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Benchmarking atlas-level data integration in single-cell genomics.

Nat. Methods 19, 41-50 (2022)
Publ. Version/Full Text DOI PMC
Open Access Gold (Paid Option)
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Single-cell atlases often include samples that span locations, laboratories and conditions, leading to complex, nested batch effects in data. Thus, joint analysis of atlas datasets requires reliable data integration. To guide integration method choice, we benchmarked 68 method and preprocessing combinations on 85 batches of gene expression, chromatin accessibility and simulation data from 23 publications, altogether representing >1.2 million cells distributed in 13 atlas-level integration tasks. We evaluated methods according to scalability, usability and their ability to remove batch effects while retaining biological variation using 14 evaluation metrics. We show that highly variable gene selection improves the performance of data integration methods, whereas scaling pushes methods to prioritize batch removal over conservation of biological variation. Overall, scANVI, Scanorama, scVI and scGen perform well, particularly on complex integration tasks, while single-cell ATAC-sequencing integration performance is strongly affected by choice of feature space. Our freely available Python module and benchmarking pipeline can identify optimal data integration methods for new data, benchmark new methods and improve method development.
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Publication type Article: Journal article
Document type Scientific Article
Corresponding Author
Keywords Rna-seq
ISSN (print) / ISBN 1548-7091
e-ISSN 1548-7105
Journal Nature Methods
Quellenangaben Volume: 19, Issue: 1, Pages: 41-50 Article Number: , Supplement: ,
Publisher Nature Publishing Group
Publishing Place New York, NY
Non-patent literature Publications
Reviewing status Peer reviewed
Grants Helmholtz Association