Please contact me if you run into trouble. My email address is below.

The procedure for installing the latest RCytoscape:

  1. Install R version 2.15   (available here; look for the CRAN link on the left of the page, then pick a mirror)

  2. Install Cytoscape 2.8.3 or later  (available here)

  3. Install Jan Bot's CytoscapeRPC plugin. You need the latest version, available from the plugins page at Place this jar file in the Cytoscape plugins directory. Plugin installation is explained at

  4. Start R and install RCytoscape and the packages upon which it depends:
      source ('')
      biocLite ('RCytoscape')

  5. Test your installation. First, make sure that

    Now, start R and type these commands:
      library (RCytoscape)
      cy = CytoscapeConnection ()
      pluginVersion (cy)
    You should see 
        [1] "1.8"
    Proceed now to read the vignette and/or browse through the cookbook examples.

    Don't hesitate to send me questions if you run into trouble: pshannon AT systemsbiology DOT org