ReactomeGSA

DOI: 10.18129/B9.bioc.ReactomeGSA    

Client for the Reactome Analysis Service for comparative multi-omics gene set analysis

Bioconductor version: Release (3.10)

The ReactomeGSA packages uses Reactome's online analysis service to perform a multi-omics gene set analysis. The main advantage of this package is, that the retrieved results can be visualized using REACTOME's powerful webapplication. Since Reactome's analysis service also uses R to perfrom the actual gene set analysis you will get similar results when using the same packages (such as limma and edgeR) locally. Therefore, if you only require a gene set analysis, different packages are more suited.

Author: Johannes Griss [aut, cre]

Maintainer: Johannes Griss <johannes.griss at meduniwien.ac.at>

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

Installation

To install this package, start R (version "3.6") and enter:

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

BiocManager::install("ReactomeGSA")

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("ReactomeGSA")

 

HTML R Script Using the ReactomeGSA package
PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews GeneExpression, GeneSetEnrichment, Proteomics, Reactome, Software, SystemsBiology, Transcriptomics
Version 1.0.0
In Bioconductor since BioC 3.10 (R-3.6) (< 6 months)
License MIT + file LICENSE
Depends
Imports jsonlite, httr, progress, ggplot2, methods
LinkingTo
Suggests testthat, knitr, rmarkdown, ReactomeGSA.data, Biobase, devtools
SystemRequirements
Enhances limma, edgeR
URL https://github.com/reactome/ReactomeGSA
BugReports https://github.com/reactome/ReactomeGSA/issues
Depends On Me ReactomeGSA.data
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package ReactomeGSA_1.0.0.tar.gz
Windows Binary ReactomeGSA_1.0.0.zip
Mac OS X 10.11 (El Capitan) ReactomeGSA_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/ReactomeGSA
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ReactomeGSA
Package Short Url https://bioconductor.org/packages/ReactomeGSA/
Package Downloads Report Download Stats

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