A travel guide to Cytoscape plugins

Abstract

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.

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Figure 1: Statistics for registered Cytoscape plugins.
Figure 2: Network analysis workflow.
Figure 3: Relationships between Cytoscape plugins and tags.
Figure 4: Examples of plugin outputs.

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Acknowledgements

Work on this review was funded by the National Resource for Network Biology (P41 GM103504) and the San Diego Center for Systems Biology (P50 GM085764). We thank J. Dutkowski, D. Emig and G. Hannum for advice and critical reading of the manuscript. Finally, the greatest thanks go to all of the plugin developers who have enriched the Cytoscape user experience with their ideas. We apologize to those plugin authors whose excellent work was not covered here because of space limitations.

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Correspondence to Trey Ideker.

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Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–6 and Supplementary Table 1 (PDF 888 kb)

Supplementary Data

Comprehensive list of Cytoscape plugins that we reviewed and tagged. (XLS 56 kb)

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Saito, R., Smoot, M., Ono, K. et al. A travel guide to Cytoscape plugins. Nat Methods 9, 1069–1076 (2012). https://doi.org/10.1038/nmeth.2212

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