Using bulk RNAseq GSEA methods on single cel RNAseq results?
I have lists of DE genes from a Seurat analysis. Is it advisable to use bulk RNAseq GSEA packages like FGSEA on such enriched results? Or is it better to use dedicated scRNAseq GSEA programs like Pagoda or iDEA?
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theodore.killian •
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Can you clarify what you mean: Do you have gene sets from single-cell data and now want to use bulk RNA-seq data (so ranked lists) to compare with these sets or visa versa, so have bulk gene sets and want to compare with ranked lists from single-cell data?
I have gene sets from single cell data.