Fig. 3. Between-method concordance.

Upset plot obtained from intersecting the top-n ranked gene-subpopulation combinations (lowest p value) across methods and simulation replicates. Here, n = min(n₁, n₂), where n₁ = number of genes simulated to be differential, and n₂ =  number of genes called differential at FDR < 0.05. Shown are the 40 most frequent interactions; coloring corresponds to (true) simulated gene categories. The bottom right annotation indicates method types (PB pseudobulk (aggregation-based) methods, MM mixed models, and AD Anderson–Darling tests).