RCy3

DOI: 10.18129/B9.bioc.RCy3    

This is the development version of RCy3; to use it, please install the devel version of Bioconductor.

Functions to Access and Control Cytoscape

Bioconductor version: Development (3.10)

Vizualize, analyze and explore networks using Cytoscape via R.

Author: Alex Pico [aut, cre] , Tanja Muetze [aut], Paul Shannon [aut], Ruth Isserlin [ctb], Shraddha Pai [ctb], Julia Gustavsen [ctb], Georgi Kolishovski [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 "3.6") and enter:

if (!requireNamespace("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")

 

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 2.5.17
In Bioconductor since BioC 3.2 (R-3.2) (4 years)
License MIT + file LICENSE
Depends
Imports httr, methods, RJSONIO, XML, utils, BiocGenerics, igraph, stats, graph, R.utils
LinkingTo
Suggests RUnit, BiocStyle, knitr, rmarkdown
SystemRequirements Cytoscape (>= 3.7.1), 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, rScudo
Links To Me
Build Report  

Package Archives

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

Source Package RCy3_2.5.17.tar.gz
Windows Binary RCy3_2.5.17.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) RCy3_2.5.17.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

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