Rank–rank hypergeometric overlap (RRHO) is a threshold-free method aiming to compare gene expression profiles across two gene lists that were ranked by the degree of differential expression from two separate differential expression analyses [44]. The original RRHO method was further modified to improve the interpretability when the differential expression patterns are discordant in the two gene lists [45]. The input gene lists for RRHO were ranked by the log2FC (computed by limma-trend, see above) comparing the gene expressions of each endocrine cell type with all the other endocrine cell types in the snRNA-seq or scRNA-seq library.
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