Bioconductor: Open Software Development for Computational Biology and Bioinformatics

Genome Biology, Vol. 5, No. 10, Article. R80, September 2004

16 Pages Posted: 26 Dec 2007

See all articles by Kurt Hornik

Kurt Hornik

Vienna University of Economics and Business Administration - Department of Statistics and Mathematics

Robert C. Gentleman

Dana-Farber/Harvard Cancer Center

Vincent J. Carey

Brigham and Women's Hopsital/Harvard Medical School - Channing Laboratory

Douglas M. Bates

University of Wisconsin - Madison - Department of Statistics

Ben Bolstad

University of California, Berkeley - Division of Biostatistics

Marcel Dettling

ETH Zurich - Seminar for Statistics

Sandrine Dudoit

affiliation not provided to SSRN

Byron Ellis

Harvard University - Department of Statistics

Laurent Gautier

Technical University of Denmark - Centre for Biological Sequence Analysis

Yongchao Ge

Mt. Sinai School of Medicine - Biomathematical Sciences

Jeff Gentry

Dana-Farber/Harvard Cancer Center

Torsten Hothorn

University of Erlangen-Nürnberg

Wolfgang Huber

DKFZ (German Cancer Research Center)

Stefano Maria Iacus

University of Milan - Department of Economics, Business and Statistics

Rafael A. Irizarry

Johns Hopkins University - Bloomberg School of Public Health

Friedrich Leisch

Vienna University of Technology

Cheng Li

Dana-Farber Cancer Institute

Martin Maechler

ETH Zentrum - Seminar für Statistik

Anthony J. Rossini

University of Washington - Department of Medical Education and Biomedical Informatics

Günther Sawitzki

Heidelberg University - StatLab Heidelberg

Colin Smith

affiliation not provided to SSRN

Gordon Smyth

affiliation not provided to SSRN

Luke Tierney

University of Iowa - Department of Statistics & Actuarial Science

Jean Y.H. Yang

The University of Sydney - School of Mathematics and Statistics; The University of Sydney - Charles Perkins Centre

Jianhua Zhang

affiliation not provided to SSRN

Abstract

The Bioconductor project is an initiative for the collaborative creation of the extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry into interdisciplinary scientific research, and promoting the achievement of remote reproducibility of research results. We describe details of our aims and methodes, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples.

Keywords: Genomic data, microarray

JEL Classification: C14, C63

Suggested Citation

Hornik, Kurt and Gentleman, Robert C. and Carey, Vincent J. and Bates, Douglas M. and Bolstad, Ben and Dettling, Marcel and Dudoit, Sandrine and Ellis, Byron and Gautier, Laurent and Ge, Yongchao and Gentry, Jeff and Hothorn, Torsten and Huber, Wolfgang and Iacus, Stefano Maria and Irizarry, Rafael A. and Leisch, Friedrich and Li, Cheng and Maechler, Martin and Rossini, Anthony J. and Sawitzki, Günther and Smith, Colin and Smyth, Gordon and Tierney, Luke and Yang, Jean Y.H. and Zhang, Jianhua, Bioconductor: Open Software Development for Computational Biology and Bioinformatics. Genome Biology, Vol. 5, No. 10, Article. R80, September 2004, Available at SSRN: https://ssrn.com/abstract=620245

Kurt Hornik

Vienna University of Economics and Business Administration - Department of Statistics and Mathematics ( email )

Vienna A-1090, Wien
Austria

Robert C. Gentleman

Dana-Farber/Harvard Cancer Center

450 Brookline Avenue
Boston, MA 02115
United States

Vincent J. Carey (Contact Author)

Brigham and Women's Hopsital/Harvard Medical School - Channing Laboratory ( email )

181 Longwood Avenue
Boston, MA 02115
United States

Douglas M. Bates

University of Wisconsin - Madison - Department of Statistics ( email )

716 Langdon Street
Madison, WI 53706-1481
United States
(608) 263-8531 (Phone)

Ben Bolstad

University of California, Berkeley - Division of Biostatistics

310 Barrows Hall
Berkeley, CA 94720
United States

Marcel Dettling

ETH Zurich - Seminar for Statistics ( email )

ETH Zentrum HG-F 42.1
Raemistr. 101
CH-8092 Zurich, 8092
Switzerland

Sandrine Dudoit

affiliation not provided to SSRN

Byron Ellis

Harvard University - Department of Statistics ( email )

Science Center 7th floor
One Oxford Street
Cambridge, MA 02138-2901
United States

Laurent Gautier

Technical University of Denmark - Centre for Biological Sequence Analysis ( email )

Anker Engelunds Vej 1
Building 101A
Lyngby, 2800
Denmark

Yongchao Ge

Mt. Sinai School of Medicine - Biomathematical Sciences ( email )

One Gustave L. Levy Place
New York, NY 10029-6574
United States

Jeff Gentry

Dana-Farber/Harvard Cancer Center

450 Brookline Avenue
Boston, MA 02115
United States

Torsten Hothorn

University of Erlangen-Nürnberg ( email )

Schloßplatz 4
Erlangen, DE Bavaria 91054
Germany

Wolfgang Huber

DKFZ (German Cancer Research Center)

Stefano Maria Iacus

University of Milan - Department of Economics, Business and Statistics ( email )

Via Conservatorio 7
Milano, 20122
Italy
+390250321461 (Phone)
+3950321505 (Fax)

HOME PAGE: http://www.economia.unimi.it/iacus

Rafael A. Irizarry

Johns Hopkins University - Bloomberg School of Public Health ( email )

615 North Wolfe Street
Baltimore, MD 21205
United States

Friedrich Leisch

Vienna University of Technology ( email )

Wien 1040
Austria

Cheng Li

Dana-Farber Cancer Institute ( email )

450 Brookline Avenue
Boston, MA 02115
United States

Martin Maechler

ETH Zentrum - Seminar für Statistik ( email )

Lausanne CH-1001
Switzerland

Anthony J. Rossini

University of Washington - Department of Medical Education and Biomedical Informatics ( email )

Seattle, WA 98195
United States

Günther Sawitzki

Heidelberg University - StatLab Heidelberg ( email )

Im Neuenheimer Feld 294
Heidelberg, 69120
Germany

Colin Smith

affiliation not provided to SSRN

Gordon Smyth

affiliation not provided to SSRN

Luke Tierney

University of Iowa - Department of Statistics & Actuarial Science ( email )

Iowa City, IA 52242-1409
United States

Jean Y.H. Yang

The University of Sydney - School of Mathematics and Statistics

Sydney, New South Wales 2006
Australia

The University of Sydney - Charles Perkins Centre ( email )

Sydney, 2006
Australia

Jianhua Zhang

affiliation not provided to SSRN

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