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More flexibility for functional enrichment analysis #77

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GentlemanOfFate opened this issue Nov 11, 2023 · 1 comment
Closed

More flexibility for functional enrichment analysis #77

GentlemanOfFate opened this issue Nov 11, 2023 · 1 comment

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@GentlemanOfFate
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GentlemanOfFate commented Nov 11, 2023

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 added a commit that referenced this issue Dec 4, 2023
@nargesr
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nargesr commented Dec 4, 2023

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()

@nargesr nargesr closed this as completed Dec 4, 2023
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