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RCX

R package implementing the Cytoscape Exchange (CX) format


Bioconductor version: Release (3.18)

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]

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 "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

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

Details

biocViews DataImport, Network, Pathways, Software
Version 1.6.0
In Bioconductor since BioC 3.15 (R-4.2) (2 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
See More
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_1.6.0.tar.gz
Windows Binary RCX_1.6.0.zip (64-bit only)
macOS Binary (x86_64) RCX_1.6.0.tgz
macOS Binary (arm64) RCX_1.6.0.tgz
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