I would like to introduce our group's new bioinformatics package to you:
This tool is designed to improve pathway enrichment analysis by firstly
identifying active subnetworksin 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.
pathfindR also creates pathway diagrams 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
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