DOI: 10.18129/B9.bioc.RCy3  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see RCy3.

Functions to Access and Control Cytoscape

Bioconductor version: 3.16

Vizualize, analyze and explore networks using Cytoscape via R. Anything you can do using the graphical user interface of Cytoscape, you can now do with a single RCy3 function.

Author: Alex Pico [aut, cre] , Tanja Muetze [aut], Paul Shannon [aut], Ruth Isserlin [ctb], Shraddha Pai [ctb], Julia Gustavsen [ctb], Georgi Kolishovski [ctb], Yihang Xin [ctb]

Maintainer: Alex Pico <alex.pico at gladstone.ucsf.edu>

Citation (from within R, enter citation("RCy3")):


To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



HTML R Script 01. Overview of RCy3 ~25 min
HTML R Script 02. Cytoscape and igraph ~5 min
HTML R Script 03. Cytoscape and graphNEL ~5 min
HTML R Script 04. Importing data ~5 min
HTML R Script 05. Network functions and visualization ~15 min
HTML R Script 06. Cancer networks and data ~40 min
HTML R Script 07. Identifier mapping ~20 min
HTML R Script 08. Upgrading existing scripts ~15 min
HTML R Script 09. Cytoscape and NDEx ~20 min
HTML R Script 10. Group nodes ~15 min
HTML R Script 11. Custom Graphics and Labels ~10 min
HTML R Script 12. Filtering Networks ~10 min
HTML R Script 13. Phylogenetic Trees ~3 min
HTML R Script 14. Jupyter Bridge and RCy3 ~10 min
PDF   Reference Manual
Text   NEWS


biocViews GraphAndNetwork, Network, Software, ThirdPartyClient, Visualization
Version 2.18.0
In Bioconductor since BioC 3.2 (R-3.2) (7.5 years)
License MIT + file LICENSE
Imports httr, methods, RJSONIO, XML, utils, BiocGenerics, stats, graph, fs, uuid, uchardet, glue, RCurl, base64url, base64enc, IRkernel, IRdisplay, RColorBrewer, gplots
Suggests BiocStyle, knitr, rmarkdown, igraph, grDevices
SystemRequirements Cytoscape (>= 3.7.1), CyREST (>= 3.8.0)
URL https://github.com/cytoscape/RCy3
BugReports https://github.com/cytoscape/RCy3/issues
Depends On Me
Imports Me categoryCompare, CeTF, fedup, MetaPhOR, MOGAMUN, NCIgraph, netZooR, regutools, TimiRGeN, transomics2cytoscape
Suggests Me graphite, netDx, rScudo
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package RCy3_2.18.0.tar.gz
Windows Binary RCy3_2.18.0.zip
macOS Binary (x86_64) RCy3_2.18.0.tgz
macOS Binary (arm64) RCy3_2.18.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/RCy3
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/RCy3
Bioc Package Browser https://code.bioconductor.org/browse/RCy3/
Package Short Url https://bioconductor.org/packages/RCy3/
Package Downloads Report Download Stats

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