R Examples

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This page is here for legacy information. For more recent info on accessing Cytoscape through R, please refer to the RCy3 library as well as the Sample R Scripts in the Cytoscape Automation repository.

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Example Workflows in R

R examples are available here:

• https://github.com/idekerlab/cy-rest-R

Basic examples are available as R Markdown documents, and we recommend to use RStudio IDE to try these.

New: RCy3 - Harmonization Layer for R and cyREST

RCy3, a successor of RCytoscape, is now available as a part of Bioconductor distribution. RCy3 provides more natural API for R users.

• RCy3 in Bioconductor project
• RCy3 source code