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ChromoScan
ChromoScan is a software implementation of a genome-based scan statistic that detects genomic regions which are statistically significant for targeted measurements such as genetic associations with disease, gene expression profiles, DNA copy number variations, as well as other genome based measurements. A Java graphic user interface (GUI) is provided to help users to select appropriate data transformation and threshold for defining the significant events.
Operating Requirements
ChromoScan requires a Java Runtime Environment version 1.5 or greater. The authors have only tested ChromoScan in Windows and Linux with the Sun JDK 1.5.006 and 1.5.007. Other versions on other platforms of 1.5 compliant JDKs or JREs should work, but have not been tested. To download Sun Java 1.5 go to http://java.sun.com .
Background Information
If you use ChromoScan or ChromoScanGWA in your study, please reference Sun, YV et. al, "ChromoScan: a scan statistic application for identifying chromosomal regions in genomic studies." Bioinformatics 2006 Dec 1. The original algorithm that ChromoScan is based on is a Scan Statistic algorithm published by Sun, YV et. al., "A scan statistic for identifying chromosomal patterns of SNP association." Genet Epidemiol. 2006 Jul 20. If you are interested in obtaining the Java source code for ChromoScan or if you have any questions related to ChromoScan or other software published by the Kardia Research Lab, please contact us via email: KardiaSoftware@umich.edu.
Note for Internet Explorer Users
For security reasons Internet Explorer will rename "chromoscan_1.0.jar" automatically to "chromoscan_1.0.zip" after downloading ChromoScan. In order to use ChromoScan, rename the downloaded zip file to "chromoscan_1.0.jar". Please note that you must have Windows Explorer configured to show file extensions to correct this issue.
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This software was developed using U.S. government grant support at the University of Michigan in the School of Public Health by Dr. Sharon L. R. Kardia's lab staff. The original algorithm implemented by this software is the Scan Statistic algorithm developed by Drs. Yan Sun, Albert Levin, and Sharon Kardia.
ChromoScan is Copyright © 2006 The Regents of the University of Michigan. All Rights Reserved.
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