ReactomePA: Reactome Pathway Analysis

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This package provides functions for pathway analysis based on REACTOME pathway database. It implements enrichment analysis, gene set enrichment analysis and several functions for visualization.

ReactomePA is released within the Bioconductor project and the source code is hosted in GitHub.

Author

Guangchuang Yu, School of Public Health, The University of Hong Kong.

Citation

Please cite the following article when using ReactomePA:

doi Altmetric citation

Yu G and He QY*. ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization. Molecular BioSystems, 2016,12(2):477-9.

Installation

Install ReactomePA is easy, follow the guide in the Bioconductor page:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
## biocLite("BiocUpgrade") ## you may need this
biocLite("ReactomePA")

Overview

Enrichment Analysis

  • Over-representation analysis
  • Gene set enrichment analysis

Visualization

  • barplot
  • cnetplot
  • dotplot
  • enrichMap
  • gseaplot
  • upsetplot
  • viewPathway

Find out details and examples on Documentation.

Projects that depend on ReactomePA

Bioconductor packages

  • bioCancer: Interactive Multi-Omics Cancers Data Visualization and Analysis
  • LINC: co-expression of lincRNAs and protein-coding genes
  • miRsponge: Identification and analysis of miRNA sponge interaction networks and modules

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