News: pathfindR - Pathway Enrichment Analysis using Active Subnetworks
gravatar for egeulgen
9 weeks ago by
egeulgen20 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.
  • As of v1.1.0, 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)
  • 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 3 days ago • written 9 weeks ago by egeulgen20
gravatar for egeulgen
6 weeks ago by
egeulgen20 wrote:


Thank you for your interest. It seems that you have duplicate genes in the input. We keep the lowest p value in such situations. Try the following:

input.2hr_updated <- input.2hr[order(input.2hr$PValue, decreasing = FALSE), ]

input.2hr_updated <- input.2hr_updated[!duplicated(input.2hr_updated$SYMBOL), ]

Hope this helps

ADD COMMENTlink written 6 weeks ago by egeulgen20

Great thanks !

ADD REPLYlink written 6 weeks ago by fawazfebin30
gravatar for fawazfebin
8 weeks 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 8 weeks ago by fawazfebin30
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