ReactomePA: Reactome Pathway Analysis
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.
Guangchuang Yu, School of Public Health, The University of Hong Kong.
Please cite the following article when using
Yu G and He QY*. ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization. Molecular BioSystems, 2016,12(2):477-9.
Find out more on Featured Articles.
ReactomePA is easy, follow the guide in the Bioconductor
## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") ## biocLite("BiocUpgrade") ## you may need this biocLite("ReactomePA")
- Over-representation analysis
- Gene set enrichment analysis
Find out details and examples on Documentation.
- clusterProfiler for Ontologies/pathways enrichment analyses
- DOSE for Disease Ontology Semantic and Enrichment analyses
- meshes for MeSH Enrichment and Semantic analysis
Find out more on projects.
Projects that depend on ReactomePA
- bioCancer: Interactive Multi-Omics Cancers Data Visualization and Analysis
- LINC: co-expression of lincRNAs and protein-coding genes