RCy3 Enrichment Map
Channel: Cytoscape
Date: 20/10/2019

RCy3 has methods to control Cytoscape apps using the command line syntax app authors choose to support.  Here we demonstrate running the Enrichment Map Pipeline, controling 4 different apps from within R. Enrichment Maps provide a way to summarize functional enrichment results as a clustered and annotated network. 

This use case is from the RCy3 paper: https://doi.org/10.12688/f1000research.20887.1. The Rmd code is available at https://cytoscape.org/cytoscape-automation/for-scripters/R/notebooks/RCy3-use-cases.nb.html

Cytoscape is a free, open source platform for network analysis and visulization.
  * Download: https://cytoscape.org
  * Lean how to use:  http://tutorials.cytoscape.org
  * Explore apps: https://apps.cytoscape.org
  * Automate with R/Python: http://automation.cytoscape.org
  * See the code: https://github.com/cytoscape/cytoscape
  * Report a bug: https://cytoscape.org/bug-report.html
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