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    • Jupyter Notebook
      MIT License
      0100Updated Apr 15, 2026Apr 15, 2026
    • FLASHMM

      Public
      Fast and Scalable Single Cell Differential Expression Analysis using Mixed-effects Models
      R
      Other
      29141Updated Apr 8, 2026Apr 8, 2026
    • GenAnT

      Public
      A tutorial on how to annotate and interpret novel mammalian reference genomes
      HTML
      MIT License
      82410Updated Mar 4, 2026Mar 4, 2026
    • Wolfram Language
      0000Updated Feb 27, 2026Feb 27, 2026
    • Analysis scripts for benchmarking FLASH-MM and applying it to case-control and cell-type-specific comparisons in scRNA-seq datasets.
      R
      MIT License
      0000Updated Dec 27, 2025Dec 27, 2025
    • R
      MIT License
      0000Updated Dec 25, 2025Dec 25, 2025
    • APA-Net

      Public
      Jupyter Notebook
      MIT License
      1200Updated Aug 14, 2025Aug 14, 2025
    • RETINA

      Public
      Jupyter Notebook
      MIT License
      0500Updated Jun 16, 2025Jun 16, 2025
    • Compute Ontario Pathway and Network Analysis Bookdown for June 2025
      CSS
      Creative Commons Zero v1.0 Universal
      11100Updated Jun 4, 2025Jun 4, 2025
    • R
      MIT License
      41600Updated May 22, 2025May 22, 2025
    • compare results from GSEA and fGSEA
      TeX
      Creative Commons Zero v1.0 Universal
      2000Updated Apr 30, 2025Apr 30, 2025
    • sciRED

      Public
      Jupyter Notebook
      MIT License
      2910Updated Mar 20, 2025Mar 20, 2025
    • simulated lineage history files
      MIT License
      0000Updated Feb 14, 2025Feb 14, 2025
    • Java
      02100Updated Jan 28, 2025Jan 28, 2025
    • cy3d-impl

      Public
      3D Graph Renderer for Cytoscape using OpenGL
      Java
      11060Updated Jan 9, 2025Jan 9, 2025
    • The AutoAnnotate Cytoscape App finds clusters of nodes and visually annotates them with semantic labels and groups.
      Java
      GNU Lesser General Public License v2.1
      18203Updated Jan 6, 2025Jan 6, 2025
    • CBW Asynchronous Pathway and Network Analysis Bookdown for November 2024
      Jupyter Notebook
      Creative Commons Zero v1.0 Universal
      11000Updated Nov 19, 2024Nov 19, 2024
    • End-User Documentation for the EnrichmentMap Cytoscape App
      Python
      1320Updated Oct 7, 2024Oct 7, 2024
    • The EnrichmentMap Cytoscape App allows you to visualize the results of gene-set enrichment as a network.
      Java
      GNU Lesser General Public License v2.1
      1235339Updated Oct 7, 2024Oct 7, 2024
    • openPIP

      Public
      The open protein interaction platform repo
      JavaScript
      MIT License
      138203Updated Aug 6, 2024Aug 6, 2024
    • CBW Pathway and Network Analysis Bookdown for June 2024
      Jupyter Notebook
      Creative Commons Zero v1.0 Universal
      11010Updated Jun 28, 2024Jun 28, 2024
    • ecuda

      Public
      STL-like containers (array, vector, matrix, cube) useable in device code.
      C++
      Other
      73301Updated Feb 23, 2024Feb 23, 2024
    • code to run the mimp webserver (mimp.baderlab.org)
      JavaScript
      GNU Lesser General Public License v3.0
      1000Updated Nov 8, 2023Nov 8, 2023
    • repo with dockers for each of the static baderlab servers
      Dockerfile
      0000Updated Oct 27, 2023Oct 27, 2023
    • ALS_APA

      Public
      Codes for APA-Net model and analysis for ALS APA atlas paper
      Jupyter Notebook
      MIT License
      0000Updated Oct 2, 2023Oct 2, 2023
    • Explore and share your scRNAseq clustering results
      R
      MIT License
      1052120Updated Sep 6, 2023Sep 6, 2023
    • R function and document for power analysis of the log-rank test in survival analysis
      R
      0000Updated Aug 24, 2023Aug 24, 2023
    • R
      0000Updated Aug 23, 2023Aug 23, 2023
    • RatLiver

      Public
      a single-cell atlas of the rat liver
      R
      0100Updated Aug 23, 2023Aug 23, 2023
    • Predicting SH3 domain mediated protein interactions in human
      Python
      GNU General Public License v3.0
      0000Updated Jul 12, 2023Jul 12, 2023
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