Issue 2, 2016
From the journal:

Molecular BioSystems

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

Guangchuang Yuab  and  Qing-Yu He*a  

* Corresponding authors

a 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, China
E-mail: [email protected]
Fax: +86-20-85227039
Tel: +86-20-85227039

b State Key Laboratory of Emerging Infectious Disease, School of Public Health, The University of Hong Kong, Hong Kong SAR, China

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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Article information

DOI
https://doi.org/10.1039/C5MB00663E
Article type
Paper
Submitted
05 Oct 2015
Accepted
20 Nov 2015
First published
23 Nov 2015

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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