Locat: Joint enrichment and depletion testing identifies localized marker genes in single-cell transcriptomics

-treated PBMCs, independent localization analysis of control and stimulated samples reveals stimulus-responsive programs and markers of shared immune populations without requiring batch correction or data integration. In retinoic acid-induced embryonic stem cell differentiation, localized genes exhibit reproducible stage-specific patterns across time points. Together, these results demonstrate that jointly assessing concentration and depletion yields specific, interpretable marker genes that enable direct cross-condition and multi-sample comparisons of marker genes across diverse biological settings.