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geneBasis: an iterative approach for unsupervised selection of targeted gene panels from scRNA-seq.

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cam.issuedOnline2021-12-06
dc.contributor.authorMissarova, Alsu
dc.contributor.authorJain, Jaison
dc.contributor.authorButler, Andrew
dc.contributor.authorGhazanfar, Shila
dc.contributor.authorStuart, Tim
dc.contributor.authorBrusko, Maigan
dc.contributor.authorWasserfall, Clive
dc.contributor.authorNick, Harry
dc.contributor.authorBrusko, Todd
dc.contributor.authorAtkinson, Mark
dc.contributor.authorSatija, Rahul
dc.contributor.authorMarioni, John
dc.contributor.orcidMarioni, John [0000-0001-9092-0852]
dc.date.accessioned2021-12-24T13:35:14Z
dc.date.available2021-12-24T13:35:14Z
dc.date.issued2021-12-06
dc.date.submitted2021-07-20
dc.date.updated2021-12-24T13:35:13Z
dc.descriptionFunder: European Molecular Biology Laboratory (EMBL) (4843)
dc.description.abstractscRNA-seq datasets are increasingly used to identify gene panels that can be probed using alternative technologies, such as spatial transcriptomics, where choosing the best subset of genes is vital. Existing methods are limited by a reliance on pre-existing cell type labels or by difficulties in identifying markers of rare cells. We introduce an iterative approach, geneBasis, for selecting an optimal gene panel, where each newly added gene captures the maximum distance between the true manifold and the manifold constructed using the currently selected gene panel. Our approach outperforms existing strategies and can resolve cell types and subtle cell state differences.
dc.identifier.doi10.17863/CAM.79237
dc.identifier.eissn1474-760X
dc.identifier.issn1474-7596
dc.identifier.others13059-021-02548-z
dc.identifier.other2548
dc.identifier.urihttps://www.repository.cam.ac.uk/handle/1810/331788
dc.languageen
dc.publisherSpringer Science and Business Media LLC
dc.subjectMethod
dc.titlegeneBasis: an iterative approach for unsupervised selection of targeted gene panels from scRNA-seq.
dc.typeArticle
dcterms.dateAccepted2021-11-19
prism.issueIdentifier1
prism.publicationNameGenome Biol
prism.volume22
pubs.funder-project-idnational institutes of health (1OT2OD026673-01, 1OT2OD026673-01, RM1HG011014-02, K99HG011489-01, U54AI142766, U54AI142766, U54AI142766, U54AI142766)
pubs.funder-project-idroyal society (gb) (NIF\R1\181950)
pubs.funder-project-idleona m. and harry b. helmsley charitable trust (2004-03813, 2004-03813)
pubs.funder-project-idcancer research uk (C9545/A29580)
rioxxterms.licenseref.urihttp://creativecommons.org/licenses/by/4.0/
rioxxterms.versionVoR
rioxxterms.versionofrecord10.1186/s13059-021-02548-z

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