Show simple item record

dc.contributor.authorStrauss, Magdalena
dc.contributor.authorReid, John
dc.contributor.authorWernisch, Lorenz
dc.date.accessioned2018-09-08T06:32:56Z
dc.date.available2018-09-08T06:32:56Z
dc.date.issued2019-02-15
dc.identifier.issn1367-4811
dc.identifier.urihttps://www.repository.cam.ac.uk/handle/1810/279864
dc.description.abstractAbstract 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 data sets. Availability and implementation: Our method is available on github: https://github.com/magStra/GPseudoRank.
dc.description.sponsorshipMS, JR and LW are funded by the UK Medical Research Council (Grant Ref MC_UU_00002/1).
dc.publisherOxford University Press
dc.rightsAttribution 4.0 International (CC BY 4.0)
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.titleGPseudoRank: a permutation sampler for single cell orderings
dc.typeArticle
prism.publicationNameBioinformatics
dc.identifier.doi10.17863/CAM.27232
dcterms.dateAccepted2018-07-19
rioxxterms.versionofrecord10.1093/bioinformatics/bty664
rioxxterms.licenseref.urihttp://creativecommons.org/licenses/by/4.0/
rioxxterms.licenseref.startdate2018-07-19
dc.contributor.orcidReid, John [0000-0002-7762-6760]
dc.identifier.eissn1367-4811
rioxxterms.typeJournal Article/Review
pubs.funder-project-idMRC (unknown)
pubs.funder-project-idMRC (unknown)
pubs.funder-project-idMRC (1647133)
cam.issuedOnline2018-07-25


Files in this item

Thumbnail
Thumbnail

This item appears in the following Collection(s)

Show simple item record

Attribution 4.0 International (CC BY 4.0)
Except where otherwise noted, this item's licence is described as Attribution 4.0 International (CC BY 4.0)