RCy3

DOI: 10.18129/B9.bioc.RCy3    

Functions to Access and Control Cytoscape

Bioconductor version: Release (3.8)

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")):

Installation

To install this package, start R and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("RCy3", version = "3.8")

Documentation

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

browseVignettes("RCy3")

 

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
Text   LICENSE

Details

biocViews GraphAndNetwork, Network, Software, ThirdPartyClient, Visualization
Version 2.2.1
In Bioconductor since BioC 3.2 (R-3.2) (3 years)
License MIT + file LICENSE
Depends R (>= 3.5)
Imports httr, methods, RJSONIO, XML, utils, BiocGenerics, igraph, stats, graph
LinkingTo
Suggests RUnit, RColorBrewer, BiocStyle, knitr, rmarkdown
SystemRequirements Cytoscape (>= 3.7.0), CyREST (>= 3.8.0)
Enhances
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_2.2.1.tar.gz
Windows Binary RCy3_2.2.1.zip
Mac OS X 10.11 (El Capitan) RCy3_2.2.1.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/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.8 Source Archive

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