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Diffusion pseudotime robustly reconstructs lineage branching.
- Source :
-
Nature methods [Nat Methods] 2016 Oct; Vol. 13 (10), pp. 845-8. Date of Electronic Publication: 2016 Aug 29. - Publication Year :
- 2016
-
Abstract
- The temporal order of differentiating cells is intrinsically encoded in their single-cell expression profiles. We describe an efficient way to robustly estimate this order according to diffusion pseudotime (DPT), which measures transitions between cells using diffusion-like random walks. Our DPT software implementations make it possible to reconstruct the developmental progression of cells and identify transient or metastable states, branching decisions and differentiation endpoints.
- Subjects :
- Algorithms
Animals
Cluster Analysis
Computer Simulation
Diffusion
Embryonic Stem Cells cytology
Mice
Numerical Analysis, Computer-Assisted
Cell Differentiation genetics
Cell Lineage genetics
High-Throughput Nucleotide Sequencing methods
Models, Genetic
Models, Statistical
Single-Cell Analysis methods
Subjects
Details
- Language :
- English
- ISSN :
- 1548-7105
- Volume :
- 13
- Issue :
- 10
- Database :
- MEDLINE
- Journal :
- Nature methods
- Publication Type :
- Academic Journal
- Accession number :
- 27571553
- Full Text :
- https://doi.org/10.1038/nmeth.3971