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


BACKGROUND
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).
Margolin
Adam A
AA
Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
Greshock
Joel
J
Naylor
Tara L
TL
Mosse
Yael
Y
Maris
John M
JM
Bignell
Graham
G
Saeed
Alexander I
AI
Quackenbush
John
J
Weber
Barbara L
BL
D000465:Algorithms; D000818:Animals; D002874:Chromosome Mapping / Q000379:methods*; D003196:Computer Graphics; D004252:DNA Mutational Analysis / Q000379:methods*; D018628:Gene Dosage; D006801:Humans; D009369:Neoplasms / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012984:Software; D014584:User-Computer Interface