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

Mol Biosyst. 2016 Feb;12(2):477-9. 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 (

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Chromatin Immunoprecipitation
  • Databases, Factual*
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Metabolic Networks and Pathways
  • Protein Interaction Maps
  • Proteomics
  • Signal Transduction