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Usage
==================
This software provides a biclustering module for microarray data. For a set of genes and a set of conditions, the program outputs a block-like structure which shows uniform pattern within the block, the block would contain only subsets of all given genes under subsets of all given conditions. 

Certain parts of the code uses open-source data structure library codes, including:
- fib <http://resnet.uoregon.edu/~gurney_j/jmpc/fib.html>, copyright information in fib.c
- Mark A. Weiss's data structure codes <http://www.cs.fiu.edu/~weiss/>

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Installation
==================
.. note::
    qubic currently will only run on linux platform, as it is dependent on GNU function.

Simply put "qubic0.1.tar.gz" in any directory, 

$ tar zxvf qubic0.1.tar.gz

enter the folder "qubic0.1" and type "make" then the compiled codes are within the same directory as the source.


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Inputs and outputs
==================
The major program in the provided package is `gcluster`, it can parse two 
formats of files, discrete data and continuous data, and examples for each
are provided. See help and look at all available options.

$ ./qubic -h

Take a look at `toy_example` (discrete data) first. And try to run clustering

$ ./qubic -i toy_example -d

-d is important here since it tells the program that this is discrete data.

Then look at a larger file `yeast_example` (continuous data). Try to run

$ ./qubic -i yeast_examaple -k 20 -q .06

This restricts the block width to be 20 and use 6% tails for quantile discretization.

The algorithm work for discrete data only so the program works by discretize first. For each row, it finds significantly small or large numbers (default 6% tail from distribution) and then adjust the data need to be discreted similar to outlier detection algorithm (see details in Algorithm design in paper), the entries which are lower (upper) than the value low (up), which we will export to a '.rules' file, are considered as down (up)-regulated. Look at a generated '.rules' file and a `.chars` file.

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Changelog
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Version 0.1 
- prototype of algorithm

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Contact
==================
Any questions, problems, bugs are welcome and should be dumped to
Qin Ma <maqin@csbl.bmb.uga.edu>

Creation: Dec. 16, 2008

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