Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics

Springer Science and Business Media LLC - Tập 19 - Trang 1-16 - 2018
Kelly Street1,2, Davide Risso3, Russell B. Fletcher4, Diya Das4,5, John Ngai4,6,7, Nir Yosef8,2, Elizabeth Purdom9,2, Sandrine Dudoit1,9,2,5
1Division of Biostatistics, School of Public Health, University of California, Berkeley, USA
2Center for Computational Biology, University of California, Berkeley, USA
3Division of Biostatistics and Epidemiology, Department of Healthcare Policy and Research, Weill Cornell Medicine, New York, USA
4Department of Molecular and Cell Biology, University of California, Berkeley, USA
5Berkeley Institute for Data Science, University of California, Berkeley, USA
6Helen Wills Neuroscience Institute, University of California, Berkeley, USA
7QB3 Berkeley Functional Genomics Laboratory, Berkeley, USA
8Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, USA
9Department of Statistics, University of California, Berkeley, USA

Tóm tắt

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. 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. 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.

Tài liệu tham khảo

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