SimHap statistics
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SimHap specifications
Information
| Unique identifier | OMICS_00246 |
|---|---|
| Name | SimHap |
| Software type | Package/Module |
| Interface | Graphical user interface |
| Restrictions to use | None |
| Operating system | Unix/Linux, Mac OS, Windows |
| Programming languages | R |
| Computer skills | Medium |
| Stability | Stable |
| Maintained | Yes |
Versioning
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Publication for SimHap
SimHap citations
(15)Association of the Common Genetic Polymorphisms and Haplotypes of the Chymase Gene with Left Ventricular Mass in Male Patients with Symptomatic Aortic Stenosis
[…] analyze the effects of multiple covariates on a continuous outcome. Haplotypes were inferred for individuals with ambiguous phase, and the haplotype frequencies were estimated and analyzed using the SimHap software . P-values <0.0125 were designated as significant based on the Bonferroni correction for multiple comparisons of the four htSNPs, which were evaluated as independent statistical tests […]
A comprehensive investigation of variants in genes encoding adiponectin (ADIPOQ) and its receptors (ADIPOR1/R2), and their association with serum adiponectin, type 2 diabetes, insulin resistance and the metabolic syndrome
[…] d using a natural logarithm transformation prior to analysis. Associations between transformed values and genotypes at each tSNP were examined using a generalised linear model approach implemented in SimHap []. Each polymorphism was modelled as a genotypic (codominant) genetic effect, accommodating the effects of age, gender, and BMI as significant covariates. We determined marginal geometric mean […]
Determinants of Human Adipose Tissue Gene Expression: Impact of Diet, Sex, Metabolic Status, and Cis Genetic Regulation
[…] ion equations displayed in the legend of the tables. Genotype frequency and Hardy-Weinberg equilibrium were tested using SNP assoc package. Genetic association to gene expression was tested using the SimHap package. The effect of sex was tested using chi2 test and Fisher's exact test. A Benjamini-Hochberg procedure was used to control the false discovery rate at 5% with the multtest package (mt.r […]
A replicated association between polymorphisms near TNFα and risk for adverse reactions to radiotherapy
[…] lained adverse reactions).Statistical analysis used SPSS v16.0 (IBM software, Armonk, NY, USA). Genetic analysis was carried out using the Plink v1.07 (http://pngu.mgh.harvard.edu/purcell/plink/) and SimHap v1.02 (http://www.genepi.meddent.uwa.edu.au/ software/simhap). For calculation of empirical P-values 20 000 permutations were performed. […]
Interleukin 1 Two Locus Haplotype Is Strongly Associated with Severe Chronic Periodontitis among Yemenis
[…] correlation coefficient (r 2), and log of the likelihood odds ratio (LOD), the later being a measure of significance (LOD > 2 is significant). Haplotyping at the subject level was performed using the SimHap software (Centre for Genetic Epidemiology and Biostatistics, University of Western Australia), which employs the estimation-maximization (EM) algorithm for the estimation of haplotypes []. […]
Disorder specific effects of polymorphisms at opposing ends of the Insulin Degrading Enzyme gene
[…] on of test statistic distributions under the null and alternative hypothesis. All association and power analyses were performed in R version 2.10.0 using the packages geepack, pwr, powerMediation and SimHap (all obtained from http://www.r-project.org). […]
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