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

2015; Royal Society of Chemistry; Volume: 12; Issue: 2 Linguagem: Inglês

10.1039/c5mb00663e

1742-206X

Guangchuang Yu, Qing‐Yu He,

Gene expression and cancer classification

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).