Benchmarking atlas-level data integration in single-cell genomics
Malte D. Luecken, Maren Büttner, Kridsadakorn Chaichoompu et al.
2021 · Nature Methods · 1,458 citations
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…
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