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A travel guide to Cytoscape plugins

Nature Methods volume 9, pages 10691076 (2012) | Download Citation

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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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.

Author information

Affiliations

  1. Department of Medicine, University of California, San Diego, La Jolla, California, USA.

    • Rintaro Saito
    • , Michael E Smoot
    • , Keiichiro Ono
    • , Johannes Ruscheinski
    • , Peng-Liang Wang
    •  & Trey Ideker
  2. Department of Bioengineering, University of California, San Diego, La Jolla, California, USA.

    • Rintaro Saito
    • , Michael E Smoot
    • , Keiichiro Ono
    • , Johannes Ruscheinski
    • , Peng-Liang Wang
    •  & Trey Ideker
  3. Gladstone Institutes, San Francisco, California, USA.

    • Samad Lotia
    •  & Alexander R Pico
  4. The Donnelly Centre, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada.

    • Gary D Bader

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Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Trey Ideker.

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–6 and Supplementary Table 1

Excel files

  1. 1.

    Supplementary Data

    Comprehensive list of Cytoscape plugins that we reviewed and tagged.

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DOI

https://doi.org/10.1038/nmeth.2212

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