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The scverse project provides a computational ecosystem for single-cell omics data analysis

Nature Biotechnology volume 41, pages 604–606 (2023)Cite this article

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Single-cell omics technologies have enabled the creation of comprehensive cell atlases across tissues and species and delivered key insights into the biological mechanisms underlying development, homeostasis and disease. Deriving such insights relied on the development of a multitude of computational tools and data structures1. However, the explosive growth of tools led to incompatibilities in data formats, application programming interfaces (APIs) and user interfaces, posing growing challenges for both tool users and developers. Here, we present scverse (https://scverse.org), a multi-institution open-source software project to address storage and analysis needs of single-cell profiling data. Scverse will help to support an omics analysis ecosystem in Python by bringing together tools and analysts into a robust community. To deliver a sustainable solution, scverse provides well-maintained core functionality including interoperable data formats and community structures. Scverse is an open community initiated by the developers of some of the most popular tools in the Python single-cell analysis ecosystem, including scanpy2, scvi-tools3 and muon4, which are successfully used in many downstream methods constructing various single-cell reference atlases of tissues, organs and organisms5.

The rapid growth, broad adoption and substantial impact of single-cell genomics depends on computational tools, as reflected in the accelerated growth of the software ecosystem1. With this growth, common obstacles of academic open-source software start to arise, including scattered and overlapping functionality across tools, poor discoverability and documentation, and lack of testing and continuous integration for some tools. These issues are exacerbated by an incentive structure in academia that rewards novelty over maintenance of essential infrastructure6. Moreover, enhancement and maintenance of widely used academic software is often limited to the original authors and a small number of direct collaborators, which can severely limit their continued reliability. However, to ensure that all newly developed tools can interact with each other, a certain amount of centralization is required, especially concerning data structures.

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Fig. 1: Scverse.

Code availability

The source code for the scverse core tools is publicly available at https://github.com/scverse. Code for determining the number of dependent packages and repositories is available from https://gist.github.com/ivirshup/4bff45c0a8d38b97c5289c8b2407dfcf.

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Acknowledgements

The authors would like to thank all scverse contributors who opened issues, contributed code or answered questions on scverse forums to guide novice and advanced users. D.B. acknowledges funding by the EMBL International PhD Programme and Darwin Trust Fellowship. G.S. was supported by a DOC fellowship from the Austrian Academy of Sciences. F.F. was supported by the Austrian Science Fund (FWF) (T 974-B30). G.P. is supported by the Helmholtz Association under the joint research school Munich School for Data Science.

Author information

Author notes

  1. These authors contributed equally: Isaac Virshup, Danila Bredikhin, Lukas Heumos, Giovanni Palla, Gregor Sturm, Adam Gayoso.

  2. These authors jointly supervised this work: Francesca Finotello, F. Alexander Wolf, Nir Yosef, Oliver Stegle, Fabian J. Theis.

Authors and Affiliations

  1. Computational Health Center, Helmholtz Center Munich, Neuherberg, Germany

    Isaac Virshup, Lukas Heumos, Giovanni Palla, Volker Bergen, Maren Büttner, David Fischer, Michal Klein, Marius Lange, Mohammad Lotfollahi, Malte D. Luecken, Sergei Rybakov, Anna C. Schaar, Philipp Weiler, F. Alexander Wolf & Fabian J. Theis

  2. European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany

    Danila Bredikhin, Max Frank & Oliver Stegle

  3. Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany

    Danila Bredikhin, Ilia Kats & Oliver Stegle

  4. Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany

    Danila Bredikhin

  5. Institute of Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive; Helmholtz Zentrum Munich, Member of the German Center for Lung Research (DZL), Munich, Germany

