Pathway enrichment analysis vs GSEA for single cell RNA sequencing data analysis
I am wondering when it is appropriate to use GSEA vs pathway enrichment analysis in single cell RNA sequencing analysis. I have generated markers lists for my clusters. The markers have no p value threshold but logfc.threshold = 0.25 and min.pct = 0.2. According to Reimand et al. 2019 (Nature Protocols; 14:482-517), partial ranked gene lists should be analyzed using pathway enrichment analysis. How does this apply to single cell data?
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