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

G Yu, QY He - Molecular BioSystems, 2016 - pubs.rsc.org
G Yu, QY He
Molecular BioSystems, 2016pubs.rsc.org
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 …
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).
The Royal Society of Chemistry