• Cytoscape minimum version 3.7 is required.

Install Cytoscape

Download and install the latest version of Cytoscape at

Install EnrichmentMap 3.3

  • Open Cytoscape
  • In the main menu select Apps > App Manager
  • In the App Manager select EnrichmentMap in the list of All Apps and click the Install button.
  • Alternatively the EnrichmentMap Pipeline Collection can be installed. This will install EnrichmentMap as well as a suite of other apps that work well with EnrichmentMap, including AutoAnnotate, WordCloud and clusterMaker2.
EnrichmentMap can also be installed from the Cytoscape App Store at