News: pathfindR - Pathway Enrichment Analysis using Active Subnetworks
gravatar for egeulgen
8 months ago by
egeulgen20 wrote:

Hi all,

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 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)
  • The package allows for clustering of enriched pathways and establishment of representative pathways. This allows for further abstraction and reduces the complexity of analysis.
  • 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. You can read more about the package and a case study in our pre-print

ADD COMMENTlink modified 5 months ago • written 8 months ago by egeulgen20
gravatar for egeulgen
7 months 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 7 months ago by egeulgen20

Great thanks !

ADD REPLYlink written 7 months ago by fawazfebin30
gravatar for fawazfebin
7 months 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 7 months ago by fawazfebin30
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