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egeulgen / pathfindR

pathfindR: Enrichment Analysis Utilizing Active Subnetworks
https://egeulgen.github.io/pathfindR/
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Microbiome shotgun genes enrichment #70

Closed mariam50411 closed 3 years ago

mariam50411 commented 3 years ago

Greetings,

Thanks for developing this package.

I know that we could use a customize a gene set with the specific organism of interest, however, I couldn't find any way to analyze microbiome related data. I have gut and nares microbiome KOs converted into gene symbols so could I use the default parameters as they already live inside the human or will this affect the reliability of the sub-networks?

Thanks in advance Mariam Oweda

egeulgen commented 3 years ago

Hey @mariam50411,

I do not have any experience with microbiome related data. I'm not sure if you're genes belong to human or microbiome. However, if you're interested in the alterations in human pathways, I would use the default PIN and gene sets. If you're interested in the alterations in microbiome pathways, I would provide a custom PIN and gene sets data.

Hope this helps, Best, -E