RCy3

DOI: 10.18129/B9.bioc.RCy3    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see RCy3.

Functions to Access and Control Cytoscape

Bioconductor version: 3.8

Vizualize, analyze and explore networks using Cytoscape via R.

Author: Alexander Pico, Tanja Muetze, Ruth Isserlin, Shraddha Pai, Julia Gustavsen, 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>

Installation

To install this package, start R (version "3.5") 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	2.2.9
In Bioconductor since	BioC 3.2 (R-3.2) (3.5 years)
License	MIT + file LICENSE
Depends	R (>= 3.5)
Imports	httr, methods, RJSONIO, XML, utils, BiocGenerics, igraph, stats, graph, R.utils
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_2.2.9.tar.gz
Windows Binary	RCy3_2.2.9.zip
Mac OS X 10.11 (El Capitan)	RCy3_2.2.9.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