A statistical framework for differential pseudotime analysis with multiple single-cell RNA-seq samples.

ABSTRACT: Pseudotime analysis with single-cell RNA-sequencing (scRNA-seq) data has been widely used to study dynamic gene regulatory programs along continuous biological processes. While many methods have been developed to infer the pseudotemporal trajectories of cells within a biological sample, it remains a challenge to compare pseudotemporal patterns with multiple samples (or replicates) across different experimental conditions. Here, we introduce Lamian, a comprehensive and statistically-rigorous computational framework for differential multi-sample pseudotime analysis. Lamian can be used to identify changes in a biological process associated with sample covariates, such as different biological conditions while adjusting for batch effects, and to detect changes in gene expression, cell density,

SUBMITTER: Hou W 

PROVIDER: S-EPMC10638410 | biostudies-literature | 2023 Nov

REPOSITORIES: biostudies-literature