Tool: pathfindR - Pathway Enrichment Analysis using Active Subnetworks
gravatar for egeulgen
7 days ago by
Acibadem University, Istanbul
egeulgen80 wrote:

Hi all,

I would like to introduce our group's new 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.
  • 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 download the package via CRAN. You can read more about the package and a case study in our pre-print

ADD COMMENTlink modified 6 days ago • written 7 days ago by egeulgen80

Can you please give a tutorial by taking some examples of a gene.

ADD REPLYlink modified 4 days ago • written 4 days ago by kalyanimeha0

You can see an example application in the vignette (vignette("pathfindr_vignette"))

ADD REPLYlink written 4 days ago by egeulgen80
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