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).