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Orchestrating Single-Cell Analysis with Bioconductor

View ORCID ProfileRobert A. Amezquita, Vince J. Carey, View ORCID ProfileLindsay N. Carpp, View ORCID ProfileLudwig Geistlinger, View ORCID ProfileAaron T. L. Lun, View ORCID ProfileFederico Marini, View ORCID ProfileKevin Rue-Albrecht, View ORCID ProfileDavide Risso, View ORCID ProfileCharlotte Soneson, View ORCID ProfileLevi Waldron, Hervé Pagès, View ORCID ProfileMike Smith, View ORCID ProfileWolfgang Huber, Martin Morgan, View ORCID ProfileRaphael Gottardo, View ORCID ProfileStephanie C. Hicks
doi: https://doi.org/10.1101/590562
Robert A. Amezquita
1Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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  • ORCID record for Robert A. Amezquita
Vince J. Carey
2Channing Division of Network Medicine, Brigham And Women’s Hospital, MA, USA
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Lindsay N. Carpp
1Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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Ludwig Geistlinger
3Graduate School of Public Health and Health Policy, City University of New York, NY, USA
4Institute for Implementation Science in Population Health, City University of New York, NY, USA
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Aaron T. L. Lun
5Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
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Federico Marini
6Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), Mainz, Germany
7Center for Thrombosis and Hemostasis, Mainz, Germany
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Kevin Rue-Albrecht
8Kennedy Institute of Rheumatology, University of Oxford, Oxford, OX3 7FY, UK
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  • ORCID record for Kevin Rue-Albrecht
Davide Risso
9Department of Statistical Sciences, University of Padua, Italy
10Division of Biostatistics and Epidemiology, Department of Healthcare Policy and Research, Weill Cornell Medicine, New York, NY, USA
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Charlotte Soneson
11Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
12SIB Swiss Institute of Bioinformatics, Basel, Switzerland
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  • ORCID record for Charlotte Soneson
Levi Waldron
3Graduate School of Public Health and Health Policy, City University of New York, NY, USA
4Institute for Implementation Science in Population Health, City University of New York, NY, USA
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Hervé Pagès
1Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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Mike Smith
13European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
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Wolfgang Huber
13European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
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Martin Morgan
14Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
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Raphael Gottardo
1Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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Stephanie C. Hicks
15Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, MD, USA
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  • For correspondence: shicks19@jhu.edu
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Abstract

Recent developments in experimental technologies such as single-cell RNA sequencing have enabled the profiling a high-dimensional number of genome-wide features in individual cells, inspiring the formation of large-scale data generation projects quantifying unprecedented levels of biological variation at the single-cell level. The data generated in such projects exhibits unique characteristics, including increased sparsity and scale, in terms of both the number of features and the number of samples. Due to these unique characteristics, specialized statistical methods are required along with fast and efficient software implementations in order to successfully derive biological insights. Bioconductor - an open-source, open-development software project based on the R programming language - has pioneered the analysis of such high-throughput, high-dimensional biological data, leveraging a rich history of software and methods development that has spanned the era of sequencing. Featuring state-of-the-art computational methods, standardized data infrastructure, and interactive data visualization tools that are all easily accessible as software packages, Bioconductor has made it possible for a diverse audience to analyze data derived from cutting-edge single-cell assays. Here, we present an overview of single-cell RNA sequencing analysis for prospective users and contributors, highlighting the contributions towards this effort made by Bioconductor.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted March 27, 2019.
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Orchestrating Single-Cell Analysis with Bioconductor
Robert A. Amezquita, Vince J. Carey, Lindsay N. Carpp, Ludwig Geistlinger, Aaron T. L. Lun, Federico Marini, Kevin Rue-Albrecht, Davide Risso, Charlotte Soneson, Levi Waldron, Hervé Pagès, Mike Smith, Wolfgang Huber, Martin Morgan, Raphael Gottardo, Stephanie C. Hicks
bioRxiv 590562; doi: https://doi.org/10.1101/590562
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Orchestrating Single-Cell Analysis with Bioconductor
Robert A. Amezquita, Vince J. Carey, Lindsay N. Carpp, Ludwig Geistlinger, Aaron T. L. Lun, Federico Marini, Kevin Rue-Albrecht, Davide Risso, Charlotte Soneson, Levi Waldron, Hervé Pagès, Mike Smith, Wolfgang Huber, Martin Morgan, Raphael Gottardo, Stephanie C. Hicks
bioRxiv 590562; doi: https://doi.org/10.1101/590562

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