Cell-connectivity-guided trajectory inference from single-cell data.

ABSTRACT:

Motivation

Single-cell RNA-sequencing enables cell-level investigation of cell differentiation, which can be modelled using trajectory inference methods. While tremendous effort has been put into designing these methods, inferring accurate trajectories automatically remains difficult. Therefore, the standard approach involves testing different trajectory inference methods and picking the trajectory giving the most biologically sensible model. As the default parameters are often suboptimal, their tuning requires methodological expertise.

Results

We introduce Totem, an open-source, easy-to-use R package designed to facilitate inference of tree-shaped trajectories from single-cell data. Totem generates a large number of clustering results, estimates their topologies as minimum

SUBMITTER: Smolander J 

PROVIDER: S-EPMC10474950 | biostudies-literature | 2023 Sep

REPOSITORIES: biostudies-literature