ASPEN: Robust detection of allelic dynamics in single cell RNA-seq.

ABSTRACT: Single-cell RNA-seq data from F1 hybrids provide a unique framework for dissecting complex regulatory mechanisms, but allelic measurements are limited by technical noise due to low counts. Here, we present ASPEN, a statistical method for modeling allelic mean and variance in single-cell transcriptomic data. ASPEN combines a sensitive mapping pipeline  with a moderated beta-binomial model and adaptive shrinkage to distinguish allelic imbalance and changes to allelic variance in single cells. In both simulated and empirical datasets, ASPEN achieves a ~30% increase in sensitivity over existing approaches for single-cell allelic imbalance detection. Applied to mouse brain organoids and T cells, ASPEN identifies genes with incomplete X inactivation, random monoallelic expression, and significan

SUBMITTER: Petrova V 

PROVIDER: S-EPMC12774380 | biostudies-literature | 2025 Dec

REPOSITORIES: biostudies-literature