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

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 appli...

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Bibliographic Details
Published in:	Molecular bioSystems Vol. 12; no. 2; p. 477
Main Authors:	Yu, Guangchuang, He, Qing-Yu
Format:	Journal Article
Language:	English
Published:	England 01-01-2016
Subjects:	Animals Chromatin Immunoprecipitation Databases, Factual High-Throughput Nucleotide Sequencing Humans Metabolic Networks and Pathways Protein Interaction Maps Proteomics Signal Transduction
Online Access:	Get more information
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Description
Summary:	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).
ISSN:	1742-2051
DOI:	10.1039/c5mb00663e