Journal
BIOINFORMATICS
Volume 38, Issue 5, Pages 1328-1335Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btab831
Keywords
-
Categories
Funding
- European Research Council ERC [677943]
- European Union [955321]
- Academy of Finland [322123, 296801, 310561, 314443, 329278, 335434, 335611]
- Sigrid Juselius Foundation
- University of Turku Graduate School (UTUGS)
- Biocenter Finland
- ELIXIR Finland
- Academy of Finland (AKA) [322123, 335611, 322123, 335434, 335611] Funding Source: Academy of Finland (AKA)
Ask authors/readers for more resources
The scShaper is a new trajectory inference method that generates a continuous smooth pseudo-time using an ensemble approach. It accurately infers various trigonometric trajectories and outperforms other methods in terms of accuracy of cell sorting and differentially expressed genes. The scShaper is a fast method with a few hyperparameters, making it a promising alternative to the principal curves method for linear pseudotemporal ordering.
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 pseudo-time 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 curves method fails. A comprehensive benchmarking with state-of-the-art methods revealed that scShaper achieved superior accuracy of the cell ordering and, in particular, the differentially expressed genes. Moreover, scShaper is a fast method with few hyperparameters, making it a promising alternative to the principal curves method for linear pseudotemporal ordering.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available