• Scikit-bio: a fundamental Pyth...

Treffer: Scikit-bio: a fundamental Python library for biological omic data analysis.

Title:
Scikit-bio: a fundamental Python library for biological omic data analysis.
Authors:
Aton M; Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, USA., McDonald D; Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA., Cañardo Alastuey J; College of Engineering and Applied Science, University of Colorado Boulder, Boulder, CO, USA.; Amazon Robotics, North Reading, MA, USA., Azom R; Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, USA., Batra P; Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, USA., Bezshapkin V; Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, Zurich, Switzerland., Bolyen E; Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA., Cagle A; Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA., Caporaso JG; Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA., Debelius JW; Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA.; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA., Gorlick K; Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA., Hamsanipally N; Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, USA., Hunger L; Gutz Analytics, LLC, Boulder, CO, USA., Keluskar A; Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, USA., Liao D; Cheriton School of Computer Science, University of Waterloo, Waterloo, Ontario, Canada., Lu YY; Cheriton School of Computer Science, University of Waterloo, Waterloo, Ontario, Canada.; Department of Biomedical Engineering and Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA., Navas-Molina JA; Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA.; Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA.; Google LLC, Mountain View, CA, USA., Pitman A; Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.; University of Utah, Salt Lake City, UT, USA., Rideout JR; Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.; One Codex, Inc., Wilmington, DE, USA., Sazonov A; Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, USA., Sathappan B; Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA., Schwarzberg Lipson K; Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.; Chasing Value Asset Management, Inc., Santa Monica, CA, USA., Sfiligoi I; San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, USA., Tapo C; Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, USA.; Department of Mathematics, College of Engineering and Polymer Science, University of Akron, Akron, OH, USA., Vázquez-Baeza Y; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.; BiomeSense Inc., Chicago, IL, USA., Wu Z; Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, USA., Xu ZZ; Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA.; State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, China., Ye MS; School of Business, Stevens Institute of Technology, Hoboken, NJ, USA., Zhao J; Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA., Knight R; Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA. rknight@ucsd.edu.; Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA. rknight@ucsd.edu.; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA. rknight@ucsd.edu.; Department of Bioengineering, University of California San Diego, La Jolla, California, USA. rknight@ucsd.edu., Morton JT; Gutz Analytics, LLC, Boulder, CO, USA. jamie@gutzanalytics.com., Zhu Q; Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, USA. qiyun.zhu@asu.edu.; School of Life Sciences, Arizona State University, Tempe, AZ, USA. qiyun.zhu@asu.edu.
Source:
Nature methods [Nat Methods] 2025 Dec 11. Date of Electronic Publication: 2025 Dec 11.
Publication Model:
Ahead of Print
Publication Type:
Letter
Language:
English
Journal Info:
Publisher: Nature Pub. Group Country of Publication: United States NLM ID: 101215604 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1548-7105 (Electronic) Linking ISSN: 15487091 NLM ISO Abbreviation: Nat Methods Subsets: MEDLINE
Imprint Name(s):
Original Publication: New York, NY : Nature Pub. Group, c2004-
References:
Quinn, T. P. et al. Gigascience 8, giz107 (2019). (PMID: 10.1093/gigascience/giz107315442126755255)
Rahnenführer, J. et al. BMC Med. 21, 182 (2023). (PMID: 10.1186/s12916-023-02858-y3718912510186672)
Cock, P. J. A. et al. Bioinformatics 25, 1422–1423 (2009). (PMID: 10.1093/bioinformatics/btp163193048782682512)
Wolf, F. A., Angerer, P. & Theis, F. J. Genome Biol. 19, 15 (2018). (PMID: 10.1186/s13059-017-1382-0294095325802054)
McDonald, D. et al. Gigascience 1, 7 (2012). (PMID: 10.1186/2047-217X-1-7235872243626512)
McDonald, D. et al. Nat. Methods 15, 847–848 (2018). (PMID: 10.1038/s41592-018-0187-8303773687250580)
Bolyen, E. et al. Nat. Biotechnol. 37, 852–857 (2019). (PMID: 10.1038/s41587-019-0209-9313412887015180)
Caporaso, J. G. et al. Nat. Methods 7, 335–336 (2010). (PMID: 10.1038/nmeth.f.303203831313156573)
Bolyen, E. et al. J. Open Source Educ. 1, 27 (2018). (PMID: 10.21105/jose.00027306878456343836)
Grant Information:
DE-SC0024320 U.S. Department of Energy (DOE); DE-SC0024320 U.S. Department of Energy (DOE)
Entry Date(s):
Date Created: 20251211 Latest Revision: 20251211
Update Code:
20251212
DOI:
10.1038/s41592-025-02981-z
PMID:
41381898
Database:
MEDLINE

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Competing interests: R.K. is a scientific advisory board member and consultant for BiomeSense, Inc., and has equity in and receives income from the company. He is a scientific advisory board member for and has equity in GenCirq. He is a consultant for and receives income from DayTwo. He has equity in and acts as a consultant for Cybele. He is a co-founder of Biota, Inc., and has equity in the company. He is a cofounder of Micronoma, and has equity in and is a scientific advisory board member for the company. The terms of these arrangements have been reviewed and approved by the University of California, San Diego, in accordance with its conflict of interest policies. D.M. is a consultant for BiomeSense, Inc., and has equity in and receives income from the company. The terms of these arrangements have been reviewed and approved by the University of California, San Diego, in accordance with its conflict of interest policies. Y.V.-B. is a full-time employee for BiomeSense, Inc., and has equity in and receives income from the company. J.R.R. is a full-time employee for One Codex, Inc., and has equity in and receives income from the company. J.G.C. and E.B. have equity in and receive income from Cymis Benefit Corp. J.C.A.’s contribution to this work was completed before he joined Amazon Robotics. All other authors declare no competing interests.