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Bioconductor: open software development for computational biology and bioinformatics

Genome biology · 2004 · Vol. 5(10) · pp. R80–R80

Robert Gentleman✉(Dana-Farber/Harvard Cancer Center)Vincent J. Carey(Brigham and Women's Hospital)Douglas M. Bates(University of Wisconsin–Madison)Ben Bolstad(University of California, Berkeley)Marcel DettlingSandrine Dudoit(University of California, Berkeley)Byron Ellis(Harvard University)Laurent Gautier(Technical University of Denmark)Yongchao Ge(Icahn School of Medicine at Mount Sinai)Jeff Gentry(Dana-Farber Cancer Institute)Kurt Hornik(Statistics Austria)Torsten Hothorn(Friedrich-Alexander-Universität Erlangen-Nürnberg)Wolfgang Huber(German Cancer Research Center)Stefano M. Iacus(University of Milan)Rafael A. Irizarry(Johns Hopkins University)Friedrich Leisch(Statistics Austria)Cheng Li(Dana-Farber Cancer Institute)Martin MaechlerAnthony Rossini(University of Washington)Günther Sawitzki(Institut für Angewandte Statistik)Colin A. Smith(Scripps Research Institute)Gordon K. Smyth(Walter and Eliza Hall Institute of Medical Research)Luke Tierney(University of Iowa)Jean YangJianhua Zhang(Dana-Farber Cancer Institute)

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Abstract

The Bioconductor project is an initiative for the collaborative creation of 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 methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples.

Scientific Computing and Data Management Genetics, Bioinformatics, and Biomedical Research Single-cell and spatial transcriptomicsBioconductorSoftwareBiologyData scienceBioinformaticsComputer scienceComputational biologySoftware engineeringGeneticsProgramming language