RCy3

DOI: 10.18129/B9.bioc.RCy3    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see RCy3.

Functions to Access and Control Cytoscape

Bioconductor version: 3.9

Vizualize, analyze and explore networks using Cytoscape via R.

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

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

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("RCy3")

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

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
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
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	GraphAndNetwork, Network, Software, ThirdPartyClient, Visualization
Version	2.4.6
In Bioconductor since	BioC 3.2 (R-3.2) (4 years)
License	MIT + file LICENSE
Depends
Imports	httr, methods, RJSONIO, XML, utils, BiocGenerics, igraph, stats, graph, R.utils
LinkingTo
Suggests	RUnit, BiocStyle, knitr, rmarkdown
SystemRequirements	Cytoscape (>= 3.7.1), 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, rScudo
Links To Me
Build Report

Package Archives

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

Source Package	RCy3_2.4.6.tar.gz
Windows Binary	RCy3_2.4.6.zip
Mac OS X 10.11 (El Capitan)	RCy3_2.4.6.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	https://bioconductor.org/packages/RCy3/
Package Downloads Report	Download Stats