GeneClust for R v1.0, Windows 98,NT,2000,NP
	Table of Contents: Description Download and Installation User Interface Input/Output
	Description: Gene Shaving is a method for clustering groups of similarly behaving genes whose changes in expression are most tightly linked to observed biological changes. The basic method is similar to observed principal components (singular value decomposition, maximum eigenvalue, etc.) with a sequential twist: a canonical "gene vector" is identified based on the eigenvectors, and the genes are ranked according to their agreement with this vector. The worst fitting are then "shaved off" and a new canonical vector is identified and fit. The GeneClust distribution for Windows consists of a simple user interface and an R back-end which calls various C functions implementing the statistical method. Installation & Requirements: Please create a folder named "GeneClust" on your main drive. Copy GeneClust.zip and expand it in that folder using WinZip (a free evaluation version can be downloaded from http://www.winzip.com/). Please note the directory structure needs to be preserved for GeneClust to run properly. You need the following installed on your PC in order to run GeneClust: -R for Windows , version 1.7.0 or later. Download -Microsoft .NET Framework Redistributable. Download Enjoy the GeneClust application. Please notify us about any problems or contact us with comments and suggestions at: GeneClustWin Return to TOC User Interface: The GeneClust application can process raw data or generate it in demo mode. The information input by the user however is checked for validity. Tooltips containing the allowed ranges are provided for all numerical variables. The set of parameters used can be saved and loaded from the File Menu into configuration files (*.cf). GeneClust in Raw Data Mode Return to TOC GeneClust in Demo Mode Return to TOC GeneClust File and Help Menus Return to TOC Input/Output: · Files: <settings>.clf: Classification file used to perform supervised shaving. <datafile>.tsv: ASCII file that contains tab-separated values. <config> .cf: Configuration file with a the full list of parameters · Directories: o <output>: Stores the output of the algorithm. If the “Postscript output” option in the File Menu is checked, postscript copies of the plots are saved also o <doc> : The directory containing the documentation o <data> : Data file directory. This directory is not needed to run properly GeneClust o <sinterpreter> : R Script directory. This directory must not be altered. Return to TOC Back to Home Page