I would like to introduce our group's new CRAN package to you: pathfindR
- This tool is designed to improve pathway enrichment analysis by firstly identifying active subnetworks in differential expression/methylation data using a protein-protein interaction network. It then performs pathway enrichment analysis (Over-Representation Analysis). By utilizing the interaction information, the tool identifies most of the involved pathways.
- As of v1.1.0, pathfindR provides the gene sets KEGG, Reactome, BioCarta as well as GO-MF, GO-BP and GO-CC for enrichment analysis
- pathfindR also creates pathway diagrams for KEGG with the involved genes colored by change values. (this is achieved using the bioconductor package pathview)
- Finally, the package allows for clustering of enriched pathways and establishment of representative pathways. This allows for further abstraction and reduces the complexity of analysis.
You can read more about the package and a case study in our pre-print