Hi all,

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 pathview)
• 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.

You can download the package via CRAN. You can read more about the package and a case study in our pre-print