[HTML][HTML] Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics

K Street, D Risso, RB Fletcher, D Das, J Ngai, N Yosef… - BMC genomics, 2018 - Springer
K Street, D Risso, RB Fletcher, D Das, J Ngai, N Yosef, E Purdom, S Dudoit
BMC genomics, 2018Springer
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 …
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.
Springer