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Bioinformatics Advance Access published online on May 19, 2005
Bioinformatics, 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@oupjournals.org
Received March 14, 2005
Revised May 2, 2005
Accepted May 13, 2005

Applications note

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*

1 Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA
2 The Children's Hospital of Philadelphia, Philadelphia, PA
3 Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
4 The Institute for Genomic Research, Rockville MD

* To whom correspondence should be addressed.
Barbara L. Weber, E-mail: weberb{at}mail.med.upenn.edu


  Abstract

Summary: This synopsis provides an overview of array-based comparative genomic hybridization (aCGH) 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 data sets, 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 (Saeed, et al., 2003) 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).


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