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

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Saeed AI, Bhagabati NK, Braisted JC, Liang W, Sharov V, Howe EA, et al. TM4 microarray software suite. Methods in Enzymology. 2006;411:134-93. Abstract

Saeed AI, Sharov V, White J, Li J, Liang W, Bhagabati N, et al. TM4: a free, open-source system for microarray data management and analysis. Vol 34.; 2003.

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

Publication Type:

Journal Article

Authors:

Margolin,Adam A; Greshock,Joel; Naylor,Tara L; Mosse,Yael; Maris,John M; Bignell,Graham; Saeed,Alexander I; Quackenbush,John; Weber,Barbara L

Source:

Bioinformatics (Oxford, England), Volume 21, Issue 15, p.3308 - 3311 (2005)

ISBN:

1367-4803

URL:

http://www.ncbi.nlm.nih.gov/pubmed/15905276

Keywords:

Comparative Genomic Hybridization

Abstract:

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).