scCODA is a Bayesian model for compositional single-cell data analysis.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
25 11 2021
25 11 2021
Historique:
received:
11
01
2021
accepted:
01
11
2021
entrez:
26
11
2021
pubmed:
27
11
2021
medline:
31
12
2021
Statut:
epublish
Résumé
Compositional changes of cell types are main drivers of biological processes. Their detection through single-cell experiments is difficult due to the compositionality of the data and low sample sizes. We introduce scCODA ( https://github.com/theislab/scCODA ), a Bayesian model addressing these issues enabling the study of complex cell type effects in disease, and other stimuli. scCODA demonstrated excellent detection performance, while reliably controlling for false discoveries, and identified experimentally verified cell type changes that were missed in original analyses.
Identifiants
pubmed: 34824236
doi: 10.1038/s41467-021-27150-6
pii: 10.1038/s41467-021-27150-6
pmc: PMC8616929
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
6876Informations de copyright
© 2021. The Author(s).
Références
Ann Appl Stat. 2020 Mar;14(1):94-115
pubmed: 32983313
Cell. 2017 Jun 15;169(7):1276-1290.e17
pubmed: 28602351
JAMA. 2020 Mar 17;323(11):1061-1069
pubmed: 32031570
Nat Med. 2020 Jun;26(6):842-844
pubmed: 32398875
Nat Commun. 2020 Jul 14;11(1):3514
pubmed: 32665548
J R Soc Interface. 2019 Jan 31;16(150):20180572
pubmed: 30958174
Brief Bioinform. 2019 Jan 18;20(1):210-221
pubmed: 28968702
BMC Bioinformatics. 2017 Feb 8;18(1):94
pubmed: 28178947
Microb Ecol Health Dis. 2015 May 29;26:27663
pubmed: 26028277
Proc Natl Acad Sci U S A. 2019 Nov 26;116(48):24242-24251
pubmed: 31719197
Immunol Today. 1995 Jan;16(1):12-6
pubmed: 7880382
J Med Virol. 2021 Feb;93(2):1070-1077
pubmed: 32910461
BMC Bioinformatics. 2019 Dec 24;20(Suppl 19):721
pubmed: 31870280
Nature. 2017 Nov 16;551(7680):333-339
pubmed: 29144463
Sci Rep. 2021 Jul 15;11(1):14505
pubmed: 34267244
Bioinformatics. 2018 Feb 1;34(3):372-380
pubmed: 28968799
Nature. 2019 Feb;566(7745):490-495
pubmed: 30787436
PLoS Comput Biol. 2021 Nov 16;17(11):e1009442
pubmed: 34784344
Genome Biol. 2018 Feb 6;19(1):15
pubmed: 29409532
Front Microbiol. 2017 Nov 15;8:2224
pubmed: 29187837
Inflamm Bowel Dis. 2006 Jun;12(6):447-56
pubmed: 16775488
Cell. 2019 Jul 25;178(3):714-730.e22
pubmed: 31348891
Biostatistics. 2004 Apr;5(2):155-76
pubmed: 15054023
J Exp Med. 2020 Jun 1;217(6):
pubmed: 32302401
Eur Respir J. 2020 May 7;55(5):
pubmed: 32269088