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ReactomeGSA

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


Bioconductor version: Release (3.18)

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 "4.3") and enter:


if (!require("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")
Analysing single-cell RNAseq data HTML R Script
Using the ReactomeGSA package HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews GeneExpression, GeneSetEnrichment, Proteomics, Reactome, Software, SystemsBiology, Transcriptomics
Version 1.16.1
In Bioconductor since BioC 3.10 (R-3.6) (4.5 years)
License MIT + file LICENSE
Depends
Imports jsonlite, httr, progress, ggplot2, methods, gplots, RColorBrewer, dplyr, tidyr
System Requirements
URL https://github.com/reactome/ReactomeGSA
Bug Reports https://github.com/reactome/ReactomeGSA/issues
See More
Suggests testthat, knitr, rmarkdown, ReactomeGSA.data, Biobase, devtools
Linking To
Enhances limma, edgeR, Seurat (>= 3.0), scater
Depends On Me ReactomeGSA.data
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 ReactomeGSA_1.16.1.tar.gz
Windows Binary ReactomeGSA_1.16.1.zip (64-bit only)
macOS Binary (x86_64) ReactomeGSA_1.16.1.tgz
macOS Binary (arm64) ReactomeGSA_1.16.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/ReactomeGSA
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ReactomeGSA
Bioc Package Browser https://code.bioconductor.org/browse/ReactomeGSA/
Package Short Url https://bioconductor.org/packages/ReactomeGSA/
Package Downloads Report Download Stats