Cytoscape
Network data integration, analysis, and visualization
Cytoscape is an open source platform for visualizing complex networks and integrating them with attribute data. It supports molecular and genetic interaction datasets in standard formats, pathway datasets such as WikiPathways, Reactome, and KEGG, and social network data assembled from tables, forms, and web service APIs. Because it is domain-independent, it can also be used for general complex network analysis.
Core capabilities include visual mappings across data, shortest path and cluster analysis, and network statistics through Apps such as NetworkAnalyzer and CentiScaPe. It integrates with tools including R (sna/igraph), NetworkX, igraph, Pajek, and GraphViz, and supports automation via CyREST, Commands, and R and Python libraries. Cytoscape is extensible through third-party Apps built on the OSGi framework using Java and its API, with source code on GitHub. Cytoscape Web is available for browser-based use, and NDEx iQuery supports gene analysis.
Cytoscape is used in bioinformatics, social network analysis, semantic web, and general network analysis. It is distributed as open source software; the pages do not describe plans, trials, or seat-based editions.
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