The ReactomeGSA package is an R client to the Reactome Analysis System. This new analysis system supports multi-species, multi-omics, comparative pathway analyses.
- For any questions surrounding the use of ReactomeGSA, please simply post it in our Q&A Section
- Should you find a bug in our tool(s) we'd be very grateful if you could report it by posting a new GitHub Issue
- If you encounter any other issues, don't hesitate to contact us at help [at] reactome [dot] org
The complete usage of the package is described in the main vignette.
If you are interested in processing single-cell RNA-seq data using ReactomeGSA, checkout this vignette
The ReactomeGSA package is part of Bioconductor since version 3.10. You can find detailed information on the latest stable version on ReactomeGSA's Bioconductor page.
To install the latest version from Bioconductor use
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ReactomeGSA")Bioconductor is updated every 6 months. You can still get the latest version of the ReactomeGSA package directly from GitHub:
# install devtools if needed
if (!require(devtools)) {
install.packages("devtools")
}
# install the ReactomeGSA package
if (!require(ReactomeGSA)) {
install_github("reactome/ReactomeGSA")
}If you used ReactomeGSA in your research, we would be grateful if you could cite the following manuscript:
Griss et al., ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis (2020), MCP 19 (12) P2115-2125, DOI: 10.1074/mcp.TIR120.002155