Tool: pathfindR - Pathway Enrichment Analysis using Active Subnetworks
11 months ago by
egeulgen • 660
egeulgen • 660 wrote:
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, GO-CC and GO-All (BP+MF+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. The available clustering approaches are hierarchical and fuzzy.
- 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.
ADD COMMENT • link •