Features

ReactomePA provides the following analysis and visualization functions for Reactome pathway enrichment:

Enrichment Analysis

  • enrichPathway(): Over-Representation Analysis (ORA) for Reactome pathways
  • gsePathway(): Gene Set Enrichment Analysis (GSEA) for Reactome pathways
  • nsePathway(): Network-based Set Enrichment Analysis (NSEA) using the Reactome reaction graph with Random Walk with Restart

Post-hoc Analysis

  • bayes_reactome(): Bayesian term selection to compress redundant pathway output
  • enrichPathway(weight = ...) and gsePathway(weight = ...): Weighted ORA/GSEA

Utilities

  • gson_Reactome(): Build a GSON gene-set annotation object from Reactome
  • prepareReactomeNetwork(): Build and cache the Reactome reaction graph for NSEA

Visualization

  • dotplot(): Dot plot of enrichment results
  • cnetplot(): Gene-concept network plot
  • emapplot(): Enrichment map
  • heatplot(): Gene-pathway heatmap
  • ridgeplot(): Ridge plot of GSEA results
  • gseaplot(): GSEA running score plot
  • viewPathway(): Topological view of a Reactome pathway

Full Vignette

Please go to https://yulab-smu.top/biomedical-knowledge-mining-book/ for the full vignette.

Citation

If you use ReactomePA [@yu_reactomepa_2016] in published research, please cite:

G Yu, QY He*. ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization. Molecular BioSystems 2016, 12(2):477-479. doi: 10.1039/C5MB00663E

Need help?

If you have questions/issues, please post to Bioconductor support site and tag your post with ReactomePA.