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SimHap specifications


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


No version available

Publication for SimHap

SimHap citations


Association of the Common Genetic Polymorphisms and Haplotypes of the Chymase Gene with Left Ventricular Mass in Male Patients with Symptomatic Aortic Stenosis

PLoS One
PMCID: 4019480
PMID: 24823657
DOI: 10.1371/journal.pone.0096306
call_split See protocol

[…] 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

BMC Med Genet
PMCID: 3598639
PMID: 23351195
DOI: 10.1186/1471-2350-14-15
call_split See protocol

[…] 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

PLoS Genet
PMCID: 3459935
PMID: 23028366
DOI: 10.1371/journal.pgen.1002959

[…] 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

Br J Cancer
PMCID: 3419947
PMID: 22767148
DOI: 10.1038/bjc.2012.290

[…] lained adverse reactions).Statistical analysis used SPSS v16.0 (IBM software, Armonk, NY, USA). Genetic analysis was carried out using the Plink v1.07 ( and SimHap v1.02 ( 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

PMCID: 3388377
PMID: 22778957
DOI: 10.1155/2012/231309
call_split See protocol

[…] 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

BMC Med Genet
PMCID: 3266204
PMID: 22107728
DOI: 10.1186/1471-2350-12-151

[…] 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 […]


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SimHap institution(s)
Western Australian Institute for Medical Research and UWA Centre for Medical Research, University of Western Australia, Perth, Australia

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