Quantifying pluripotency landscape of cell differentiation from scRNA-seq data by continuous birth-death process.

ABSTRACT: Modeling cell differentiation from omics data is an essential problem in systems biology research. Although many algorithms have been established to analyze scRNA-seq data, approaches to infer the pseudo-time of cells or quantify their potency have not yet been satisfactorily solved. Here, we propose the Landscape of Differentiation Dynamics (LDD) method, which calculates cell potentials and constructs their differentiation landscape by a continuous birth-death process from scRNA-seq data. From the viewpoint of stochastic dynamics, we exploited the features of the differentiation process and quantified the differentiation landscape based on the source-sink diffusion process. In comparison with other scRNA-seq methods in seven benchmark datasets, we found that LDD could accurately and effic

SUBMITTER: Shi J 

PROVIDER: S-EPMC6876891 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature