DOI: 10.18129/B9.bioc.RCy3    

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see RCy3.

Functions to Access and Control Cytoscape

Bioconductor version: 3.7

Vizualize, analyze and explore networks using Cytoscape via R.

Author: Alexander Pico, Tanja Muetze, Georgi Kolishovski, Paul Shannon

Maintainer: Alexander Pico <alex.pico at gladstone.ucsf.edu>, Tanja Muetze <tanja.muetze14 at alumni.imperial.ac.uk>, Paul Shannon <pshannon at systemsbiology.org>

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


To install this package, start R and enter:

## try http:// if https:// URLs are not supported


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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
PDF   Reference Manual
Text   NEWS


biocViews GraphAndNetwork, Network, Software, ThirdPartyClient, Visualization
Version 2.0.88
In Bioconductor since BioC 3.2 (R-3.2) (3 years)
License MIT + file LICENSE
Depends R (>= 3.4)
Imports httr, methods, RJSONIO, XML, utils, BiocGenerics, igraph, stats, graph
Suggests RUnit, RColorBrewer, BiocStyle, knitr, rmarkdown
SystemRequirements Cytoscape (>= 3.6.0), CyREST (>= 3.6.0)
URL https://github.com/cytoscape/RCy3
BugReports https://github.com/cytoscape/RCy3/issues
Depends On Me
Imports Me categoryCompare, NCIgraph
Suggests Me graphite
Links To Me
Build Report  

Package Archives

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

Source Package RCy3_2.0.88.tar.gz
Windows Binary RCy3_2.0.88.zip
Mac OS X 10.11 (El Capitan) RCy3_2.0.88.tgz
Source Repository git clone https://git.bioconductor.org/packages/RCy3
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/RCy3
Package Short Url http://bioconductor.org/packages/RCy3/
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