RCy3

This is the released version of RCy3; for the devel version, see RCy3.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2

Functions to Access and Control Cytoscape

Bioconductor version: Release (3.23)

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: Jing Chen [cre], Alex Pico [aut] ORCID: 0000-0001-5706-2163 , Tanja Muetze [aut], Paul Shannon [aut], Ruth Isserlin [ctb], Shraddha Pai [ctb], Julia Gustavsen [ctb], Georgi Kolishovski [ctb], Yihang Xin [ctb]

Maintainer: Jing Chen <jingjingbic at gmail.com>

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

Alex Pico, Tanja Muetze, Paul Shannon. RCy3: Functions to Access and Control Cytoscape. doi:10.18129/B9.bioc.RCy3, R package version 2.32.0, https://bioconductor.org/packages/RCy3.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("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")

06. Cancer networks and data ~40 min	HTML	R Script
11. Custom Graphics and Labels ~10 min	HTML	R Script
03. Cytoscape and graphNEL ~5 min	HTML	R Script
02. Cytoscape and igraph ~5 min	HTML	R Script
09. Cytoscape and NDEx ~20 min	HTML	R Script
12. Filtering Networks ~10 min	HTML	R Script
10. Group nodes ~15 min	HTML	R Script
07. Identifier mapping ~20 min	HTML	R Script
04. Importing data ~5 min	HTML	R Script
14. Jupyter Bridge and RCy3 ~10 min	HTML	R Script
05. Network functions and visualization ~15 min	HTML	R Script
01. Overview of RCy3 ~25 min	HTML	R Script
13. Phylogenetic Trees ~3 min	HTML	R Script
08. Upgrading existing scripts ~15 min	HTML	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GraphAndNetwork, Network, Software, ThirdPartyClient, Visualization
Version	2.32.0
In Bioconductor since	BioC 3.2 (R-3.2) (11 years)
License	MIT + file LICENSE
Depends
Imports	httr, methods, RJSONIO, XML, utils, BiocGenerics, stats, graph, fs, uuid, stringi, glue, RCurl, base64url, base64enc, IRkernel, IRdisplay, RColorBrewer, gplots
System Requirements	Cytoscape (>= 3.7.1), CyREST (>= 3.8.0)
URL	https://github.com/cytoscape/RCy3
Bug Reports	https://github.com/cytoscape/RCy3/issues

Suggests	BiocStyle, knitr, rmarkdown, igraph, grDevices
Linking To
Enhances
Depends On Me
Imports Me	categoryCompare, CeTF, dendroNetwork, enrichViewNet, fedup, GeneNetworkBuilder, lilikoi, MetaPhOR, MOGAMUN, NCIgraph, netgsa, netZooR, regutools, ScriptMapR, transomics2cytoscape
Suggests Me	graphite, rScudo, sharp, tidysbml
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	RCy3_2.32.0.tar.gz
Windows Binary (x86_64)	RCy3_2.32.0.zip
macOS Binary (big-sur-x86_64)	RCy3_2.32.0.tgz
macOS Binary (sonoma-arm64)	RCy3_2.32.0.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