RCy3

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

Functions to Access and Control Cytoscape

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DOI: 10.18129/B9.bioc.RCy3

Bioconductor version: Release (3.22)

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] ORCID iD 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: Alex Pico <alex.pico at gladstone.ucsf.edu>

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

Installation

To install this package, start R (version "4.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews GraphAndNetwork, Network, Software, ThirdPartyClient, Visualization

Version 2.30.0

In Bioconductor since BioC 3.2 (R-3.2) (10 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, enrichViewNet, fedup, GeneNetworkBuilder, MetaPhOR, MOGAMUN, MSstatsBioNet, NCIgraph, regutools, transomics2cytoscape, dendroNetwork, lilikoi, netgsa, ScriptMapR

Suggests Me graphite, rScudo, tidysbml, sharp

Links To Me

Build Report Build Report

Package Archives

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

Source Package RCy3_2.30.0.tar.gz

Windows Binary (x86_64) RCy3_2.30.0.zip (64-bit only)

macOS Binary (x86_64) RCy3_2.30.0.tgz

macOS Binary (arm64) RCy3_2.30.0.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