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Bioinformatics Advance Access published online on August 27, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth495
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received April 2, 2004
Revised August 18, 2004
Accepted August 19, 2004

Applications note

OntologyTraverser: an R package for GO analysis

A. Young 1, N. Whitehouse 1, J. Cho 1, C. Shaw 1*

1 Baylor College of Medicine, Department of Molecular and Human Genetics, Houston, Texas, USA

* To whom correspondence should be addressed. E-mail: cashaw{at}bcm.tmc.edu.


  Abstract

Gene Ontology annotations have become a major tool for analysis of genome scale experiments. We have created OntologyTraverser - an R package for GO analysis of gene lists. Our system is a major advance over previous work because (a) the system can be installed as an R package (b) the system uses Java to instantiate the GO structure and the SJava system to integrate R and Java and (c) the system is also deployed as a publicly available web-tool.

Availability Our software is academically available through http://franklin.imgen.bcm.tmc.edu/OntologyTraverser/. Both the R package and the web-tool are accessible.


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