RCy3

This package is for version 3.6 of Bioconductor; for the stable, up-to-date release version, see RCy3.

Display and manipulate graphs in Cytoscape>= 3.3.0

Bioconductor version: 3.6

Vizualize, analyze and explore graphs, connecting R to Cytoscape (>= 3.3.0).

Author: Tanja Muetze, Georgi Kolishovski, Paul Shannon

Maintainer: Tanja Muetze <tanja.muetze14 at alumni.imperial.ac.uk>, Georgi Kolishovski <g_kolishv at yahoo.com>, Paul Shannon <pshannon at systemsbiology.org>

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

Installation

To install this package, start R (version "3.4") 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")

RCy3 Overview PDF R Script

Reference Manual PDF

README Text

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews GraphAndNetwork, Network, Software, ThirdPartyClient, Visualization

Version 1.8.0

In Bioconductor since BioC 3.2 (R-3.2) (8.5 years)

License Artistic-2.0

Depends R (>= 3.2), graph(>= 1.48.0)

Imports httr, methods, RCurl, RJSONIO

System Requirements Cytoscape (>= 3.3.0), CyREST (>= 3.3.7), Java (>=8)

URL https://github.com/tmuetze/Bioconductor_RCy3_the_new_RCytoscape

Bug Reports https://github.com/tmuetze/Bioconductor_RCy3_the_new_RCytoscape/issues

Suggests BiocGenerics, RUnit, knitr, igraph, RColorBrewer, paxtoolsr, rmarkdown

Linking To

Enhances

Depends On Me

Imports Me categoryCompare, NCIgraph

Suggests Me graphite

Links To Me

Build Report Build Report

Package Archives

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

Source Package RCy3_1.8.0.tar.gz

Windows Binary RCy3_1.8.0.zip

Mac OS X 10.11 (El Capitan) RCy3_1.8.0.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

Old Source Packages for BioC 3.6 Source Archive