Repositories list

• Multiscale_human_liver_vEM

  Public
  Jupyter Notebook

  •

  MIT License

  •00 forks•11 star•00 issues•00 pull requests•Updated Apr 15, 2026Apr 15, 2026

• FLASHMM

  Public
  Fast and Scalable Single Cell Differential Expression Analysis using Mixed-effects Models

  R

  •

  Other

  •22 forks•99 stars•1414 issues•11 pull request•Updated Apr 8, 2026Apr 8, 2026

• GenAnT

  Public
  A tutorial on how to annotate and interpret novel mammalian reference genomes

  HTML

  •

  MIT License

  •88 forks•2424 stars•11 issue•00 pull requests•Updated Mar 4, 2026Mar 4, 2026

• Lineage_Theory

  Public
  Wolfram Language

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 27, 2026Feb 27, 2026

• FLASH-MM-analysis

  Public
  Analysis scripts for benchmarking FLASH-MM and applying it to case-control and cell-type-specific comparisons in scRNA-seq datasets.

  R

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Dec 27, 2025Dec 27, 2025

• phase_contrast_collective_organization_GSCs_incucyte_August2025

  Public
  R

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Dec 25, 2025Dec 25, 2025

• APA-Net

  Public
  Jupyter Notebook

  •

  MIT License

  •11 fork•22 stars•00 issues•00 pull requests•Updated Aug 14, 2025Aug 14, 2025

• RETINA

  Public
  Jupyter Notebook

  •

  MIT License

  •00 forks•55 stars•00 issues•00 pull requests•Updated Jun 16, 2025Jun 16, 2025

• ComputeOntario_Pathways_2025

  Public
  Compute Ontario Pathway and Network Analysis Bookdown for June 2025

  CSS

  •

  Creative Commons Zero v1.0 Universal

  •1111 forks•11 star•00 issues•00 pull requests•Updated Jun 4, 2025Jun 4, 2025

• MALAT1_threshold

  Public
  R

  •

  MIT License

  •44 forks•1616 stars•00 issues•00 pull requests•Updated May 22, 2025May 22, 2025

• GSEA_vs_fGSEA

  Public
  compare results from GSEA and fGSEA

  TeX

  •

  Creative Commons Zero v1.0 Universal

  •22 forks•00 stars•00 issues•00 pull requests•Updated Apr 30, 2025Apr 30, 2025

• sciRED

  Public
  Jupyter Notebook

  •

  MIT License

  •22 forks•99 stars•11 issue•00 pull requests•Updated Mar 20, 2025Mar 20, 2025

• Lineage_Vis

  Public
  simulated lineage history files

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 14, 2025Feb 14, 2025

• EnrichmentMap_monthlyGenesetBuild

  Public
  Java

  •00 forks•22 stars•1010 issues•00 pull requests•Updated Jan 28, 2025Jan 28, 2025

• cy3d-impl

  Public
  3D Graph Renderer for Cytoscape using OpenGL

  javaopenglcytoscape+ 2

  javaopenglcytoscapejogl3d-renderer

  Java

  •11 fork•1010 stars•66 issues•00 pull requests•Updated Jan 9, 2025Jan 9, 2025

• AutoAnnotateApp

  Public
  The AutoAnnotate Cytoscape App finds clusters of nodes and visually annotates them with semantic labels and groups.

  javacytoscape

  javacytoscape

  Java

  •

  GNU Lesser General Public License v2.1

  •11 fork•88 stars•2020 issues•33 pull requests•Updated Jan 6, 2025Jan 6, 2025

• CBW_Pathways_2024_asynchronous

  Public
  CBW Asynchronous Pathway and Network Analysis Bookdown for November 2024

  Jupyter Notebook

  •

  Creative Commons Zero v1.0 Universal

  •1111 forks•00 stars•00 issues•00 pull requests•Updated Nov 19, 2024Nov 19, 2024

• EnrichmentMap_docs

  Public
  End-User Documentation for the EnrichmentMap Cytoscape App

  Python

  •11 fork•33 stars•22 issues•00 pull requests•Updated Oct 7, 2024Oct 7, 2024

• EnrichmentMapApp

  Public
  The EnrichmentMap Cytoscape App allows you to visualize the results of gene-set enrichment as a network.

  javaenrichmentcytoscape

  javaenrichmentcytoscape

  Java

  •

  GNU Lesser General Public License v2.1

  •1212 forks•3535 stars•3333 issues•99 pull requests•Updated Oct 7, 2024Oct 7, 2024

• openPIP

  Public
  The open protein interaction platform repo

  JavaScript

  •

  MIT License

  •1313 forks•88 stars•2020 issues•33 pull requests•Updated Aug 6, 2024Aug 6, 2024

• CBW_Pathways_2024

  Public
  CBW Pathway and Network Analysis Bookdown for June 2024

  Jupyter Notebook

  •

  Creative Commons Zero v1.0 Universal

  •1111 forks•00 stars•11 issue•00 pull requests•Updated Jun 28, 2024Jun 28, 2024

• ecuda

  Public
  STL-like containers (array, vector, matrix, cube) useable in device code.

  c-plus-pluscuda

  c-plus-pluscuda

  C++

  •

  Other

  •77 forks•3333 stars•00 issues•11 pull request•Updated Feb 23, 2024Feb 23, 2024

• mimp_webserver

  Public
  code to run the mimp webserver (mimp.baderlab.org)

  JavaScript

  •

  GNU Lesser General Public License v3.0

  •11 fork•00 stars•00 issues•00 pull requests•Updated Nov 8, 2023Nov 8, 2023

• Baderlab_static_webservers

  Public
  repo with dockers for each of the static baderlab servers

  Dockerfile

  •00 forks•00 stars•00 issues•00 pull requests•Updated Oct 27, 2023Oct 27, 2023

• ALS_APA

  Public
  Codes for APA-Net model and analysis for ALS APA atlas paper

  Jupyter Notebook

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Oct 2, 2023Oct 2, 2023

• scClustViz

  Public
  Explore and share your scRNAseq clustering results

  ruishiny+ 6

  ruishinyscrna-seqsingle-celldifferential-expressionclustering-evaluationscrnaseqscrna-seq-analysis

  R

  •

  MIT License

  •1010 forks•5252 stars•1212 issues•00 pull requests•Updated Sep 6, 2023Sep 6, 2023

• logrank.test_power

  Public
  R function and document for power analysis of the log-rank test in survival analysis

  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 24, 2023Aug 24, 2023

• HealthyRatLiverMap

  Public
  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 23, 2023Aug 23, 2023

• RatLiver

  Public
  a single-cell atlas of the rat liver

  R

  •00 forks•11 star•00 issues•00 pull requests•Updated Aug 23, 2023Aug 23, 2023

• DoMo-Pred-Human

  Public
  Predicting SH3 domain mediated protein interactions in human

  Python

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 12, 2023Jul 12, 2023