RCX

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

R package implementing the Cytoscape Exchange (CX) format

Bioconductor version: Development (3.21)

Create, handle, validate, visualize and convert networks in the Cytoscape exchange (CX) format to standard data types and objects. The package also provides conversion to and from objects of iGraph and graphNEL. The CX format is also used by the NDEx platform, a online commons for biological networks, and the network visualization software Cytocape.

Author: Florian Auer [aut, cre] (ORCID: )

Maintainer: Florian Auer <florian.auer at informatik.uni-augsburg.de>

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

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("RCX")

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("RCX")

01. RCX - an R package implementing the Cytoscape Exchange (CX) format	HTML	R Script
02. Creating RCX from scratch	HTML	R Script
03. Extending the RCX Data Model	HTML	R Script
Appendix: The RCX and CX Data Model	HTML	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport, Network, Pathways, Software
Version	1.11.0
In Bioconductor since	BioC 3.15 (R-4.2) (2.5 years)
License	MIT + file LICENSE
Depends	R (>= 4.2.0)
Imports	jsonlite, plyr, igraph, methods
System Requirements
URL	https://github.com/frankkramer-lab/RCX
Bug Reports	https://github.com/frankkramer-lab/RCX/issues

Suggests	BiocStyle, testthat, knitr, rmarkdown, base64enc, graph
Linking To
Enhances
Depends On Me	ndexr
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	RCX_1.11.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/RCX
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/RCX
Bioc Package Browser	https://code.bioconductor.org/browse/RCX/
Package Short Url	https://bioconductor.org/packages/RCX/
Package Downloads Report	Download Stats