Cytoscape supports many use cases in molecular and systems biology, genomics, and proteomics:

• Load molecular and genetic interaction data sets in many formats
• Project and integrate global datasets and functional annotations
• Establish powerful visual mappings across these data
• Perform advanced analysis and modeling using Cytoscape plugins
• Visualize and analyze human-curated pathway datasets such as Reactome or KEGG.

Cytoscape is used by social scientists to:

• Visualize and analyze large social networks of interpersonal relationships
• Assemble social networks from tables and forms
• Gather social interactions from the web by variety of web service API and scripted web crawlers within Cytoscape
• Calculate network statistics using plugins
• Use with other tools, such as R with sna/ igraph package, for more advanced analysis

Cytoscape is also a tool of choice for the semantic web community, since the semantic web is encoded and viewed as a network of knowledge and resources.

• Load and visualize Resource Description Framework (RDF) data as networks
• Import data from Triplestore through simple text table or XML-RDF
• Query RDF data by SPARQL
• Perform reasoning by plugins
• Platform to develop custom semantic web applications with other semantic web frameworks including Jena and Sesame

Cytoscape is domain-independent and therefore is a powerful tool for complex network analysis in general.

• Calculate statistics for networks by plugins such as NetworkAnalyzer or CentiScaPe
• Find shortest path
• Find clusters by various kinds of algorithms
• Use with other tools for more advanced analysis
• Import data files from other popular network analysis tools, including igraph, Pajek, and GraphViz (by standard file formats like GML)

Cytoscape is expandable and extensible. Cytoscape has a vibrant plugin developer community and over a hundred plugins developed by third parties.

• Build Cytoscape from source code
• Develop simple and complex plugins in Java
• Rich Cytoscape Application Programming Interface ( API)
• Active developer community
• Write simple functions with scripting languages, including Ruby, Python, Groovy, and JavaScript