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Bioinformatics Advance Access originally published online on February 26, 2004
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Bioinformatics 20(11) © Oxford University Press 2004; all rights reserved.

GeneCluster 2.0: an advanced toolset for bioarray analysis

M. Reich , K. Ohm , M. Angelo {dagger}, P. Tamayo and J. P. Mesirov *

The Eli and Edythe L. Broad Institute, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02141, USA

Received on September 3, 2003; accepted on December 3, 2003
Advance Access Publication February 26, 2004

Summary: 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 standalone Java application and runs on any platform that supports the Java Runtime Environment version 1.3.1 or greater.

Availability: http://www.broad.mit.edu/cancer/software

Contact: gc-info{at}broad.wi.mit.edu

* To whom correspondence should be addressed.

{dagger} Present address: Google, Mountain View, CA 94043, USA


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