Bioconductor: open software development for computational biology and bioinformatics

Robert C. Gentleman
Vincent J. Carey
Douglas M. Bates
Ben Bolstad
Marcel Dettling
Sandrine Dudoit, Division of Biostatistics, School of Public Health, University of California, Berkeley
Byron Ellis
Laurent Gautier
Yongchao Ge
Jeff Gentry
Kurt Hornik
Torsten Hothorn
Wolfgang Huber
Stefano Iacus
Rafael Irizarry
Friedrich Leisch
Cheng Li
Martin Maechler
Anthony J. Rossini
Gunther Sawitzki
Colin Smith
Gordon Smyth
Luke Tierney
Jean Y. H. Yang
Jianhua Zhang

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.