A travel guide to Cytoscape plugins

Nat Methods. 2012 Nov;9(11):1069-76. doi: 10.1038/nmeth.2212. Epub 2012 Nov 6.


Cytoscape is open-source software for integration, visualization and analysis of biological networks. It can be extended through Cytoscape plugins, enabling a broad community of scientists to contribute useful features. This growth has occurred organically through the independent efforts of diverse authors, yielding a powerful but heterogeneous set of tools. We present a travel guide to the world of plugins, covering the 152 publicly available plugins for Cytoscape 2.5-2.8. We also describe ongoing efforts to distribute, organize and maintain the quality of the collection.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Algorithms
  • Computational Biology
  • Computer Simulation
  • Data Mining
  • Database Management Systems
  • Gene Expression Profiling
  • Gene Regulatory Networks*
  • Genes / physiology*
  • Genomics / methods*
  • Models, Biological
  • Software*