Repositories list

• js4cytoscape

  Public
  JavaScript library for calling Cytoscape Automation via CyREST

  JavaScript

  •

  MIT License

  •4•4•1•0•Updated Sep 8, 2025Sep 8, 2025

• network-ptm-integration

  Public
  This repo tracks the work of data-driven addition of phosphorylation sites to proteins in networks (and pathways).

  R

  •

  MIT License

  •0•0•7•0•Updated Sep 8, 2025Sep 8, 2025

• cytoscape-web

  Public
  A browser-based implementation of Cytoscape for network visualization and analysis. Runs entirely in your browser with data-driven styling, collaborative workflows, and Cytoscape ecosystem integration.

  systems-biologydata-visualizationcytoscape+ 2network-analysisnetwork-biology

  TypeScript

  •

  MIT License

  •10•19•0•3•Updated Sep 4, 2025Sep 4, 2025

• cytoscape-home

  Public
  JavaScript

  •

  MIT License

  •1•1•7•0•Updated Sep 4, 2025Sep 4, 2025

• cytoscape.js-dagre

  Public
  The Dagre layout for DAGs and trees for Cytoscape.js

  cytoscapejscytoscapejs-extension

  JavaScript

  •

  MIT License

  •80•262•0•2•Updated Aug 28, 2025Aug 28, 2025

• cytoscape.js-klay

  Public
  The Klay layout algorithm for Cytoscape.js

  JavaScript

  •

  MIT License

  •42•94•0•3•Updated Aug 24, 2025Aug 24, 2025

• cytoscape.js-popper

  Public
  A wrapper for Popper.js that lets you position divs relative to Cytoscape elements

  JavaScript

  •

  MIT License

  •23•104•0•4•Updated Aug 24, 2025Aug 24, 2025

• cytoscape.js-automove

  Public
  An extension for Cytoscape.js that automatically updates node positions based on specified rules

  cytoscapejscytoscapejs-extension

  JavaScript

  •

  MIT License

  •10•35•0•3•Updated Aug 24, 2025Aug 24, 2025

• cytoscape.js-pdf-export

  Public
  PDF export extension for Cytoscape.js

  JavaScript

  •

  MIT License

  •0•2•3•0•Updated Aug 21, 2025Aug 21, 2025

• cytoscape.js

  Public
  Graph theory (network) library for visualisation and analysis

  visualizationjavascriptanalysis+ 4networkvisualisationgraph-theorycytoscapejs

  JavaScript

  •

  MIT License

  •1.6k•11k•12•2•Updated Aug 21, 2025Aug 21, 2025

• cytoscape.js-cxtmenu

  Public
  Context menu for Cytoscape.js

  cytoscapejscytoscapejs-extension

  JavaScript

  •

  MIT License

  •83•173•0•2•Updated Aug 21, 2025Aug 21, 2025

• cytoscape.js-cola

  Public
  The Cola.js physics simulation layout for Cytoscape.js

  cytoscapejscytoscapejs-extension

  JavaScript

  •

  MIT License

  •68•164•0•2•Updated Aug 21, 2025Aug 21, 2025

• cytoscape.js-edgehandles

  Public
  Edge creation UI extension for Cytoscape.js

  cytoscapejscytoscapejs-extension

  HTML

  •

  MIT License

  •85•177•0•2•Updated Aug 21, 2025Aug 21, 2025

• py4cytoscape

  Public
  Python library for calling Cytoscape Automation via CyREST

  workflowworkflow-automationpython+ 3cytoscapepy2cytoscapecytoscape-interfaces

  Python

  •

  Other

  •15•85•26•1•Updated Aug 16, 2025Aug 16, 2025

• cytoscape-manual

  Public
  Markdown version of Cytoscape manual

  Creative Commons Zero v1.0 Universal

  •22•12•0•0•Updated Aug 14, 2025Aug 14, 2025

• cytoscape-impl

  Public
  Cytoscape 3 implementation bundles.

  Java

  •

  GNU Lesser General Public License v2.1

  •40•40•0•0•Updated Aug 7, 2025Aug 7, 2025

• cytoscape.js-compound-drag-and-drop

  Public
  Compound node drag-and-drop UI for adding and removing children

  JavaScript

  •

  MIT License

  •16•33•0•1•Updated Aug 6, 2025Aug 6, 2025

• cytoscape-gui-distribution

  Public
  Cytoscape 3 desktop version.

  Java

  •18•17•0•3•Updated Jul 31, 2025Jul 31, 2025

• cyREST

  Public
  Core App: REST API module for Cytoscape

  JavaScript

  •

  MIT License

  •13•31•50•0•Updated Jul 31, 2025Jul 31, 2025

• cytoscape.js-blog

  Public
  The Cytoscape.js blog, using Github pages and Jekyll

  JavaScript

  •

  MIT License

  •49•18•0•4•Updated Jul 29, 2025Jul 29, 2025

• cx

  Public
  CX serialization and de-serialization in Cytoscape

  Java

  •1•3•8•1•Updated Jul 23, 2025Jul 23, 2025

• cytoscape.js-panzoom

  Public
  Panzoom extension for Cytoscape.js

  cytoscapejscytoscapejs-extension

  CSS

  •

  MIT License

  •33•68•0•1•Updated Jul 22, 2025Jul 22, 2025

• iregulon-webapp

  Public
  JavaScript

  •

  MIT License

  •0•1•17•0•Updated Jul 16, 2025Jul 16, 2025

• ipycytoscape

  Public
  A Cytoscape Jupyter widget

  binderjupyter-notebookcytoscape

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •63•283•60•14•Updated Jul 7, 2025Jul 7, 2025

• cytoscape-app-samples

  Public
  Cytoscape 3 sample code for App developers.

  Java

  •301•22•1•0•Updated Jul 7, 2025Jul 7, 2025

• cytocontainer-rest-server

  Public
  Java

  •0•0•0•0•Updated Jul 3, 2025Jul 3, 2025

• cytocontainer-rest-model

  Public
  Java

  •0•0•0•0•Updated Jun 26, 2025Jun 26, 2025

• RCy3

  Public
  New version of RCy3, redesigned and collaboratively maintained by Cytoscape developer community

  R

  •

  MIT License

  •20•54•5•0•Updated Jun 24, 2025Jun 24, 2025

• enrichment-map-webapp

  Public
  JavaScript

  •

  MIT License

  •1•9•9•0•Updated Jun 6, 2025Jun 6, 2025

• web-cytoscape-manual

  Public
  Holds documentation for Cytoscape Web

  Makefile

  •

  Creative Commons Zero v1.0 Universal

  •0•1•0•0•Updated May 30, 2025May 30, 2025