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RCy3

Functions to Access and Control Cytoscape


Bioconductor version: Release (3.18)

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>

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

Installation

To install this package, start R (version "4.3") 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")
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 HTML R Script
14. Jupyter Bridge and RCy3 ~10 min HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews GraphAndNetwork, Network, Software, ThirdPartyClient, Visualization
Version 2.22.1
In Bioconductor since BioC 3.2 (R-3.2) (8.5 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
See More
Suggests BiocStyle, knitr, rmarkdown, igraph, grDevices
Linking To
Enhances
Depends On Me
Imports Me categoryCompare, CeTF, enrichViewNet, fedup, MetaPhOR, MOGAMUN, NCIgraph, netZooR, regutools, TimiRGeN, transomics2cytoscape
Suggests Me graphite, netDx, rScudo
Links To Me
Build Report Build Report

Package Archives

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

Source Package RCy3_2.22.1.tar.gz
Windows Binary RCy3_2.22.1.zip
macOS Binary (x86_64) RCy3_2.22.1.tgz
macOS Binary (arm64) RCy3_2.22.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/RCy3
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/RCy3
Bioc Package Browser https://code.bioconductor.org/browse/RCy3/
Package Short Url https://bioconductor.org/packages/RCy3/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.18 Source Archive