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Open Access Green as soon as Postprint is submitted to ZB.
Modeling fragment counts improves single-cell ATAC-seq analysis.
Nat. Methods 21, 28–31 (2024)
Single-cell ATAC sequencing coverage in regulatory regions is typically binarized as an indicator of open chromatin. Here we show that binarization is an unnecessary step that neither improves goodness of fit, clustering, cell type identification nor batch integration. Fragment counts, but not read counts, should instead be modeled, which preserves quantitative regulatory information. These results have immediate implications for single-cell ATAC sequencing analysis.
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Publication type
Article: Journal article
Document type
Scientific Article
Keywords
Accessibility
ISSN (print) / ISBN
1548-7091
e-ISSN
1548-7105
Journal
Nature Methods
Quellenangaben
Volume: 21,
Pages: 28–31
Publisher
Nature Publishing Group
Publishing Place
New York, NY
Non-patent literature
Publications
Reviewing status
Peer reviewed
Institute(s)
Institute of Computational Biology (ICB)
Grants
European Union
Helmholtz Association's Initiative and Networking Fund through Helmholtz AI
Deutsche Forschungsgemeinschaft
Helmholtz Association under the joint research school Munich School for Data Science
Deutsche Forschungsgemeinschaft (German Research Foundation)
Helmholtz Association's Initiative and Networking Fund through Helmholtz AI
Deutsche Forschungsgemeinschaft
Helmholtz Association under the joint research school Munich School for Data Science
Deutsche Forschungsgemeinschaft (German Research Foundation)