RCy3

DOI: 10.18129/B9.bioc.RCy3    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see RCy3.

Functions to Access and Control Cytoscape

Bioconductor version: 3.13

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>

Installation

To install this package, start R (version "4.1") 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	2.12.4
In Bioconductor since	BioC 3.2 (R-3.2) (6 years)
License	MIT + file LICENSE
Depends
Imports	httr, methods, RJSONIO, XML, utils, BiocGenerics, igraph, stats, graph, R.utils, dplR, uchardet, glue, RCurl, base64url, base64enc, IRkernel, RColorBrewer
LinkingTo
Suggests	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, CeTF, fedup, MOGAMUN, NCIgraph, netDx, regutools, TimiRGeN, transomics2cytoscape
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_2.12.4.tar.gz
Windows Binary	RCy3_2.12.4.zip
macOS 10.13 (High Sierra)	RCy3_2.12.4.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