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Bioinformatics Advance Access originally published online on May 19, 2005
Bioinformatics 2005 21(15):3308-3311; doi:10.1093/bioinformatics/bti500
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

CGHAnalyzer: a stand-alone software package for cancer genome analysis using array-based DNA copy number data

Adam A. Margolin 1, Joel Greshock 1, Tara L. Naylor 1, Yael Mosse 2, John M. Maris 2, Graham Bignell 3, Alexander I. Saeed 4, John Quackenbush 4 and Barbara L. Weber 1,*

1Abramson Family Cancer Research Institute, University of Pennsylvania 514 BRB II/III, 421 Curie Blrd, Philadelphia, PA 19104, USA
2The Children's Hospital of Philadelphia Philadelphia, PA, USA
3Wellcome Trust Sanger Institute Hinxton, Cambridgeshire, UK
4The Institute for Genomic Research Rockville, MD, USA

*To whom correspondence should be addressed.

Summary: This synopsis provides an overview of array-based comparative genomic hybridization data display, abstraction and analysis using CGHAnalyzer, a software suite, designed specifically for this purpose. CGHAnalyzer can be used to simultaneously load copy number data from multiple platforms, query and describe large, heterogeneous datasets and export results. Additionally, CGHAnalyzer employs a host of algorithms for microarray analysis that include hierarchical clustering and class differentiation.

Availability: CGHAnalyzer, the accompanying manual, documentation and sample data are available for download at http://acgh.afcri.upenn.edu. This is a Java-based application built in the framework of the TIGR MeV that can run on Microsoft Windows, Macintosh OSX and a variety of Unix-based platforms. It requires the installation of the free Java Runtime Environment 1.4.1 (or more recent) (http://www.java.sun.com).

Contact: weberb{at}mail.med.upenn.edu

Received on March 14, 2005; revised on May 2, 2005; accepted on May 13, 2005

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