A Python library for probabilistic analysis of single-cell omics data

Adam Gayoso^#¹, Romain Lopez^#², Galen Xing^#^{1

3}, Pierre Boyeau^{2

4}, Valeh Valiollah Pour Amiri^{1

2}, Justin Hong^{1

2}, Katherine Wu², Michael Jayasuriya², Edouard Mehlman^{4

5}, Maxime Langevin^{5

6

7}, Yining Liu^{2

8}, Jules Samaran⁹, Gabriel Misrachi^{5

10}, Achille Nazaret^{5

8}, Oscar Clivio^{4

11}, Chenling Xu¹, Tal Ashuach¹, Mariano Gabitto^{1

2}, Mohammad Lotfollahi^{12

13}, Valentine Svensson¹⁴, Eduardo da Veiga Beltrame¹⁵, Vitalii Kleshchevnikov¹⁶, Carlos Talavera-López^{16

17}, Lior Pachter^{15

18}, Fabian J Theis^{12

13}, Aaron Streets^{1

3

19}, Michael I Jordan^{1

2

20}, Jeffrey Regier²¹, Nir Yosef^{22

23

24

25}

Affiliations

¹ Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA.
² Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA.
³ Chan Zuckerberg Biohub, San Francisco, CA, USA.
⁴ École Normale Supérieure Paris-Saclay, Gif-sur-Yvette, France.
⁵ Centre de Mathématiques Appliquées, École polytechnique, Palaiseau, France.
⁶ Pasteur, Department of Chemistry, École Normale Supérieure, PSL University, Paris, France.
⁷ Molecular Design Sciences - Integrated Drug Discovery, Sanofi R&D, Vitry-sur-Seine, France.
⁸ Department of Computer Science, Columbia University, New York, NY, USA.
⁹ Mines Paristech, PSL University, Paris, France.
¹⁰ Gleamer, Paris, France.
¹¹ Department of Statistics, University of Oxford, Oxford, UK.
¹² Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany.
¹³ School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany.
¹⁴ Serqet Therapeutics, Cambridge, MA, USA.
¹⁵ Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
¹⁶ Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
¹⁷ EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK.
¹⁸ Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA.
¹⁹ Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.
²⁰ Department of Statistics, University of California, Berkeley, Berkeley, CA, USA.
²¹ Department of Statistics, University of Michigan, Ann Arbor, MI, USA.
²² Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA. niryosef@berkeley.edu.
²³ Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA. niryosef@berkeley.edu.
²⁴ Chan Zuckerberg Biohub, San Francisco, CA, USA. niryosef@berkeley.edu.
²⁵ Ragon Institute of Massachusetts General Hospital, MIT and Harvard, Cambridge, MA, USA. niryosef@berkeley.edu.

^# Contributed equally.

PMID: 35132262
DOI: 10.1038/s41587-021-01206-w

A Python library for probabilistic analysis of single-cell omics data

Adam Gayoso et al. Nat Biotechnol. 2022 Feb.

. 2022 Feb;40(2):163-166.

doi: 10.1038/s41587-021-01206-w.

Authors

Affiliations

¹ Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA.
² Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA.
³ Chan Zuckerberg Biohub, San Francisco, CA, USA.
⁴ École Normale Supérieure Paris-Saclay, Gif-sur-Yvette, France.
⁵ Centre de Mathématiques Appliquées, École polytechnique, Palaiseau, France.
⁶ Pasteur, Department of Chemistry, École Normale Supérieure, PSL University, Paris, France.
⁷ Molecular Design Sciences - Integrated Drug Discovery, Sanofi R&D, Vitry-sur-Seine, France.
⁸ Department of Computer Science, Columbia University, New York, NY, USA.
⁹ Mines Paristech, PSL University, Paris, France.
¹⁰ Gleamer, Paris, France.
¹¹ Department of Statistics, University of Oxford, Oxford, UK.
¹² Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany.
¹³ School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany.
¹⁴ Serqet Therapeutics, Cambridge, MA, USA.
¹⁵ Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
¹⁶ Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
¹⁷ EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK.
¹⁸ Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA.
¹⁹ Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.
²⁰ Department of Statistics, University of California, Berkeley, Berkeley, CA, USA.
²¹ Department of Statistics, University of Michigan, Ann Arbor, MI, USA.
²² Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA. niryosef@berkeley.edu.
²³ Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA. niryosef@berkeley.edu.
²⁴ Chan Zuckerberg Biohub, San Francisco, CA, USA. niryosef@berkeley.edu.
²⁵ Ragon Institute of Massachusetts General Hospital, MIT and Harvard, Cambridge, MA, USA. niryosef@berkeley.edu.

^# Contributed equally.

PMID: 35132262
DOI: 10.1038/s41587-021-01206-w

No abstract available

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References

1. Svensson, V., da Veiga Beltrame, E. & Pachter, L. Database 2020, baaa073 (2020). - DOI
1. Lee, J., Hyeon, D. Y. & Hwang, D. Exp. Mol. Med. 52, 1428–1442 (2020). - DOI
1. Wagner, A., Regev, A. & Yosef, N. Nat. Biotechnol. 34, 1145–1160 (2016). - DOI
1. Zappia, L., Phipson, B. & Oshlack, A. PLOS Comput. Biol. 14 (2018).
1. Lopez, R., Gayoso, A. & Yosef, N. Mol. Syst. Biol. 16, e9198 (2020). - DOI

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A Python library for probabilistic analysis of single-cell omics data

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A Python library for probabilistic analysis of single-cell omics data

Authors

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References

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