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GPseudoRank: a permutation sampler for single cell orderings

MOTIVATION: A number of pseudotime methods have provided point estimates of the ordering of cells for scRNA-seq data. A still limited number of methods also model the uncertainty of the pseudotime estimate. However, there is still a need for a method to sample from complicated and multi-modal distri...

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Detalles Bibliográficos
Autores principales: Strauß, Magdalena E, Reid, John E, Wernisch, Lorenz
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6230469/
https://www.ncbi.nlm.nih.gov/pubmed/30052778
http://dx.doi.org/10.1093/bioinformatics/bty664
Descripción
Sumario:MOTIVATION: A number of pseudotime methods have provided point estimates of the ordering of cells for scRNA-seq data. A still limited number of methods also model the uncertainty of the pseudotime estimate. However, there is still a need for a method to sample from complicated and multi-modal distributions of orders, and to estimate changes in the amount of the uncertainty of the order during the course of a biological development, as this can support the selection of suitable cells for the clustering of genes or for network inference. RESULTS: In applications to scRNA-seq data we demonstrate the potential of GPseudoRank to sample from complex and multi-modal posterior distributions and to identify phases of lower and higher pseudotime uncertainty during a biological process. GPseudoRank also correctly identifies cells precocious in their antiviral response and links uncertainty in the ordering to metastable states. A variant of the method extends the advantages of Bayesian modelling and MCMC to large droplet-based scRNA-seq datasets. AVAILABILITY AND IMPLEMENTATION: Our method is available on github: https://github.com/magStra/GPseudoRank. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.