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Bioconductor - RCy3 (development version)

RCy3

This is the development version of RCy3; for the stable release version, see RCy3.

Functions to Access and Control Cytoscape

Bioconductor version: Development (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: 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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

Details biocViews GraphAndNetwork, Network, Software, ThirdPartyClient, Visualization Version 2.29.1 In Bioconductor since BioC 3.2 (R-3.2) (9.5 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, 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.

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