title: CGHAnalyzer: a stand-alone software package for cancer genome analysis using array-based DNA copy number data.
abstract: 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).
authors.affiliation: Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors.forename: Adam A
authors.initials: AA
authors.lastname: Margolin
authors.forename: Joel
authors.initials: J
authors.lastname: Greshock
authors.forename: Tara L
authors.initials: TL
authors.lastname: Naylor
authors.forename: Yael
authors.initials: Y
authors.lastname: Mosse
authors.forename: John M
authors.initials: JM
authors.lastname: Maris
authors.forename: Graham
authors.initials: G
authors.lastname: Bignell
authors.forename: Alexander I
authors.initials: AI
authors.lastname: Saeed
authors.forename: John
authors.initials: J
authors.lastname: Quackenbush
authors.forename: Barbara L
authors.initials: BL
authors.lastname: Weber
mesh_terms: 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