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ReactomeGSA

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

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

Bioconductor version: Development (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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("ReactomeGSA")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

Reference Manual PDF

Details

biocViews GeneExpression, GeneSetEnrichment, Proteomics, Reactome, Software, SystemsBiology, Transcriptomics
Version 1.15.0
In Bioconductor since BioC 3.10 (R-3.6) (4 years)
License MIT + file LICENSE
Depends
Imports jsonlite, httr, progress, ggplot2, methods, gplots, RColorBrewer, dplyr, tidyr
Linking To
Suggests testthat, knitr, rmarkdown, ReactomeGSA.data, Biobase, devtools
System Requirements
Enhances limma, edgeR, Seurat (>= 3.0), scater
URL https://github.com/reactome/ReactomeGSA
Bug Reports https://github.com/reactome/ReactomeGSA/issues
See More
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
Windows Binary ReactomeGSA_1.15.0.zip
macOS Binary (x86_64) ReactomeGSA_1.15.0.tgz
macOS Binary (arm64)
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