Repositories list

• CBW_Pathways_2024_asynchronous

  Public
  CBW Asynchronous Pathway and Network Analysis Bookdown for November 2024

  Jupyter Notebook

  •

  Creative Commons Zero v1.0 Universal

  •6•0•0•0•Updated Oct 11, 2024Oct 11, 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.

  enrichmentcytoscapejava

  Java

  •

  GNU Lesser General Public License v2.1

  •12•32•29•9•Updated Oct 7, 2024Oct 7, 2024

• 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•6•20•3•Updated Oct 7, 2024Oct 7, 2024

• EnrichmentMap_monthlyGenesetBuild

  Public
  Java

  •0•2•9•0•Updated Sep 17, 2024Sep 17, 2024

• openPIP

  Public
  The open protein interaction platform repo

  JavaScript

  •

  MIT License

  •9•7•16•0•Updated Aug 6, 2024Aug 6, 2024

• MALAT1_threshold

  Public
  R

  •

  MIT License

  •1•9•0•0•Updated Jul 22, 2024Jul 22, 2024

• CBW_Pathways_2024

  Public
  CBW Pathway and Network Analysis Bookdown for June 2024

  Jupyter Notebook

  •

  Creative Commons Zero v1.0 Universal

  •6•0•1•0•Updated Jun 28, 2024Jun 28, 2024

• ecuda

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

  cudac-plus-plus

  C++

  •

  Other

  •5•31•0•0•Updated Feb 23, 2024Feb 23, 2024

• APA-Net

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Jan 2, 2024Jan 2, 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

  ruishiny+ 6scrna-seqsingle-celldifferential-expressionclustering-evaluationscrnaseqscrna-seq-analysis

  R

  •

  MIT License

  •9•46•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•7•3•1•Updated Jun 28, 2023Jun 28, 2023

• CBW_Pathways_2023

  Public
  CBW Pathway and Network Analysis Bookdown for June 2023

  Jupyter Notebook

  •

  Creative Commons Zero v1.0 Universal

  •6•1•18•0•Updated Jun 6, 2023Jun 6, 2023

• Chan-Covid19

  Public
  Code for Chan lab collaboration for Covid-19 research

  R

  •0•0•0•0•Updated Mar 28, 2023Mar 28, 2023

• Cytoscape_workflows

  Public
  collection of notebooks with different cytoscape workflows

  HTML

  •

  Creative Commons Zero v1.0 Universal

  •36•48•7•0•Updated Mar 22, 2023Mar 22, 2023

• CellAnnotationTutorial

  Public
  Accompanying code for the tutorial: Annotating single cell transcriptomic maps using automated and manual methods

  HTML

  •

  MIT License

  •25•88•0•0•Updated Mar 18, 2023Mar 18, 2023

• GeneEval

  Public
  A Python library for evaluating gene embeddings.

  Python

  •

  Apache License 2.0

  •0•4•2•11•Updated Mar 6, 2023Mar 6, 2023

• SocialNetworkApp

  Public
  dropbox

  Java

  •4•7•26•5•Updated Feb 24, 2023Feb 24, 2023

• netDx

  Public
  R package with netDx software and data for examples

  R

  •

  Other

  •9•12•16•1•Updated Feb 22, 2023Feb 22, 2023

• CCInx

  Public
  Build predicted cell-cell interaction networks from single-cell data.

  HTML

  •

  MIT License

  •3•9•0•0•Updated Jan 31, 2023Jan 31, 2023

• cy3d-impl

  Public
  3D Graph Renderer for Cytoscape using OpenGL

  openglcytoscapejogl+ 23d-rendererjava

  Java

  •1•9•6•0•Updated Dec 22, 2022Dec 22, 2022

• docker-deploy

  Public
  Automatic docker deployments on git push

  Shell

  •0•0•0•0•Updated Nov 23, 2022Nov 23, 2022

• GeneMANIA_build

  Public
  all scripts and code required to build Genemania database

  Python

  •0•0•1•0•Updated Aug 8, 2022Aug 8, 2022