Software

GaneSh

GaneSh - a software to cluster expression data by Gibbs sampling procedure
Copyright (C) 2006-2007 Flanders Interuniversitary Intsitute for Biotechnology (VIB)

This source code is freely distributed under the terms of the GNU General Public License. See the files COPYRIGHT and LICENSE for details.

Written by Anagha Joshi and Tom Michoel

Content

GaneSh.jarGaneSh java jar archive
GaneSh.properties GaneSh properties file
lib java libraries directory
be source code and java classes directory
COPYRIGHT Copyright statement
LICENSE GPL license
MakefuzzyClusters.m matlab script to generate fuzzy clusters

Installation and Usage

You will need the java version 1.5 installed on your system.
The current version of GaneSh is a command-line program. There's no graphical user interface.
First, unzip the package in a given directory, let's say /home/anjos/GaneSh. Then go into the directory where you would like to run an analysis, and call the program with the command:

java -jar /home/anjos/GaneSh/GaneSh.jar

Optionally, you can pass memory size parameters to the java virtual machine, it might help if you have a big dataset:

java -Xmx512m -jar /home/anjos/GaneSh/GaneSh.jar

All the necessary parameters are contained in the file GaneSh.properties. You need to copy this file to the directory where you are going to run GaneSh. That's a simple text file with all the option set with an option=value line. You'll have to edit this file to set the data directory, data file name and so on. There is an example in the GaneSh package.

File formats

All data files are simple tab-delimited text files.
- The datafile contain expression values for every gene.

Structure:
<header line>
gene_id1 description value1 value2 .... valueN
gene_id2 description value1 value2 .... valueN
...
gene_idM description value1 value2 .... valueN

Examples

There is an example data file in the directory "examples". You can give it a try simply by running the following command in the directory where you unzipped the package:

java -jar GaneSh.jar

The GaneSh.property file is set by default to use the example file.

This will generate 10 clusters. Fuzzy clusters could be generated using MakefuzzyClusters.m matlab script.

Last but not least, have fun with GaneSh !!!
Anagha and Tom.





Joshi, A., Van de Peer, Y., Michoel, T. (2008) Analysis of a Gibbs sampler method for model based clustering of gene expression data. Bioinformatics 24(2):176-83.




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