    Lukas Heumos

  6. School of Life Sciences, Technical University of Munich, Munich, Germany

    Lukas Heumos, Giovanni Palla, David Fischer & Fabian J. Theis

  7. Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria

    Gregor Sturm

  8. Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA

    Adam Gayoso, Justin Hong, Valeh Valiollah Pour Amiri, Galen Xing & Nir Yosef

  9. Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark

    Mikaela Koutrouli

  10. Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA

    Bonnie Berger

  11. Harvard-MIT Health Sciences and Technology Program, Cambridge, MA, USA

    Bonnie Berger

  12. Broad Institute of MIT and Harvard, Cambridge, MA, USA

    Bonnie Berger

  13. Computational and Systems Biology Program, Sloan Kettering Institute, New York, NY, USA

    Dana Pe’er

  14. Howard Hughes Medical Institute, Chevy Chase, MD, USA

    Dana Pe’er

  15. Genentech Research and Early Development, Genentech Inc, South San Francisco, CA, USA

    Gokcen Eraslan, Romain Lopez & Aviv Regev

  16. Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK

    Sarah A. Teichmann, Oliver Stegle & Fabian J. Theis

  17. Cavendish Laboratory, University of Cambridge, Cambridge, UK

    Sarah A. Teichmann

  18. Institute of Molecular Biology, University of Innsbruck, Innsbruck, Austria

    Francesca Finotello

  19. Digital Science Center (DiSC), University of Innsbruck, Innsbruck, Austria

    Francesca Finotello

  20. Lamin Labs, Munich, Germany

    F. Alexander Wolf

  21. Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA

    Pierre Boyeau, Justin Hong, Valeh Valiollah Pour Amiri & Nir Yosef

  22. Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA

    Nir Yosef

  23. Chan Zuckerberg Biohub, San Francisco, CA, USA

    Nir Yosef

  24. Faculty of Biosciences, Heidelberg University, Heidelberg, Germany

    Oliver Stegle

  25. School of Computation, Information and Technology, Technical University of Munich, Munich, Germany

    Marius Lange, Sergei Rybakov, Anna C. Schaar, Philipp Weiler & Fabian J. Theis

  26. Cellarity, Somerville, MA, USA

    Philipp Angerer & Volker Bergen

  27. Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany

    Maren Büttner

  28. Department of Genetics, Stanford University, Stanford, CA, USA

    Romain Lopez

  29. Department of Global Computational Biology and Digital Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany

    Fidel Ramirez

  30. Department of Statistics, University of Michigan, Ann Arbor, MI, USA

    Jeffrey Regier

  31. Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA

    Galen Xing

Authors
  1. Isaac Virshup
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  2. Danila Bredikhin
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  3. Lukas Heumos
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  4. Giovanni Palla
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  5. Gregor Sturm
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  6. Adam Gayoso
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  7. Ilia Kats
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  8. Mikaela Koutrouli
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  9. Bonnie Berger
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  10. Dana Pe’er
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  11. Aviv Regev
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  12. Sarah A. Teichmann
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  13. Francesca Finotello
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  14. F. Alexander Wolf
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  15. Nir Yosef
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  16. Oliver Stegle
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  17. Fabian J. Theis
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Consortia

Scverse Community

  • Philipp Angerer
  • , Volker Bergen
  • , Pierre Boyeau
  • , Maren Büttner
  • , Gokcen Eraslan
  • , David Fischer
  • , Max Frank
  • , Justin Hong
  • , Michal Klein
  • , Marius Lange
  • , Romain Lopez
  • , Mohammad Lotfollahi
  • , Malte D. Luecken
  • , Fidel Ramirez
  • , Jeffrey Regier
  • , Sergei Rybakov
  • , Anna C. Schaar
  • , Valeh Valiollah Pour Amiri
  • , Philipp Weiler
  •  & Galen Xing

Contributions

B.B., D.P., A.R. and S.A.T. are members of the scverse Advisory Committee. F.F., F.A.W., N.Y., O.S. and F.J.T. are members of the scverse Management Committee. Members of the scverse community are listed in alphabetical order.

Corresponding authors

Correspondence to Isaac Virshup, Danila Bredikhin or Lukas Heumos.

Ethics declarations

Competing interests

F.J.T. consults for Immunai Inc., Singularity Bio B.V., CytoReason Ltd and Omniscope Ltd, and has ownership interest in Dermagnostix GmbH and Cellarity. A.R. is a co-founder of and equity holder in Celsius Therapeutics, an equity holder in Immunitas, and until 31 July 2020 was a scientific advisory board member of Thermo Fisher Scientific, Syros Pharmaceuticals, Neogene Therapeutics and Asimov. From 1 August 2020, A.R. has been an employee of Genentech and a member of the Roche Group, and has equity in Roche. M.D.L is a part-time contractor for the Chan Zuckerberg Initiative. V.B. reports being employed by and having ownership interest in Cellarity. G.E. has been an employee of Genentech since 4 April 2022. R.L. has been an employee of Genentech since 31 August 2021. F.A.W. holds equity in Lamin Labs, Cellarity, Retro Biosciences and Doloromics. N.Y. is an advisor to and/or has equity in Cellarity, Celsius Therapeutics and Rheos Medicines. The remaining authors declare no competing interests.

Peer review

Peer review information

Nature Methods thanks Martin Hemberg and Wolfgang Huber for their contribution to the peer review of this work.

Supplementary information

Supplementary Table 1

List of unique PyPI packages that depend on scverse core tools. Determined by looking at reverse dependencies from https://www.wheelodex.org/.

Supplementary Table 2

List of unique GitHub repositories that depend on scverse core tools. Determined by scraping the dependent repositories from the core tools GitHub repositories.

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Virshup, I., Bredikhin, D., Heumos, L. et al. The scverse project provides a computational ecosystem for single-cell omics data analysis. Nat Biotechnol 41, 604–606 (2023). https://doi.org/10.1038/s41587-023-01733-8

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