Repositories list

• cytoscape-desktop-mcp

  Public

  cytoscape/cytoscape-desktop-mcp’s past year of commit activity
  App which provides an MCP server for integration of desktop with agents

  Java

  •

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

  •0•0•0•0•Updated Mar 3, 2026Mar 3, 2026

• cytoscape-web

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

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

  TypeScript

  •

  MIT License

  •12•27•0•1•Updated Mar 3, 2026Mar 3, 2026

• cytoscape.js-compound-drag-and-drop

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

  JavaScript

  •

  MIT License

  •15•33•0•4•Updated Mar 2, 2026Mar 2, 2026

• cytoscape.js-klay

  Public
  The Klay layout algorithm for Cytoscape.js

  JavaScript

  •

  MIT License

  •42•97•0•5•Updated Mar 2, 2026Mar 2, 2026

• cytoscape.js-cola

  Public

  cytoscape/cytoscape.js-cola’s past year of commit activity
  The Cola.js physics simulation layout for Cytoscape.js

  cytoscapejscytoscapejs-extension

  JavaScript

  •

  MIT License

  •67•170•0•3•Updated Mar 2, 2026Mar 2, 2026

• cytoscape.js-edgehandles

  Public
  Edge creation UI extension for Cytoscape.js

  cytoscapejscytoscapejs-extension

  HTML

  •

  MIT License

  •82•179•0•6•Updated Mar 2, 2026Mar 2, 2026

• cytoscape.js-panzoom

  Public
  Panzoom extension for Cytoscape.js

  cytoscapejscytoscapejs-extension

  CSS

  •

  MIT License

  •31•68•0•4•Updated Mar 2, 2026Mar 2, 2026

• cytoscape.js-dagre

  Public

  cytoscape/cytoscape.js-dagre’s past year of commit activity
  The Dagre layout for DAGs and trees for Cytoscape.js

  cytoscapejscytoscapejs-extension

  JavaScript

  •

  MIT License

  •81•276•1•5•Updated Mar 2, 2026Mar 2, 2026

• cytoscape.js-cose-bilkent

  Public
  The CoSE layout for Cytoscape.js by Bilkent with enhanced compound node placement.

  cytoscapejscytoscapejs-extension

  HTML

  •

  MIT License

  •45•137•20•11•Updated Mar 1, 2026Mar 1, 2026

• cytoscape-desktop-website

  Public

  cytoscape/cytoscape-desktop-website’s past year of commit activity
  The new "Cytoscape Desktop" website

  JavaScript

  •

  MIT License

  •0•0•0•0•Updated Feb 26, 2026Feb 26, 2026

• cytoscape-home

  Public
  JavaScript

  •

  MIT License

  •4•1•10•3•Updated Feb 20, 2026Feb 20, 2026

• cytoscape.js-cxtmenu

  Public
  Context menu for Cytoscape.js

  cytoscapejscytoscapejs-extension

  JavaScript

  •

  MIT License

  •80•179•0•3•Updated Feb 18, 2026Feb 18, 2026

• cytoscape.js-popper

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

  JavaScript

  •

  MIT License

  •22•104•0•4•Updated Feb 17, 2026Feb 17, 2026

• 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 Feb 17, 2026Feb 17, 2026

• jupyter-bridge

  Public
  Bridge enables Jupyter code on remote server to execute HTTP calls on local PC

  Python

  •

  MIT License

  •3•4•0•0•Updated Feb 12, 2026Feb 12, 2026

• cytoscape-admin-scripts

  Public
  Build and maintenance scripts for Cytoscape core developers.

  Jupyter Notebook

  •4•2•1•0•Updated Feb 11, 2026Feb 11, 2026

• cytocontainer-rest-server

  Public
  Java

  •0•0•0•0•Updated Feb 4, 2026Feb 4, 2026

• py4cytoscape

  Public
  Python library for calling Cytoscape Automation via CyREST

  pythonworkflowcytoscape+ 3workflow-automationpy2cytoscapecytoscape-interfaces

  Python

  •

  Other

  •16•85•27•1•Updated Feb 3, 2026Feb 3, 2026

• cytoscape.js-automove

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

  cytoscapejscytoscapejs-extension

  JavaScript

  •

  MIT License

  •8•37•0•5•Updated Jan 24, 2026Jan 24, 2026

• appstore

  Public
  Cytoscape App Store web application code

  Python

  •21•17•26•6•Updated Jan 22, 2026Jan 22, 2026

• cytoscape.js

  Public
  Graph theory (network) library for visualisation and analysis

  visualizationjavascriptanalysis+ 4networkvisualisationgraph-theorycytoscapejs

  JavaScript

  •

  MIT License

  •1.7k•11k•19•7•Updated Jan 21, 2026Jan 21, 2026

• ipycytoscape

  Public
  A Cytoscape Jupyter widget

  binderjupyter-notebookcytoscape

  Python

  •

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

  •61•288•60•14•Updated Jan 5, 2026Jan 5, 2026

• cytoscape-impl

  Public
  Cytoscape 3 implementation bundles.

  Java

  •

  GNU Lesser General Public License v2.1

  •40•41•0•0•Updated Jan 1, 2026Jan 1, 2026

• whiteboardREST

  Public
  Java

  •0•0•0•0•Updated Dec 18, 2025Dec 18, 2025

• cytoscape-api

  Public
  Cytoscape 3 API bundles.

  Java

  •

  GNU Lesser General Public License v2.1

  •34•26•0•1•Updated Dec 17, 2025Dec 17, 2025

• cytoscape-gui-distribution

  Public
  Cytoscape 3 desktop version.

  Java

  •17•17•0•3•Updated Dec 17, 2025Dec 17, 2025

• cx

  Public
  CX serialization and de-serialization in Cytoscape

  Java

  •0•3•8•1•Updated Dec 11, 2025Dec 11, 2025

• cyweb-mcp

  Public
  0•0•0•0•Updated Dec 8, 2025Dec 8, 2025

• RCy3

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

  R

  •

  MIT License

  •19•58•5•0•Updated Dec 3, 2025Dec 3, 2025

• cytoscape-tutorials

  Public
  Collection of modular Cytoscape tutorials for online presentation using reveal.js

  HTML

  •

  Creative Commons Zero v1.0 Universal

  •117•326•26•13•Updated Nov 6, 2025Nov 6, 2025