Software

SimHap GUI: An intuitive graphical user interface for genetic association analysis

Kim W Carter^1,4 , Pamela A McCaskie^2,3 and Lyle J Palmer³

¹  Western Australian Institute for Medical Research and UWA Centre for Medical Research, University of Western Australia, Perth, Australia

²  School of Mathematics and Statistics, University of Western Australia, Perth, Australia

³  Centre for Genetic Epidemiology and Biostatistics, University of Western Australia, Perth, Australia

⁴  Telethon Institute for Child Health Research, UWA Centre for Child Health Research, University of Western Australia, 100 Roberts Rd, Subiaco, Western Australia 6008, Australia

author email corresponding author email

BMC Bioinformatics 2008, 9:557doi:10.1186/1471-2105-9-557

Published:	25 December 2008

Abstract

Background

Researchers wishing to conduct genetic association analysis involving single nucleotide polymorphisms (SNPs) or haplotypes are often confronted with the lack of user-friendly graphical analysis tools, requiring sophisticated statistical and informatics expertise to perform relatively straightforward tasks. Tools, such as the SimHap package for the R statistics language, provide the necessary statistical operations to conduct sophisticated genetic analysis, but lacks a graphical user interface that allows anyone but a professional statistician to effectively utilise the tool.

Results

We have developed SimHap GUI, a cross-platform integrated graphical analysis tool for conducting epidemiological, single SNP and haplotype-based association analysis. SimHap GUI features a novel workflow interface that guides the user through each logical step of the analysis process, making it accessible to both novice and advanced users. This tool provides a seamless interface to the SimHap R package, while providing enhanced functionality such as sophisticated data checking, automated data conversion, and real-time estimations of haplotype simulation progress.

Conclusion

SimHap GUI provides a novel, easy-to-use, cross-platform solution for conducting a range of genetic and non-genetic association analyses. This provides a free alternative to commercial statistics packages that is specifically designed for genetic association analysis.