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Issue 2, 2016

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

Author affiliations

Abstract

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).

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

Article information


Submitted
05 Oct 2015
Accepted
20 Nov 2015
First published
23 Nov 2015

Mol. BioSyst., 2016,12, 477-479
Article type
Paper

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

G. Yu and Q. He, Mol. BioSyst., 2016, 12, 477 DOI: 10.1039/C5MB00663E

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