Installing

Install Cytoscape

• If you don’t have Cytoscape please download and install the latest release from http://www.cytoscape.org/download.html.

Install AutoAnnotate from the Cytoscape App Store

• AutoAnnotate: http://apps.cytoscape.org/apps/autoannotate

• This will also automatically install the WordCloud and clusterMaker2 apps.

Optional Apps that work well with AutoAnnotate

• The MCODE App is a popular clustering App that works well with AutoAnnotate.

  • MCODE: https://apps.cytoscape.org/apps/mcode

• AutoAnnotate is part of the EnrichmentMap Collection. AutoAnnotate will automatically choose appropriate defaults for networks created by the EnrichmentMap App.

  • EnrichmentMap Collection: https://apps.cytoscape.org/apps/enrichmentmappipelinecollection

  • EnrichmentMap: https://apps.cytoscape.org/apps/enrichmentmap