custom signatures and ssGSEA method

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from GSVA import gmt_to_dataframe
import gseapy as gp

Gene Symbols Conversion for the GMT file

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custom_signatures = gmt_to_dataframe("tests/extdata/enrichr.KEGG_2016.gmt")

ssGSEA method

ref: https://gseapy.readthedocs.io/en/latest/singlecell_example.html

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res = gp.gsea(data=adata.to_df().T, # row -> genes, column-> samples
        gene_sets="tests/extdata/enrichr.KEGG_2016.gmt",
        cls=adata.obs.stim,
        permutation_num=1000,
        permutation_type='phenotype',
        outdir=None,
        method='s2n', # signal_to_noise
        threads= 16)

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