ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization

February 15, 2016
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(This article was first published on R on G. Yu, and kindly contributed to R-bloggers)

My R/Bioconductor package,
ReactomePA, published in
Molecular BioSystems.

ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization

G Yu, QY He. Molecular BioSystems 2016, 12:477-479

Received: 05 Oct 2015 Accepted: 20 Nov 2015 Online: 23 Nov 2015

DOI: 10.1039/C5MB00663E

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).

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