ReactomePA引用过百

Reactome is a manually curated pathway annotation database for unveiling high-order biological pathways from high-throughput data. ReactomePA is an R/Bioconductor package providing enrichment analyses, including hypergeometric test and gene set enrichment analyses. A functional analysis can be applied to the genomic coordination obtained from a sequencing experiment to analyze the functional significance of genomic loci including cis-regulatory elements and non-coding regions. Comparison among different experiments is also supported. Moreover, ReactomePA provides several visualization functions to produce highly customizable, publication-quality figures. The source code and documents of ReactomePA are freely available through Bioconductor (http://www.bioconductor.org/packages/ReactomePA).

google scholar上引用已经过百，wos上的引用也有62，且是ESI高被引文章

写这个包是在KEGG刚转向收费的时候，当时Bioconductor的mailing-list上各种KEGG走向封闭，我们该怎么办的各种问号，于是我顺手就写了个富集分析的包去占位，顺手是因为有clusterProfiler的基础，代码可以说是现成的，而当年我在用IPA，所以取了ReactomePA这个名字，我其实是有想法的，是想要实现一些网络分析的，然而我还没学会（更不用谈去实现了），就跑去读博了，然后就没有然后了。

还是有 然后，就一直放着，终于某一天我想写文章了，而这催生我写文章的，其实是ChIPseeker，所谓一点即成文，写一篇文章，总想介绍点新东西，而这篇文章写的新东西就是结合ChIPseeker，我们可以做genomic loci的富集分析。当然这种东西一打通，我的系列包都可以，包括大家熟知的clusterProfiler，然而clusterProfiler的文章非常老了，那是当年最简单的版本，你看ReactomePA的文章，也是有助于了解clusterProfiler的相应功能的。

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