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Bioconductor - ReactomeGSA (development version)

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 (3.22)

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] ORCID: 0000-0003-2206-9511

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

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

To install this package, start R (version "4.5") 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

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("ReactomeGSA")
Details biocViews GeneExpression, GeneSetEnrichment, Proteomics, Reactome, Software, SystemsBiology, Transcriptomics Version 1.23.0 In Bioconductor since BioC 3.10 (R-3.6) (5.5 years) License MIT + file LICENSE Depends Imports Biobase, BiocSingular, dplyr, ggplot2, gplots, httr, igraph, jsonlite, methods, progress, RColorBrewer, SummarizedExperiment, tidyr System Requirements URL https://github.com/reactome/ReactomeGSA Bug Reports https://github.com/reactome/ReactomeGSA/issues See More Suggests devtools, knitr, ReactomeGSA.data, rmarkdown, scater, scran, scRNAseq, scuttle, Seurat (>= 3.0), SingleCellExperiment, testthat Linking To Enhances Depends On Me ReactomeGSA.data Imports Me scPipeline Suggests Me Links To Me Build Report Build Report Package Archives

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


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