{"id":628004,"date":"2023-04-11T11:56:43","date_gmt":"2023-04-11T16:56:43","guid":{"rendered":"https:\/\/news.sellorbuyhomefast.com\/index.php\/2023\/04\/11\/the-scverse-project-provides-a-computational-ecosystem-for-single-cell-omics-data-analysis\/"},"modified":"2023-04-11T11:56:43","modified_gmt":"2023-04-11T16:56:43","slug":"the-scverse-project-provides-a-computational-ecosystem-for-single-cell-omics-data-analysis","status":"publish","type":"post","link":"https:\/\/newsycanuse.com\/index.php\/2023\/04\/11\/the-scverse-project-provides-a-computational-ecosystem-for-single-cell-omics-data-analysis\/","title":{"rendered":"The scverse project provides a computational ecosystem for single-cell omics data analysis"},"content":{"rendered":"

Science & Nature <\/p>\n

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<\/a><\/sup>. 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>), 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<\/a><\/sup>, scvi-tools3<\/a><\/sup> and muon4<\/a><\/sup>, which are successfully used in many downstream methods constructing various single-cell reference atlases of tissues, organs and organisms5<\/a><\/sup>.<\/p>\n

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Code availability<\/h2>\n
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The source code for the scverse core tools is publicly available at https:\/\/github.com\/scverse<\/a>. Code for determining the number of dependent packages and repositories is available from https:\/\/gist.github.com\/ivirshup\/4bff45c0a8d38b97c5289c8b2407dfcf<\/a>.<\/p>\n<\/p><\/div>\n<\/div>\n

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    Acknowledgements<\/h2>\n

    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.<\/p>\n<\/div>\n

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    Author information<\/h2>\n
    \n

    Author notes<\/span><\/p>\n

      \n
    1. \n

      These authors contributed equally: Isaac Virshup, Danila Bredikhin, Lukas Heumos, Giovanni Palla, Gregor Sturm, Adam Gayoso.<\/p>\n<\/li>\n

    2. \n

      These authors jointly supervised this work: Francesca Finotello, F. Alexander Wolf, Nir Yosef, Oliver Stegle, Fabian J. Theis.<\/p>\n<\/li>\n<\/ol>\n

      Authors and Affiliations<\/h3>\n
        \n
      1. \n

        Computational Health Center, Helmholtz Center Munich, Neuherberg, Germany<\/p>\n

        Isaac Virshup,\u00a0Lukas Heumos,\u00a0Giovanni Palla,\u00a0Volker Bergen,\u00a0Maren B\u00fcttner,\u00a0David Fischer,\u00a0Michal Klein,\u00a0Marius Lange,\u00a0Mohammad Lotfollahi,\u00a0Malte D. Luecken,\u00a0Sergei Rybakov,\u00a0Anna C. Schaar,\u00a0Philipp Weiler,\u00a0F. Alexander Wolf\u00a0&\u00a0Fabian J. Theis<\/p>\n<\/li>\n

      2. \n

        European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany<\/p>\n

        Danila Bredikhin,\u00a0Max Frank\u00a0&\u00a0Oliver Stegle<\/p>\n<\/li>\n

      3. \n

        Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany<\/p>\n

        Danila Bredikhin,\u00a0Ilia Kats\u00a0&\u00a0Oliver Stegle<\/p>\n<\/li>\n

      4. \n

        Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany<\/p>\n

        Danila Bredikhin<\/p>\n<\/li>\n

      5. \n

        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<\/p>\n

        Lukas Heumos<\/p>\n<\/li>\n

      6. \n

        School of Life Sciences, Technical University of Munich, Munich, Germany<\/p>\n

        Lukas Heumos,\u00a0Giovanni Palla,\u00a0David Fischer\u00a0&\u00a0Fabian J. Theis<\/p>\n<\/li>\n

      7. \n

        Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria<\/p>\n

        Gregor Sturm<\/p>\n<\/li>\n

      8. \n

        Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA<\/p>\n

        Adam Gayoso,\u00a0Justin Hong,\u00a0Valeh Valiollah Pour Amiri,\u00a0Galen Xing\u00a0&\u00a0Nir Yosef<\/p>\n<\/li>\n

