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mortazavilab / PyWGCNA

PyWGCNA is a Python package designed to do Weighted Gene Correlation Network analysis (WGCNA)
https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btad415/7218311
MIT License
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More flexibility for functional enrichment analysis #77

Closed GentlemanOfFate closed 6 months ago

GentlemanOfFate commented 7 months ago

Hello once again =)

Currently, the functional_enrichment_analysis function allows performing Enrichr search only using GO, KEGG, and REACTOME.

In my case, none of them yielded good enough results, so I'd like to analyse functional enrichment with other available GSEApy datasets.

To me, it seems rather simple to add an opportunity to search through any of them by passing user-defined gene sets and dataset names into variables that will be transferred to the gp.enrichr() function (as it is almost done now), not just be confined to GO, KEGG, and REACTOME.

So, I'd be very glad to see these features in future, thanks again for the package!

nargesr commented 6 months ago

Hi,

The type only indicates the type of databases but you can pass the Enrichr Library name(s) using sets.

I also added the **kwargs to the functional_enrichment_analysis() to pass all the parameters used in gseapy.enrichr()