ReactomeGSA

DOI: 10.18129/B9.bioc.ReactomeGSA    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see ReactomeGSA.

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

Bioconductor version: 3.13

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>

Installation

To install this package, start R (version "4.1") 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	Analysing single-cell RNAseq data
HTML	R Script	Using the ReactomeGSA package
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	GeneExpression, GeneSetEnrichment, Proteomics, Reactome, Software, SystemsBiology, Transcriptomics
Version	1.6.1
In Bioconductor since	BioC 3.10 (R-3.6) (2 years)
License	MIT + file LICENSE
Depends
Imports	jsonlite, httr, progress, ggplot2, methods, gplots, RColorBrewer
LinkingTo
Suggests	testthat, knitr, rmarkdown, ReactomeGSA.data, Biobase, devtools
SystemRequirements
Enhances	limma, edgeR, Seurat (>= 3.0), scater
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_1.6.1.tar.gz
Windows Binary	ReactomeGSA_1.6.1.zip
macOS 10.13 (High Sierra)	ReactomeGSA_1.6.1.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