Discover cytoscape/cytoscape-manual Open Source project

Cytoscape: an open source platform for network analysis and visualization

10,035

cytoscape

Shell

518

cytoscape-tutorials

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

A Cytoscape Jupyter widget

309

ipycytoscape

The Dagre layout for DAGs and trees for Cytoscape.js

263

cytoscape.js-dagre

Python utilities for Cytoscape and Cytoscape.js

225

py2cytoscape

Edge creation UI extension for Cytoscape.js

178

cytoscape.js-edgehandles

Context menu for Cytoscape.js

160

cytoscape.js-cxtmenu

The Cola.js physics simulation layout for Cytoscape.js

155

cytoscape.js-cola

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

133

cytoscape.js-cose-bilkent

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

116

cytoscape.js-popper

An R/shiny widget for cytoscape.js

cyjShiny

Collection of scripts that include programmatic io and control of Cytoscape

cytoscape-automation

The Klay layout algorithm for Cytoscape.js

cytoscape.js-klay

wineandcheesemap

Panzoom extension for Cytoscape.js

cytoscape.js-panzoom

CSS

cytoscape.js-navigator

Bird's eye view pan and zoom control for Cytoscape.js.

Python library for calling Cytoscape Automation via CyREST

py4cytoscape

A Node.js package that renders images of Cytoscape.js graphs on the server using Puppeteer

cytosnap

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

RCy3

cytoscape.js-elk

The ELK layout algorithm adapter for Cytoscape.js

A Cytoscape.js extension that wraps the QTip jQuery library

cytoscape.js-qtip

Out of date. Refer to https://blog.js.cytoscape.org/tutorials/

cytoscape.js-tutorial-demo

Cytoscape.js based network visualizer for Jupyter Notebook

cytoscape-jupyter-widget

Cytoscape 3 implementation bundles.

cytoscape-impl

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

cytoscape.js-automove

Euler is a fast, high-quality force-directed (physics simulation) layout for Cytoscape.js

cytoscape.js-euler

Core App: REST API module for Cytoscape

cyREST

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

cytoscape.js-compound-drag-and-drop

The speedy Spread physics simulation layout for Cytoscape.js

cytoscape.js-spread

Jupyter lab widget for rendering graphs (networks)

cy-jupyterlab

cytoscape.github.com

Cytoscape org web site.

cytoscape-api

Cytoscape 3 API bundles.

Cytoscape 3 sample code for App developers.

cytoscape-app-samples

The Cytoscape.js blog, using Github pages and Jekyll

cytoscape.js-blog

Cytoscape 3 desktop version.

cytoscape-gui-distribution

Cytoscape App Store web application code

appstore

Cytoscape.js tutorials project for GSOC 2016

cytoscape.js-tutorials

Network visualization webapp.

cytoscape-explore

cyjs-sample

A comparison of JS graph libs

js-graph-lib-comparison

Cytoscape.js API support in JS, Python, and R Jupyter kernels

jupyter-cytoscape

A Cytoscape.js extension for the hierarchical clustering algorithm

cytoscape.js-hierarchical

A Cytoscape.js extension generator

slush-cytoscape-extension

A Cytoscape.js extension for the k-means, k-medoids, & fuzzy c-means family of algorithms

cytoscape.js-k-means

Creates a new table for performing, storing and viewing functional enrichment analysis

enrichment-table-app

enrichment-map-webapp

Flash-based graph visualization tool which can be integrated in HTML via its Javascript API (http://cytoscapeweb.cytoscape.org).

cytoscapeweb

ActionScript

cytoscape.js-leaflet

A Cytoscape.js extension to overlay a graph (network) on top of a Leaflet map

Community Detection App for Cytoscape

wiki-plugin-cytodemo

CoffeeScript

cytoscape-web

TypeScript

cy-community-detection

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

jupyter-bridge

Parent project for all Cytoscape.js export options.

web-export-templates

The Arbor physics simulation layout for Cytoscape.js

cytoscape.js-arbor

JavaScript library for calling Cytoscape Automation via CyREST

js4cytoscape

biopax

Core App: BioPAX support

A CX to Cytoscape JS library

cx2js

Zugzwang (German: forced to make a move) is a new OpenGL-accelerated renderer for Cytoscape that prioritizes rapid visual feedback above all else – thus the name.

zugzwang

The Springy physics simulation layout for Cytoscape.js

cytoscape.js-springy

A starting point for building graphs with Cytoscape.js during the MozFest 2015 open science session

mozfest2015-session

R functions for Cytoscape automation

fgsea-service

r2cytoscape

cytoscape.js-reveal-slides

Reveal.js for presentation "Displaying interactive networks on the web"

A Cytoscape.js extension for the Markov cluster algorithm

cytoscape.js-markov-cluster

A Cytoscape app to interface with the heat diffusion service

diffusion

Map the locations of nodes (and the network view) from one network to another. Easily compare networks side by side by positioning the views similarly.

copycat-layout

idmapper

Identifier mapping

DEPRECATED!! (Was used for for Core Apps)

cytoscape-app

cxio

CX serialization and de-serialization

interactive histogram and scatter charts to select nodes or create filters

mcode-service

cytosnap-demo

A demo Cytosnap server

cyChart

Build and maintenance scripts for Cytoscape core developers.

cytoscape-admin-scripts

User-submitted demos of Cytoscape.js

cytoscape.js-demos

CX serialization and de-serialization in Cytoscape

cx-viz-converter

Reveal.js testing webapp for running platform tests on Cytoscape via CyREST calls

cytoscape-platform-tests-js

Cytoscape3 app to create legends as annotations

legend-creator

file-transfer-app

A Cytoscape.js extension generator

sbml

Core App: SBML Reader

cytoscape.js-matter

cyBrowser

cytoscape-home-mock

generator-cytoscape-extension

Automatically exported from code.google.com/p/foograph

foograph

Client for Id Mapping Service

idmap

Select Largest Subnetwork App

LargestSubnetwork

Cytoscape 3 project files for App developers.

cytoscape-app-template

cytoscape2

Cytoscape 2.x series code.

EnrichmentMap microservice

enrichmentmap-service

repo for src and poms defining collections of apps

app-collections

Template code for simple export from Cytoscape 3.2.

cyjs-export-simple

ApacheConf

js-perf

Rendering and layout performance test page for Cytoscape.js

Use JSON-RPC to drive a remote instance of Cytoscape.js

cytoscape.js-rpc

Demonstration of a script-app

script-app-demo

cytoscape-ismb-2020

A Jekyll site for publishing JS notebooks for Cytoscape automation via js4cytoscape

javascript-notebooks

A Cytoscape.js extension for the affinity propagation algorithm

cytoscape.js-affinity-propagation

100

cytoscape-home