GeneClust

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Description

GeneClust is a piece of computer software which can be used as a tool for exploratory analysis of gene expression microarray data. The development of GeneClust was motivated by surging interest to search for interpretable biological structure in gene expression microarray data.

GeneClust includes two basic functions:

1. Implementation of clustering methods
   1. Hierarchical clustering
   2. Gene shaving
2. Simulation to assess performance of the above methods.

GeneClust is a suite of S-plus functions and C routines with a graphical user interface. This allows the user the ability to interact directly with the program, to have visualization power of the data and resulting clusters, and to have control of numerous intermediate output results.

Screenshots

Taken from our laptop running RedHat 7.1 and S-plus 6.0.
Multiple resolutions for all images are available:

• Starting Up
• About System Info
• Running in Demo Mode
• Gene Expression Matrix
• Cluster Plots
• Gap Curve Graphs
• Variance Graphs
• Principal Component Graphs

GeneClust for S-PLUS

Documentation

• GeneClust for S-PLUS User's Guide

Requirements

• UNIX
  • S-plus 5.1 or 6.0
  • JRE SE 1.3.1 or later
• Win2000
  • S-plus 2000 or 6.0

Download Packages

The current version for S-PLUS is 1.0b11, available as of 28 March 2002. Here are some links to download various binary packages. The source package is not publicly available at this time; contact Dr. Kim-Anh Do for private access to the source package. The following are the supported platforms.

• Sun Solaris 2.8
• Compaq Tru64 4.0f
• RedHat Linux 7.1 (IA32)
• Win2000
• Win2000 (R/.NET version)

GeneClust for R

Documentation

• GeneClust for R User's Guide

Requirements

The R version is available only as a source code package. Instructions are provided for compiling the source code for your platform. Any recent version of R and Linux should work.

Download Packages

The current (only) version for R is 1.0.0, available as of August 2006.

• Release 1.0.0

Credits

• Kim-Anh Do, Ph.D.
• Rumiana Nikolova
• Paul Roebuck
• Bradley Broom, Ph.D.

References

• Trevor Hastie, Robert Tibshirani, Michael Eisen, Patrick Brown, Doug Ross,
  Uwe Scherf, John Weinstein, Ash Alizadeh, Louis Staudt and David Botstein (2000).
  

  Gene Shaving: a New Class of Clustering Methods for Expression Arrays (HTML)

  Technical Report, Department of Statistics, Stanford University

  
  
• Robert Tibshirani, Trevor Hastie, Mike Eisen, Doug Ross, David Botstein and Patrick Brown (1999).
  

  Clustering Methods for the Analysis of DNA Microarray Data (PS)

  Technical Report, Department of Statistics, Stanford University

  
  
• Laura Lazzeroni and Art Owen (2000).
  

  Plaid Model for Gene Expression Data (PS, PDF)

  Technical Report, Department of Statistics, Stanford University

  
  

Created by P. Roebuck.

Contact me by email: roebuck@mdanderson.org

Last updated by B. Broom.

Contact me by email: bmbroom@mdanderson.org