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    96 repositories

    • GenAnT

      Public
      A tutorial on how to annotate and interpret novel mammalian reference genomes
      HTML
      •
      MIT License
      •3•7•1•0•Updated Jan 9, 2026Jan 9, 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
      •0•0•0•0•Updated Dec 27, 2025Dec 27, 2025

    • phase_contrast_collective_organization_GSCs_incucyte_August2025

      Public
      R
      •
      MIT License
      •0•0•0•0•Updated Dec 25, 2025Dec 25, 2025

    • FLASHMM

      Public
      Fast and Scalable Single Cell Differential Expression Analysis using Mixed-effects Models
      R
      •
      Other
      •1•7•11•1•Updated Aug 27, 2025Aug 27, 2025

    • APA-Net

      Public
      Jupyter Notebook
      •
      MIT License
      •0•2•0•0•Updated Aug 14, 2025Aug 14, 2025

    • RETINA

      Public
      Jupyter Notebook
      •
      MIT License
      •0•3•0•0•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
      •11•1•0•0•Updated Jun 4, 2025Jun 4, 2025

    • MALAT1_threshold

      Public
      R
      •
      MIT License
      •4•15•0•0•Updated May 22, 2025May 22, 2025

    • GSEA_vs_fGSEA

      Public
      compare results from GSEA and fGSEA
      TeX
      •
      Creative Commons Zero v1.0 Universal
      •2•0•0•0•Updated Apr 30, 2025Apr 30, 2025

    • sciRED

      Public
      Jupyter Notebook
      •
      MIT License
      •2•8•1•0•Updated Mar 20, 2025Mar 20, 2025

    • Lineage_Vis

      Public
      simulated lineage history files
      MIT License
      •0•0•0•0•Updated Feb 14, 2025Feb 14, 2025

    • EnrichmentMap_monthlyGenesetBuild

      Public
      Java
      •0•2•9•0•Updated Jan 28, 2025Jan 28, 2025

    • Lineage_Theory

      Public
      0•0•0•0•Updated Jan 21, 2025Jan 21, 2025

    • cy3d-impl

      Public
      3D Graph Renderer for Cytoscape using OpenGL
      javaopenglcytoscapejogl3d-renderer
      Java
      •1•10•6•0•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
      Java
      •
      GNU Lesser General Public License v2.1
      •1•7•20•3•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
      •11•0•0•0•Updated Nov 19, 2024Nov 19, 2024

    • EnrichmentMap_docs

      Public
      End-User Documentation for the EnrichmentMap Cytoscape App
      Python
      •1•3•2•0•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
      Java
      •
      GNU Lesser General Public License v2.1
      •12•35•32•9•Updated Oct 7, 2024Oct 7, 2024

    • openPIP

      Public
      The open protein interaction platform repo
      JavaScript
      •
      MIT License
      •10•8•16•1•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
      •11•0•1•0•Updated Jun 28, 2024Jun 28, 2024

    • ecuda

      Public
      STL-like containers (array, vector, matrix, cube) useable in device code.
      c-plus-pluscuda
      C++
      •
      Other
      •7•33•0•1•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
      •1•0•0•0•Updated Nov 8, 2023Nov 8, 2023

    • Baderlab_static_webservers

      Public
      repo with dockers for each of the static baderlab servers
      Dockerfile
      •0•0•0•0•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
      •0•0•0•0•Updated Oct 2, 2023Oct 2, 2023

    • scClustViz

      Public
      Explore and share your scRNAseq clustering results
      ruishinyscrna-seqsingle-celldifferential-expressionclustering-evaluationscrnaseqscrna-seq-analysis
      R
      •
      MIT License
      •9•50•12•0•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
      •0•0•0•0•Updated Aug 24, 2023Aug 24, 2023

    • HealthyRatLiverMap

      Public
      R
      •0•0•0•0•Updated Aug 23, 2023Aug 23, 2023

    • RatLiver

      Public
      a single-cell atlas of the rat liver
      R
      •0•1•0•0•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
      •0•0•0•0•Updated Jul 12, 2023Jul 12, 2023

    • MCODE

      Public
      Cytoscape app that clusters a given network based on topology to find densely connected regions
      Java
      •6•10•3•1•Updated Jun 28, 2023Jun 28, 2023