https://github.com/reactome/reactomegsa
R client for the REACTOME Analysis Service for comparative multi-omics gene set analysis
https://github.com/reactome/reactomegsa
Last synced: 5 months ago
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R client for the REACTOME Analysis Service for comparative multi-omics gene set analysis
- Host: GitHub
- URL: https://github.com/reactome/reactomegsa
- Owner: reactome
- License: other
- Created: 2019-07-01T11:12:19.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2024-11-27T19:03:33.000Z (over 1 year ago)
- Last Synced: 2025-10-14T01:51:37.410Z (6 months ago)
- Language: R
- Size: 1020 KB
- Stars: 29
- Watchers: 2
- Forks: 5
- Open Issues: 23
-
Metadata Files:
- Readme: README.md
- Changelog: NEWS
- License: LICENSE
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README
# ReactomeGSA
The `ReactomeGSA` package is an R client to the `Reactome Analysis System`. This new analysis system supports **multi-species, multi-omics, comparative pathway analyses**.
## Getting Help
* For any questions surrounding the use of ReactomeGSA, please simply post it in our [Q&A Section](https://github.com/reactome/ReactomeGSA/discussions)
* 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](https://github.com/reactome/ReactomeGSA/issues/new)
* If you encounter any other issues, don't hesitate to contact us at help [at] reactome [dot] org
## Documnetation
The complete usage of the package is described in the [main vignette](https://bioconductor.org/packages/release/bioc/vignettes/ReactomeGSA/inst/doc/using-reactomegsa.html).
If you are interested in processing single-cell RNA-seq data using ReactomeGSA, checkout [this vignette](https://bioconductor.org/packages/release/bioc/vignettes/ReactomeGSA/inst/doc/using-reactomegsa.html)
## Installation
### Bioconductor
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](https://doi.org/doi:10.18129/B9.bioc.ReactomeGSA).
To install the latest version from Bioconductor use
```r
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ReactomeGSA")
```
### Latest Version
Bioconductor is updated every 6 months. You can still get the latest version of the ReactomeGSA package directly from GitHub:
```r
# install devtools if needed
if (!require(devtools)) {
install.packages("devtools")
}
# install the ReactomeGSA package
if (!require(ReactomeGSA)) {
install_github("reactome/ReactomeGSA")
}
```
## Citation
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](https://doi.org/10.1074/mcp.TIR120.002155)