Bioconductor: open software development for computational biology and bioinformatics - PubMed (original) (raw)
doi: 10.1186/gb-2004-5-10-r80. Epub 2004 Sep 15.
Vincent J Carey, Douglas M Bates, Ben Bolstad, Marcel Dettling, Sandrine Dudoit, 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
Affiliations
- PMID: 15461798
- PMCID: PMC545600
- DOI: 10.1186/gb-2004-5-10-r80
Bioconductor: open software development for computational biology and bioinformatics
Robert C Gentleman et al. Genome Biol. 2004.
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.
Figures
Figure 1
Limma analysis of the ALL data. The leftmost numbers are row indices, ID is the Affymetrix HGU95av2 accession number, M is the log ratio of expression, A is the log average expression, and B is the log odds of differential expression.
Figure 2
Heat map (produced by the Bioconductor function heatmap()) of the ALL leukemia data.
Figure 3
Hypergeometric analysis of molecular function enrichment of genes selected in the analysis described in Figure 1.
References
- Bioconductor http://www.bioconductor.org
- GNU operating system - Free Software Foundation http://www.gnu.org
- Dafermos GN. Management and virtual decentralised networks: The Linux project. First Monday. 2001;6(11) http://www.firstmonday.org/issues/issue6_11/dafermos/index.html
- Free Software Project Management HOWTO http://www.tldp.org/HOWTO/Software-Proj-Mgmt-HOWTO
- Torvalds L. The Linux edge. Comm Assoc Comput Machinery. 1999;42:38–39. doi: 10.1145/299157.299165. - DOI
MeSH terms
LinkOut - more resources
Full Text Sources
Other Literature Sources