Gene set enrichment analysis was performed for each cell type that underwent differential expression analysis, using the fgsea R package85. The log2 fold changes from the differential expression analysis were used as the ranks, and pathways from the Reactome database were used as gene sets (Supplementary Data 9, all pathways with FDR < 0.2 are shown). For visualization, the top 30 enriched pathways (based on the smallest FDR) in each cell type were selected and hierarchically clustered based on the number of genes shared between the pathways. Clustered pathways were then manually labeled into 25 groups. FDR correction of p values was performed using the BH procedure.
