News: pathfindR - Pathway Enrichment Analysis using Active Subnetworks
gravatar for egeulgen
10 days ago by
egeulgen10 wrote:

Hi all,

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

ADD COMMENTlink modified 2 days ago by fawazfebin30 • written 10 days ago by egeulgen10
gravatar for fawazfebin
2 days ago by
fawazfebin30 wrote:


Great to know about the new package for pathway analysis. I installed the program from GitHub and ran the 'run_pathfindR' command on input ( a dataframe with gene symbols, logFC and adjusted p-values ) but got the following error:

> result2hr = run_pathfindR(input.2hr)
## Testing input

Error in input_testing(input, p_val_threshold) : Duplicated genes found!!


The input dataframe looks as below:

> head(input.2hr)
   SYMBOL       logFC            PValue
1    PDK4        8.676410     0.000000e+00
2  TSC22D3    5.105050     0.000000e+00
3    KLF9        3.944955      3.228586e-258
4   CEBPB      3.146205      2.349587e-251
5   DDIT4       2.790518      2.434831e-246
6   FKBP5       3.529769      1.882829e-224

What solution is suggested for the above error? Great thanks in advance.


ADD COMMENTlink written 2 days ago by fawazfebin30
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