LVPT: Lazy Velocity Pseudotime Inference Method

Authors

Shuainan Mao
Jiajia Liu
Weiling Zhao
Xiaobo Zhou

Publication Date

8-12-2023

Journal

Biomolecules

Abstract

The emergence of RNA velocity has enriched our understanding of the dynamic transcriptional landscape within individual cells. In light of this breakthrough, we embarked on integrating RNA velocity with cellular pseudotime inference, aiming to improve the prediction of cell orders along biological trajectories beyond existing methods. Here, we developed LVPT, a novel method for pseudotime and trajectory inference. LVPT introduces a lazy probability to indicate the probability that the cell stays in the original state and calculates the transition matrix based on RNA velocity to provide the probability and direction of cell differentiation. LVPT shows better and comparable performance of pseudotime inference compared with other existing methods on both simulated datasets with different structures and real datasets. The validation results were consistent with prior knowledge, indicating that LVPT is an accurate and efficient method for pseudotime inference.

Keywords

Cell Differentiation, Probability, RNA, single cell, trajectory inference, pseudotime inference, random walk

DOI

10.3390/biom13081242

PMID

37627306

PMCID

PMC10452358

PubMedCentral® Posted Date

8-12-2023

PubMedCentral® Full Text Version

Post-print

Published Open-Access

yes