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Orchestrating single-cell analysis with Bioconductor

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

in 631/1647/2217 / 631/1647/794 / Analysis / Bioinformatics / Biological Microscopy / Biological Techniques / Biomedical and Life Sciences / Biomedical Engineering/Biotechnology / Computer applications / Computer programs / Data visualization / Gene Expression Profiling / Genome / Genomes / Genomics / High-Throughput Nucleotide Sequencing / Infrastructure / Life Sciences / Open source software / Perspective / Proteomics / Public domain / Public software / Scientific visualization / Single-Cell Analysis - methods / Software / Source code

2020

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2020

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2020

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Journal Article

Orchestrating single-cell analysis with Bioconductor

Pagès, Hervé,

Waldron, Levi,

Geistlinger, Ludwig,

Risso, Davide,

Huber, Wolfgang,

Carpp, Lindsay N.,

Carey, Vince J.,

Gottardo, Raphael,

Becht, Etienne,

Marini, Federico,

Smith, Mike L.,

Lun, Aaron T. L.,

Rue-Albrecht, Kevin,

Soneson, Charlotte,

Hicks, Stephanie C.,

Amezquita, Robert A.,

Morgan, Martin

2020

Overview

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. This Perspective highlights open-source software for single-cell analysis released as part of the Bioconductor project, providing an overview for users and developers.

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Publisher

Nature Publishing Group US,Nature Publishing Group

Subject

/ Biological Microscopy

/ Biological Techniques

/ Biomedical and Life Sciences