Orchestrating single-cell analysis with Bioconductor

Robert A. Amezquita; Aaron T.L. Lun; Etienne Becht; Vince J. Carey; Lindsay N. Carpp; Ludwig Geistlinger; Federico Marini; Kevin Rue-Albrecht; Davide Risso; Charlotte Soneson; Levi Waldron; Hervé Pagès; Mike L. Smith; Wolfgang Huber; Martin Morgan; Raphael Gottardo; Stephanie C. Hicks

doi:10.1038/s41592-019-0654-x

Orchestrating single-cell analysis with Bioconductor

Robert A. Amezquita, Aaron T.L. Lun, Etienne Becht, Vince J. Carey, Lindsay N. Carpp, Ludwig Geistlinger, Federico Marini, Kevin Rue-Albrecht, Davide Risso, Charlotte Soneson, Levi Waldron, Hervé Pagès, Mike L. Smith, Wolfgang Huber, Martin Morgan, Raphael Gottardo, Stephanie C. Hicks

Bloomberg School of Public Health

Research output: Contribution to journal › Article › peer-review

39 Scopus citations

Abstract

Recent technological advancements have enabled the profiling of a large number of genome-wide features in individual cells. However, single-cell data present unique challenges that require the development of specialized methods and software infrastructure to successfully derive biological insights. The Bioconductor project has rapidly grown to meet these demands, hosting community-developed open-source software distributed as R packages. Featuring state-of-the-art computational methods, standardized data infrastructure and interactive data visualization tools, we present an overview and online book (https://osca.bioconductor.org) of single-cell methods for prospective users.

Original language	English (US)
Pages (from-to)	137-145
Number of pages	9
Journal	Nature Methods
Volume	17
Issue number	2
DOIs	https://doi.org/10.1038/s41592-019-0654-x
State	Published - Feb 1 2020

ASJC Scopus subject areas

Biotechnology
Biochemistry
Molecular Biology
Cell Biology

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abstract = "Recent technological advancements have enabled the profiling of a large number of genome-wide features in individual cells. However, single-cell data present unique challenges that require the development of specialized methods and software infrastructure to successfully derive biological insights. The Bioconductor project has rapidly grown to meet these demands, hosting community-developed open-source software distributed as R packages. Featuring state-of-the-art computational methods, standardized data infrastructure and interactive data visualization tools, we present an overview and online book (https://osca.bioconductor.org) of single-cell methods for prospective users.",

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AU - Lun, Aaron T.L.

AU - Becht, Etienne

AU - Carey, Vince J.

AU - Carpp, Lindsay N.

AU - Geistlinger, Ludwig

AU - Marini, Federico

AU - Rue-Albrecht, Kevin

AU - Risso, Davide

AU - Soneson, Charlotte

AU - Waldron, Levi

AU - Pagès, Hervé

AU - Smith, Mike L.

AU - Huber, Wolfgang

AU - Morgan, Martin

AU - Gottardo, Raphael

AU - Hicks, Stephanie C.

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Orchestrating single-cell analysis with Bioconductor

Abstract

ASJC Scopus subject areas

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