ScShaper: an ensemble method for fast and accurate linear trajectory inference from single-cell RNA-seq data.

ABSTRACT:

Motivation

Computational models are needed to infer a representation of the cells, i.e. a trajectory, from single-cell RNA-sequencing data that model cell differentiation during a dynamic process. Although many trajectory inference methods exist, their performance varies greatly depending on the dataset and hence there is a need to establish more accurate, better generalizable methods.

Results

We introduce scShaper, a new trajectory inference method that enables accurate linear trajectory inference. The ensemble approach of scShaper generates a continuous smooth pseudotime based on a set of discrete pseudotimes. We demonstrate that scShaper is able to infer accurate trajectories for a variety of trigonometric trajectories, including many for which the commonly used principal

SUBMITTER: Smolander J 

PROVIDER: S-EPMC8825760 | biostudies-literature | 2022 Feb

REPOSITORIES: biostudies-literature