Journal
BMC GENOMICS
Volume 19, Issue -, Pages -Publisher
BIOMED CENTRAL LTD
DOI: 10.1186/s12864-018-4772-0
Keywords
RNA-Seq; Single cell; Lineage inference; Pseudotime inference
Funding
- National Institute of Mental Health BRAIN Initiative grant [U01MH105979]
- National Institute on Deafness and Other Communication Disorders [RO1DC007235]
- National Center for Research Resources [S10RR029668]
- Siebel Foundation
- National Institute on Aging [K01AG045344]
- National Human Genome Research Institute [T32HG000047]
- California Institute of Regenerative Medicine
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Background: Single-cell transcriptomics allows researchers to investigate complex communities of heterogeneous cells. It can be applied to stem cells and their descendants in order to chart the progression from multipotent progenitors to fully differentiated cells. While a variety of statistical and computational methods have been proposed for inferring cell lineages, the problem of accurately characterizing multiple branching lineages remains difficult to solve. Results: We introduce Slingshot, a novel method for inferring cell lineages and pseudotimes from single-cell gene expression data. In previously published datasets, Slingshot correctly identifies the biological signal for one to three branching trajectories. Additionally, our simulation study shows that Slingshot infers more accurate pseudotimes than other leading methods. Conclusions: Slingshot is a uniquely robust and flexible tool which combines the highly stable techniques necessary for noisy single- cell data with the ability to identify multiple trajectories. Accurate lineage inference is a critical step in the identification of dynamic temporal gene expression.
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