articleMolecular BioSystemsNov 23, 2015Closed access

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

GYGuangchuang YuQHQing‐Yu He

Department of Health · Jinan University · +1 more institution

PubMed
Indexed incrossrefpubmed

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…

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Topics & keywords

Topics
Keywords
  • Bioconductor
  • Visualization
  • Computer science
  • Annotation
  • Computational biology
  • Set (abstract data type)
  • Coding (social sciences)
  • Source code
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