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Mol Biosyst. 2016 Feb;12(2):477-9. doi: 10.1039/c5mb00663e.

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

Author information

1
Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China. tqyhe@jnu.edu.cn and State Key Laboratory of Emerging Infectious Disease, School of Public Health, The University of Hong Kong, Hong Kong SAR, China.
2
Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China. tqyhe@jnu.edu.cn.

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).

PMID:
26661513
DOI:
10.1039/c5mb00663e
[Indexed for MEDLINE]

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