Application of scPS to PBMC data from HIV-positive people with and without atherosclerosis (AS). (A) scPS performance of a T-cell cluster-specific gene set across all cell subpopulations. Two-sample Wilcoxon signed-rank test, * indicates a P-value < 0.05, while **** signifies a P-value < 0.0001. (B) KEGG pathways (y-axis) dysregulated in CD8+ T cells from HIV-positive people with and without AS across the seven methods with an adjusted P-value of 0.01. (C) The distribution of the sparsity and average gene expression of the gene set in CD8+ T cells from HIV-positive people with (red) and without AS (blue). The top panel shows the number of genes (y-axis) across the gene set’s non-zero gene ratio (x-axis). The bottom panel shows the number of cells (y-axis) across the average gene expression (log-normalized) of the gene set (x-axis).