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Hrovatin, K. ; Sikkema, L. ; Shitov, V.A. ; Heimberg, G.* ; Shulman, M. ; Oliver, A.J.* ; Müller, M. ; Ibarra Del Rio, I.A. ; Wang, H.* ; Ramirez Suastegui, C. ; He, P.* ; Schaar, A. ; Teichmann, S.A.* ; Theis, F.J. ; Luecken, M.

Considerations for building and using integrated single-cell atlases.

Nat. Methods, DOI: 10.1038/s41592-024-02532-y (2024)
DOI PMC
The rapid adoption of single-cell technologies has created an opportunity to build single-cell 'atlases' integrating diverse datasets across many laboratories. Such atlases can serve as a reference for analyzing and interpreting current and future data. However, it has become apparent that atlasing approaches differ, and the impact of these differences are often unclear. Here we review the current atlasing literature and present considerations for building and using atlases. Importantly, we find that no one-size-fits-all protocol for atlas building exists, but rather we discuss context-specific considerations and workflows, including atlas conceptualization, data collection, curation and integration, atlas evaluation and atlas sharing. We further highlight the benefits of integrated atlases for analyses of new datasets and deriving biological insights beyond what is possible from individual datasets. Our overview of current practices and associated recommendations will improve the quality of atlases to come, facilitating the shift to a unified, reference-based understanding of single-cell biology.
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Publikationstyp Artikel: Journalartikel
Dokumenttyp Review
Korrespondenzautor
ISSN (print) / ISBN 1548-7091
e-ISSN 1548-7105
Zeitschrift Nature Methods
Verlag Nature Publishing Group
Verlagsort New York, NY
Nichtpatentliteratur Publikationen
Begutachtungsstatus Peer reviewed
Institut(e) Institute of Computational Biology (ICB)
Helmholtz Artifical Intelligence Cooperation Unit (HAICU)