GaneSh - a software to cluster expression data by Gibbs sampling procedure
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
Installation and Usage
You will need the java version 1.5 installed on your system.
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.
All data files are simple tab-delimited text files.
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 !!!
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.
VIB / UGent
Bioinformatics & Evolutionary Genomics
+32 (0) 9 33 13807 (phone)
+32 (0) 9 33 13809 (fax)