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("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 | ||
NEWS | Text | |
LICENSE | Text |
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 |
See More
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 | 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 |