GeneCluster 2.0: an advanced toolset for bioarray analysis.
CONCLUSIONS
GeneCluster 2.0 is a software package for analyzing gene expression and other bioarray data, giving users a variety of methods to build and evaluate class predictors, visualize marker lists, cluster data and validate results. GeneCluster 2.0 greatly expands the data analysis capabilities of GeneCluster 1.0 by adding classification, class discovery and permutation test methods. It includes algorithms for building and testing supervised models using weighted voting and k-nearest neighbor algorithms, a module for systematically finding and evaluating clustering via self-organizing maps, and modules for marker gene selection and heat map visualization that allow users to view and sort samples and genes by many criteria. GeneCluster 2.0 is a stand-alone Java application and runs on any platform that supports the Java Runtime Environment version 1.3.1 or greater.


BACKGROUND
http://www.broad.mit.edu/cancer/software
Reich
M
M
The Eli and Edythe L. Broad Institute, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02141, USA.
Ohm
K
K
Angelo
M
M
Tamayo
P
P
Mesirov
J P
JP
D000465:Algorithms; D016000:Cluster Analysis; D003196:Computer Graphics; D004247:DNA / Q000032:analysis / Q000737:chemistry / Q000145:classification; D020869:Gene Expression Profiling / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010363:Pattern Recognition, Automated; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D014584:User-Computer Interface
D004247:DNA