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Issue 2, 2016
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ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization

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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

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Publication details

The article was received on 05 Oct 2015, accepted on 20 Nov 2015 and first published on 23 Nov 2015


Article type: Paper
DOI: 10.1039/C5MB00663E
Citation: Mol. BioSyst., 2016,12, 477-479
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    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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