Get the Software

You need the following software to run RCytoscape:
  1. Cytoscape 2.8.2  (available here)

  2. Jan Bot's CytoscapeRPC plugin, version 1.8  (available here)

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

  4. RCytoscape and its dependencies. Start up R version 2.12 and enter these two lines of code:

              source("http://bioconductor.org/biocLite.R")
              biocLite("RCytoscape")

    All the R packages you need, for the proper architecture, will be downloaded and installed, including Biocondcutor's graph and Duncan Temple Lang's XMLRPC.

    Do the Install

    By following the steps listed below, in the order they are presented, the installation should proceed smoothly.

    Questions? Contact pshannon AT systemsbiology DOT org

    1. Cytoscape:   the download you performed will have installed the application as well.

    2. CytoscapeRPC plugin:
      • You can manage and install plugins from menus within the Cytoscape application.
      • Or you can simply download the plugin jar file, and copy it to the Cytoscape plugins directory, nested right below the main install directory -- which is unfortunately an architecture-specific location. On mac osx, this will be

        /Applications/Cytoscape_v2.7.0/plugins/

    3. R:   as with Cytoscape, downloading will have performed the install.

    4. RCytoscape (and dependencies):   as with R and Cytoscape, downloading will have performed the install as well.