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GenePool

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GenePool is a software package that provides analysis tools for the detection of shifts in relative allele frequency between pooled genomic DNA from cases and controls using SNP-based genotyping microarrays.

Version 0.9.1 is the beta release of the redesigned GenePool. This version strives to be multi-plaform. Runnable on OSX, Windows, and Unix like systems. The source code is C++, and to facilitate cross platform operability, the boost library is used and is an additional dependency when compiling. The purpose of the GenePool redesign was to implement changes in development and usability. The current object orient code design facilitates modification and extension of algorithms. The usability of Version 0.9.1 differs drastically from that of 0.8.1. There are three major usability differences.

First, there is only one executable. In order to run an extraction, a normalization, and an analysis, a different option must be used; namely -e, -n, and -a.

Second, extraction and analysis parameters are specified in a formatted text file that can be saved, modified and reused. Third, the extraction process creates a universal data file (.udf). This file contains experimental information, annotations and the raw data of the the chip sets being used for an experiment.

To start using this version please download the examples. Use the "--help" option with the GenePool executable to view options.

This is beta software, and we would appreciate any feedback concerning bugs and or design issues. If you have any problems installing or using GenePool or you have suggestions about how to improve the software, please contact the development team at: genepool-help@tgen.org.