Is it possible to include leading edge genes in decoupler.run_gsea output?

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Hi, everyone,

I have been following the section of Gene set enrichment and pathway analysis in single-cell best practices. Specifically, I am trying to use decoupler.run_gsea to perform pathway enrichment with scRNA-seq data. The results look very good and consistent with our understanding of the data. But I wish I can include the leading edge genes in the output somehow? I searched around but could not really figure out how to achieve that, at least using decoupler. Maybe GSEApy is better route for this? Any suggestions would be very much appreciated. Sorry if I missed anything obvious.

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Hi @resolsc

Unfortunately it is still not available in decoupler yet but it is in our list. Will let you know once it is ready.

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Hi @resolsc

Better late than never. Now decoupler 1.5.0 includes leading edge results with the function decoupler.get_gsea_df and you can plot them with the function decoupler.plot_running_score

Hope this is helpful!

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This is amazing! Thank you so much! With the addition of Pseudobulk, decoupler is all I need for the DGE and pathway analysis!!

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