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Luecken MD, Büttner M, Chaichoompu K, Danese A, Interlandi M, Mueller MF, Strobl DC, Zappia L, Dugas M, Colomé-Tatché M, Theis FJ. Benchmarking atlas-level data integration in single-cell genomics. Nat Methods 2022; 19:41-50. [PMID: 34949812 PMCID: PMC8748196 DOI: 10.1038/s41592-021-01336-8] [Citation(s) in RCA: 263] [Impact Index Per Article: 131.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 11/01/2021] [Indexed: 12/12/2022]
Abstract
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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Affiliation(s)
- Malte D. Luecken
- grid.4567.00000 0004 0483 2525Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - M. Büttner
- grid.4567.00000 0004 0483 2525Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - K. Chaichoompu
- grid.4567.00000 0004 0483 2525Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - A. Danese
- grid.4567.00000 0004 0483 2525Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - M. Interlandi
- grid.5949.10000 0001 2172 9288Institute of Medical Informatics, University of Münster, Münster, Germany
| | - M. F. Mueller
- grid.4567.00000 0004 0483 2525Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - D. C. Strobl
- grid.4567.00000 0004 0483 2525Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - L. Zappia
- grid.4567.00000 0004 0483 2525Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany ,grid.6936.a0000000123222966Department of Mathematics, Technische Universität München, Garching bei München, München, Germany
| | - M. Dugas
- grid.5253.10000 0001 0328 4908Institute of Medical Informatics, Heidelberg University Hospital, Heidelberg, Germany
| | - M. Colomé-Tatché
- grid.4567.00000 0004 0483 2525Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany ,grid.6936.a0000000123222966TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany ,grid.5252.00000 0004 1936 973XBiomedical Center (BMC), Physiological Chemistry, Faculty of Medicine, Ludwig Maximilian University of Munich, Planegg-Martinsried, Germany
| | - Fabian J. Theis
- grid.4567.00000 0004 0483 2525Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany ,grid.6936.a0000000123222966Department of Mathematics, Technische Universität München, Garching bei München, München, Germany ,grid.6936.a0000000123222966TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
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Ferronika P, van den Bos H, Taudt A, Spierings DCJ, Saber A, Hiltermann TJN, Kok K, Porubsky D, van der Wekken AJ, Timens W, Foijer F, Colomé-Tatché M, Groen HJM, Lansdorp PM, van den Berg A. Copy number alterations assessed at the single-cell level revealed mono- and polyclonal seeding patterns of distant metastasis in a small-cell lung cancer patient. Ann Oncol 2018; 28:1668-1670. [PMID: 28419234 DOI: 10.1093/annonc/mdx182] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Indexed: 11/14/2022] Open
Affiliation(s)
- P Ferronika
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands.,Department of Pathology, Faculty of Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - H van den Bos
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - A Taudt
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands.,Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - D C J Spierings
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - A Saber
- Department of Pathology and Medical Biology
| | - T J N Hiltermann
- Department of Pulmonary Diseases, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - K Kok
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - D Porubsky
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - A J van der Wekken
- Department of Pulmonary Diseases, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - W Timens
- Department of Pathology and Medical Biology
| | - F Foijer
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - M Colomé-Tatché
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands.,Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - H J M Groen
- Department of Pulmonary Diseases, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - P M Lansdorp
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands.,Department of Medical Genetics, University of British Columbia and Terry Fox Laboratory, BC Cancer Research Centre, Vancouver, Canada
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Colomé-Tatché M, Petrov DS. Parametric excitation of a 1D gas in integrable and nonintegrable cases. Phys Rev Lett 2011; 106:125302. [PMID: 21517321 DOI: 10.1103/physrevlett.106.125302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Revised: 02/07/2011] [Indexed: 05/30/2023]
Abstract
We study the response of a highly excited 1D gas with pointlike interactions to a periodic modulation of the coupling constant. We calculate the corresponding dynamic structure factors and show that their low-frequency behavior differs dramatically for integrable and nonintegrable models. Nonintegrable systems are sensitive to excitations with frequencies as low as the mean level spacing, whereas much higher frequencies are required to excite an integrable system. This effect can be used as a probe of integrability for mesoscopic 1D systems and can be observed experimentally by measuring the heating rate of a parametrically excited gas.
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Affiliation(s)
- M Colomé-Tatché
- Institut für Theoretische Physik, Leibniz Universität Hannover, Appelstrasse 2 D-30167, Hannover, Germany
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Rodríguez K, Argüelles A, Colomé-Tatché M, Vekua T, Santos L. Mott-insulator phases of spin-3/2 fermions in the presence of quadratic Zeeman coupling. Phys Rev Lett 2010; 105:050402. [PMID: 20867897 DOI: 10.1103/physrevlett.105.050402] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2010] [Revised: 06/03/2010] [Indexed: 05/29/2023]
Abstract
We study the influence of the quadratic Zeeman effect on the Mott-insulator phases of hard-core 1D spin-3/2 fermions. We show that, contrary to spinor bosons, the quadratic Zeeman coupling preserves an SU(2)⊗SU(2) symmetry, leading for large-enough quadratic Zeeman coupling to an isotropic pseudo-spin-1/2 Heisenberg antiferromagnet. Decreasing the quadratic Zeeman coupling, this phase undergoes, depending on the scattering lengths, either a Kosterlitz-Thouless transition into a gapped dimerized phase or a commensurate-incommensurate transition into a gapless spin liquid. This rich phase diagram can be observed experimentally in four-component fermions in optical lattices under similar entropy constraints to those needed for Néel order in spin-1/2 gases.
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Affiliation(s)
- K Rodríguez
- Institut für Theoretische Physik, Leibniz Universität Hannover, Appelstrasse 2 D-30167, Hannover, Germany
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