ReactomeGSA
This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see ReactomeGSA.
Client for the Reactome Analysis Service for comparative multi-omics gene set analysis
Bioconductor version: 3.10
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 "3.6") 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")| Using the ReactomeGSA package | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GeneExpression, GeneSetEnrichment, Proteomics, Reactome, Software, SystemsBiology, Transcriptomics |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (4.5 years) |
| License | MIT + file LICENSE |
| Depends | |
| Imports | jsonlite, httr, progress, ggplot2, methods |
| 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 |
| 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_1.0.0.tar.gz |
| Windows Binary | ReactomeGSA_1.0.0.zip |
| Mac OS X 10.11 (El Capitan) | ReactomeGSA_1.0.0.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 |
| Old Source Packages for BioC 3.10 | Source Archive |