      9. \n

        Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark<\/p>\n

        Mikaela Koutrouli<\/p>\n<\/li>\n

      10. \n

        Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA<\/p>\n

        Bonnie Berger<\/p>\n<\/li>\n

      11. \n

        Harvard-MIT Health Sciences and Technology Program, Cambridge, MA, USA<\/p>\n

        Bonnie Berger<\/p>\n<\/li>\n

      12. \n

        Broad Institute of MIT and Harvard, Cambridge, MA, USA<\/p>\n

        Bonnie Berger<\/p>\n<\/li>\n

      13. \n

        Computational and Systems Biology Program, Sloan Kettering Institute, New York, NY, USA<\/p>\n

        Dana Pe\u2019er<\/p>\n<\/li>\n

      14. \n

        Howard Hughes Medical Institute, Chevy Chase, MD, USA<\/p>\n

        Dana Pe\u2019er<\/p>\n<\/li>\n

      15. \n

        Genentech Research and Early Development, Genentech Inc, South San Francisco, CA, USA<\/p>\n

        Gokcen Eraslan,\u00a0Romain Lopez\u00a0&\u00a0Aviv Regev<\/p>\n<\/li>\n

      16. \n

        Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK<\/p>\n

        Sarah A. Teichmann,\u00a0Oliver Stegle\u00a0&\u00a0Fabian J. Theis<\/p>\n<\/li>\n

      17. \n

        Cavendish Laboratory, University of Cambridge, Cambridge, UK<\/p>\n

        Sarah A. Teichmann<\/p>\n<\/li>\n

      18. \n

        Institute of Molecular Biology, University of Innsbruck, Innsbruck, Austria<\/p>\n

        Francesca Finotello<\/p>\n<\/li>\n

      19. \n

        Digital Science Center (DiSC), University of Innsbruck, Innsbruck, Austria<\/p>\n

        Francesca Finotello<\/p>\n<\/li>\n

      20. \n

        Lamin Labs, Munich, Germany<\/p>\n

        F. Alexander Wolf<\/p>\n<\/li>\n

      21. \n

        Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA<\/p>\n

        Pierre Boyeau,\u00a0Justin Hong,\u00a0Valeh Valiollah Pour Amiri\u00a0&\u00a0Nir Yosef<\/p>\n<\/li>\n

      22. \n

        Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA<\/p>\n

        Nir Yosef<\/p>\n<\/li>\n

      23. \n

        Chan Zuckerberg Biohub, San Francisco, CA, USA<\/p>\n

        Nir Yosef<\/p>\n<\/li>\n

      24. \n

        Faculty of Biosciences, Heidelberg University, Heidelberg, Germany<\/p>\n

        Oliver Stegle<\/p>\n<\/li>\n

      25. \n

        School of Computation, Information and Technology, Technical University of Munich, Munich, Germany<\/p>\n

        Marius Lange,\u00a0Sergei Rybakov,\u00a0Anna C. Schaar,\u00a0Philipp Weiler\u00a0&\u00a0Fabian J. Theis<\/p>\n<\/li>\n

      26. \n

        Cellarity, Somerville, MA, USA<\/p>\n

        Philipp Angerer\u00a0&\u00a0Volker Bergen<\/p>\n<\/li>\n

      27. \n

        Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany<\/p>\n

        Maren B\u00fcttner<\/p>\n<\/li>\n

      28. \n

        Department of Genetics, Stanford University, Stanford, CA, USA<\/p>\n

        Romain Lopez<\/p>\n<\/li>\n

      29. \n

        Department of Global Computational Biology and Digital Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany<\/p>\n

        Fidel Ramirez<\/p>\n<\/li>\n

      30. \n

        Department of Statistics, University of Michigan, Ann Arbor, MI, USA<\/p>\n

        Jeffrey Regier<\/p>\n<\/li>\n

      31. \n

        Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA<\/p>\n

        Galen Xing<\/p>\n<\/li>\n<\/ol>\n

        Consortia<\/h3>\n
        \n

        Scverse Community<\/h3>\n