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PMID: 25633503 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. Review

Orchestrating high-throughput genomic analysis with Bioconductor.

Nature methods ·Vol. 12 ·No. 2 ·2015-02-00 ·Pages 115-21

Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M

Abstract

Bioconductor is an open-source, open-development software project for the analysis and comprehension of high-throughput data in genomics and molecular biology. The project aims to enable interdisciplinary research, collaboration and rapid development of scientific software. Based on the statistical programming language R, Bioconductor comprises 934 interoperable packages contributed by a large, diverse community of scientists. Packages cover a range of bioinformatic and statistical applications. They undergo formal initial review and continuous automated testing. We present an overview for prospective users and contributors.

MeSH Terms
Computational Biology Gene Expression Profiling Genomics/methods High-Throughput Screening Assays/methods Programming Languages Software User-Computer Interface
Authors & Affiliations
26 authors, click to expand affiliations / ORCID
Huber Wolfgang ORCID
European Molecular Biology Laboratory, Heidelberg, Germany.
Carey Vincent J
1] Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA. [2] Harvard School of Public Health, Boston, Massachusetts, USA.
Gentleman Robert
Genentech, South San Francisco, California, USA.
Anders Simon ORCID
European Molecular Biology Laboratory, Heidelberg, Germany.
Carlson Marc
Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.
Carvalho Benilton S ORCID
Department of Medical Genetics, School of Medical Sciences, State University of Campinas, Campinas, Brazil.
Bravo Hector Corrada
Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA.
Davis Sean ORCID
Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA.
Gatto Laurent ORCID
Department of Biochemistry, University of Cambridge, Cambridge, UK.
Girke Thomas
Institute for Integrative Genome Biology, University of California, Riverside, Riverside, California, USA.
Gottardo Raphael
Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.
Hahne Florian
Novartis Institutes for Biomedical Research, Basel, Switzerland.
Hansen Kasper D
1] McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, USA. [2] Department of Biostatistics, Johns Hopkins University, Baltimore, Maryland, USA.
Irizarry Rafael A
1] Harvard School of Public Health, Boston, Massachusetts, USA. [2] Dana-Farber Cancer Institute, Boston, Massachusetts, USA.
Lawrence Michael
Genentech, South San Francisco, California, USA.
Love Michael I ORCID
1] Harvard School of Public Health, Boston, Massachusetts, USA. [2] Dana-Farber Cancer Institute, Boston, Massachusetts, USA.
MacDonald James
Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, USA.
Obenchain Valerie
Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.
Oleś Andrzej K
European Molecular Biology Laboratory, Heidelberg, Germany.
Pagès Hervé
Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.
Reyes Alejandro
European Molecular Biology Laboratory, Heidelberg, Germany.
Shannon Paul
Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.
Smyth Gordon K
1] Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia. [2] Department of Mathematics and Statistics, University of Melbourne, Parkville, Victoria, Australia.
Tenenbaum Dan
Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.
Waldron Levi
School of Urban Public Health at Hunter College, City University of New York, New York, New York, USA.
Morgan Martin ORCID
Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.
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Article Info
Journal
Nature methods
Abbr.
Nat Methods
ISSN
1548-7105
DOI
10.1038/nmeth.3252
Published
2015-02-00
Pages
115-21
Language
English
Region
United States
NLM ID
101215604
PMCID
PMC4509590
Subset
IM
Grants
NCI NIH HHS · P30 CA016056 · United States
NHGRI NIH HHS · P41 HG004059 · United States
NHGRI NIH HHS · U41 HG004059 · United States
NHGRI NIH HHS · U41HG004059 · United States
External Links
PubMed source DOI: 10.1038/nmeth.3252 PMC Full Text View journal details
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