PT  - JOURNAL ARTICLE
AU  - Wenpin Hou
AU  - Zhicheng Ji
AU  - Zeyu Chen
AU  - E. John Wherry
AU  - Stephanie C. Hicks
AU  - Hongkai Ji
TI  - A statistical framework for differential pseudotime analysis with multiple single-cell RNA-seq samples
AID  - 10.1101/2021.07.10.451910
DP  - 2021 Jan 01
TA  - bioRxiv
PG  - 2021.07.10.451910
4099  - http://biorxiv.org/content/early/2021/07/12/2021.07.10.451910.short
4100  - http://biorxiv.org/content/early/2021/07/12/2021.07.10.451910.full
AB  - 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 computational methods have been developed to infer the pseudo-temporal trajectories of cells within a biological sample, methods that compare pseudo-temporal patterns with multiple samples (or replicates) across different experimental conditions are lacking. Lamian is a comprehensive and statistically-rigorous computational framework for differential multi-sample pseudotime analysis. It can be used to identify changes in a biological process associated with sample covariates, such as different biological conditions, and also to detect changes in gene expression, cell density, and topology of a pseudotemporal trajectory. Unlike existing methods that ignore sample variability, Lamian draws statistical inference after accounting for cross-sample variability and hence substantially reduces sample-specific false discoveries that are not generalizable to new samples. Using both simulations and real scRNA-seq data, including an analysis of differential immune response programs between COVID-19 patients with different disease severity levels, we demonstrate the advantages of Lamian in decoding cellular gene expression programs in continuous biological processes.Competing Interest StatementE.J.W. has consulting agreements with and/or is on the scientific advisory board for Merck, Roche, Pieris, Elstar, and Surface Oncology. E.J.W. is a founder of Surface Oncology and Arsenal Biosciences. E.J.W. has a patent licensing agreement on the PD-1 pathway with Roche/Genentech. Other authors declare no competing interests.