PseudotimeDE-fast: fast testing of differential gene expression along cell pseudotime.

ABSTRACT:

Summary

Identifying differentially expressed (DE) genes along cell pseudotime is crucial for understanding dynamic biological processes captured by single-cell RNA sequencing. However, existing DE methods either produce invalid P-values by ignoring the uncertainty in pseudotime inference or struggle to scale with the growing size of modern datasets. To address these limitations, we introduce PseudotimeDE-fast, a scalable method for detecting DE genes along pseudotime with well-calibrated P-values. Through comprehensive simulations and real-data analyses, we demonstrate that PseudotimeDE-fast delivers comparable or superior performance to existing approaches while offering substantial improvements in computational efficiency.

Availability and implementation

PseudotimeDE-fast

SUBMITTER: Lai Y 

PROVIDER: S-EPMC12619992 | biostudies-literature | 2025 Nov

REPOSITORIES: biostudies-literature