I would like to introduce our group's pathway enrichment 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, 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
- The package allows for clustering of enriched pathways and establishment of representative pathways. This allows for further abstraction and reduces the complexity of analysis.
- As of v1.2, pathfindR provides functionality to score pathways for individual samples and plot a heatmap of the scores. This allows the user to gain insight into the activity of a pathway overall and per each sample.