RT Journal Article
SR Electronic
T1 Totem: a user-friendly tool for clustering-based inference of tree-shaped trajectories from single-cell data
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2022.09.19.508535
DO 10.1101/2022.09.19.508535
A1 Smolander, Johannes
A1 Junttila, Sini
A1 Elo, Laura L
YR 2022
UL http://biorxiv.org/content/early/2022/09/19/2022.09.19.508535.abstract
AB 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. 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 spanning trees, and uses them to measure the connectivity of the cells. Besides automatic selection of an appropriate trajectory, cell connectivity enables to visually pinpoint branching points and milestones relevant to the trajectory. Furthermore, testing different trajectories with Totem is fast, easy, and does not require in-depth methodological knowledge.Competing Interest StatementThe authors have declared no competing interest.