ReactomeGSA

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

Bioconductor version: Release (3.19)

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 "4.4") 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
Loading and re-analysing public data through ReactomeGSA	HTML	R Script
Using the ReactomeGSA package	HTML	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GeneExpression, GeneSetEnrichment, Proteomics, Reactome, Software, SystemsBiology, Transcriptomics
Version	1.18.0
In Bioconductor since	BioC 3.10 (R-3.6) (5 years)
License	MIT + file LICENSE
Depends
Imports	jsonlite, httr, progress, ggplot2, methods, gplots, RColorBrewer, dplyr, tidyr, Biobase
System Requirements
URL	https://github.com/reactome/ReactomeGSA
Bug Reports	https://github.com/reactome/ReactomeGSA/issues

Suggests	testthat, knitr, rmarkdown, ReactomeGSA.data, 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_1.18.0.tar.gz
Windows Binary (x86_64)	ReactomeGSA_1.18.0.zip (64-bit only)
macOS Binary (x86_64)	ReactomeGSA_1.18.0.tgz
macOS Binary (arm64)	ReactomeGSA_1.18.0.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