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egeulgen / pathfindR

pathfindR: Enrichment Analysis Utilizing Active Subnetworks
https://egeulgen.github.io/pathfindR/
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fold change filtering possibility #179

Closed abedkurdi closed 9 months ago

abedkurdi commented 9 months ago

Hi there!

I would like to ask if adding a threshold on the log2 fold change (for instance, absolute log2 fold change of 1) before running run_pathfindR is acceptable or not.

Thanks in advance!

ozanozisik commented 9 months ago

Hello, Sure, you can apply thresholds to the data and then run pathfindR. As a note, by default, pathfindR only applies a p-value threshold of 0.05. Regards.

abedkurdi commented 9 months ago

Thanks a lot!