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Bioinformatics Advance Access published online on August 5, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth458
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received May 28, 2004
Revised July 12, 2004
Accepted July 27, 2004

Article

Network structures and algorithms in Bioconductor

Vincent J. Carey 1*, Jeff Gentry 2, Elizabeth Whalen 2, Robert Gentleman 2

1 Channing Laboratory, Brigham and Women's Hospital, 75 Francis Street, Boston, 02115, USA
2 Division of Biostatistics, Dana Farber Cancer Institute, 44 Binney Street, Boston, 02115, USA

* To whom correspondence should be addressed. E-mail: stvjc{at}channing.harvard.edu.


  Abstract

Summary: This paper reviews the central concepts and implementations of tools for working with network structures in Bioconductor. Interfaces to open source resources for visualization (AT&T Graphviz) and network algorithms (Boost) have been developed to support analysis of graphical structures in genomics and computational biology.

Availability: Packages graph, Rgraphviz, RBGL of Bioconductor (www.bioconductor.org). Open source.


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