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

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...

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Detalles Bibliográficos
Autores principales: Street, Kelly, Risso, Davide, Fletcher, Russell B., Das, Diya, Ngai, John, Yosef, Nir, Purdom, Elizabeth, Dudoit, Sandrine
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6007078/
https://www.ncbi.nlm.nih.gov/pubmed/29914354
http://dx.doi.org/10.1186/s12864-018-4772-0
Descripción
Sumario: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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-018-4772-0) contains supplementary material, which is available to authorized users.