct 17, 2025

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

  Public
  HTML

  •

  Other

  •0•0•0•0•Updated Oct 16, 2025Oct 16, 2025

• scaling-up-image-analysis

  Public
  Self paced tutorial on scaling up bioimage analysis pipelines with Python

  pythondeep-learningsegmentation+ 4daskimagingzarrdask-distributed

  Jupyter Notebook

  •

  MIT License

  •0•1•0•0•Updated Oct 1, 2025Oct 1, 2025

• sennet-demo

  Public
  Demo notebooks for using SenNet data

  Jupyter Notebook

  •

  MIT License

  •1•4•0•0•Updated Sep 29, 2025Sep 29, 2025

• 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 Sep 18, 2025Sep 18, 2025

• Spoti-find

  Public
  Python

  •

  GNU General Public License v2.0

  •0•1•5•0•Updated Sep 18, 2025Sep 18, 2025

• pdxnet-image-analysis-aacr2022

  Public
  Regional classification and other analysis of PDXNet H&E images for AACR 2022

  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Sep 12, 2025Sep 12, 2025

• jax-omerometrics

  Public
  Repo for generating OMERO reports/dashboards

  omeroomero-serveromero-web+ 2ezomeroimaging-solutions

  Python

  •

  MIT License

  •0•1•0•0•Updated Sep 4, 2025Sep 4, 2025

• quilt-nf

  Public
  R

  •0•1•0•0•Updated Sep 3, 2025Sep 3, 2025

• loinchpo

  Public
  Python version of LOINC2HPO

  Python

  •

  GNU General Public License v3.0

  •1•8•6•0•Updated Sep 2, 2025Sep 2, 2025

• nf-tenx

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

  bioinformaticspipeline

  Groovy

  •

  MIT License

  •1•7•4•1•Updated Aug 29, 2025Aug 29, 2025

• imaging_applications

  Public
  repository for Imaging Applications Github Page

  Lua

  •

  GNU General Public License v3.0

  •0•0•0•1•Updated Aug 12, 2025Aug 12, 2025

• DccXmlGenerator

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

  Python

  •0•0•0•0•Updated Jul 31, 2025Jul 31, 2025

• 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•5•1•0•Updated Jul 25, 2025Jul 25, 2025