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README.md
# ReactomePA: Reactome Pathway Analysis [![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ReactomePA/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ReactomePA/) [![](https://img.shields.io/badge/release%20version-1.40.0-green.svg)](https://www.bioconductor.org/packages/ReactomePA) [![](https://img.shields.io/badge/devel%20version-1.41.1-green.svg)](https://github.com/guangchuangyu/ReactomePA) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/clusterProfiler.svg)](https://www.bioconductor.org/packages/devel/bioc/html/clusterProfiler.html#since) [![platform](http://www.bioconductor.org/shields/availability/devel/ReactomePA.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ReactomePA.html#archives) [![Last-changedate](https://img.shields.io/badge/last%20change-2022--10--30-green.svg)](https://github.com/GuangchuangYu/ReactomePA/commits/master) [![Build Status](http://www.bioconductor.org/shields/build/devel/bioc/ReactomePA.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/ReactomePA/) [![Linux/Mac Travis Build Status](https://img.shields.io/travis/GuangchuangYu/ReactomePA/master.svg?label=Mac%20OSX%20%26%20Linux)](https://travis-ci.org/GuangchuangYu/ReactomePA) [![AppVeyor Build Status](https://img.shields.io/appveyor/ci/Guangchuangyu/ReactomePA/master.svg?label=Windows)](https://ci.appveyor.com/project/GuangchuangYu/ReactomePA) This package provides functions for pathway analysis based on REACTOME pathway database. It implements enrichment analysis, gene set enrichment analysis and several functions for visualization. For details, please visit <https://yulab-smu.top/biomedical-knowledge-mining-book/>. ## :writing_hand: Authors Guangchuang YU School of Basic Medical Sciences, Southern Medical University <https://yulab-smu.top> [![Twitter](https://img.shields.io/twitter/url/http/shields.io.svg?style=social&logo=twitter)](https://twitter.com/intent/tweet?hashtags=ReactomePA&url=http://pubs.rsc.org/en/Content/ArticleLanding/2016/MB/C5MB00663E#!divAbstract) [![saythanks](https://img.shields.io/badge/say-thanks-ff69b4.svg)](https://saythanks.io/to/GuangchuangYu) [![](https://img.shields.io/badge/follow%20me%20on-WeChat-green.svg)](https://guangchuangyu.github.io/blog_images/biobabble.jpg) ------------------------------------------------------------------------ Please cite the following article when using `ReactomePA`: ***G Yu***, QY He<sup>\*</sup>. ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization. ***Molecular BioSystems*** 2016, 12(2):477-479. [![](https://img.shields.io/badge/doi-10.1039/c5mb00663e-green.svg)](https://doi.org/10.1039/c5mb00663e) <!-- r badge_altmetric("4796667", "green") ------------------------------------------------------------------------ <img src="https://guangchuangyu.github.io/software/citation_trend/ReactomePA.png" width="890"/> ### Download stats [![download](http://www.bioconductor.org/shields/downloads/ReactomePA.svg)](https://bioconductor.org/packages/stats/bioc/ReactomePA/) r badge_bioc_download("ReactomePA", "total", "blue") r badge_bioc_download("ReactomePA", "month", "blue") <img src="https://guangchuangyu.github.io/software/dlstats/ReactomePA.png" width="890"/> -->