Combining Cytoscape with R

[katieannemills]

What: How to combine Cytoscape, a powerful network and graph drawing tool, with R.
Author: @jooolia
Lesson: https://github.com/jooolia/R_cytoscape_tutorial (see the .Rmd file for the complete walkthrough)
Setup Instructions:
Please install the following:

• Java 8 (http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html)
• Cytoscape 3.2.1 or later (http://www.cytoscape.org/download.php)
• CyREST (used to communicate between Cytoscape and R):
  • Start Cytoscape
  • Apps → App Manager
  • Select cyREST
  • Click install
• R packages: RJSONIO and igraph
  • from R run: install.packages(c("RJSONIO", "igraph"))