A SNP-set (e.g., a gene or a region) level test for association between a set of rare (or common) variants and dichotomous or quantitative phenotypes. SKAT aggregates individual score test statistics of SNPs in a SNP set and efficiently computes SNP-set level p-values, e.g. a gene or a region level p-value, while adjusting for covariates, such as principal components to account for population stratification. SKAT also allows for power/sample size calculations for designing for sequence association studies.
Provides various next-generation sequencing (NGS) data analysis applications which are developed or optimized by Illumina, or from a growing ecosystem of third-party app providers. BAseSpace is a cloud platform that can be integrated with the industry’s leading sequencing platforms, without cumbersome or time consuming data transfer steps.
A suite of R routines for the analysis of indirectly measured haplotypes. The statistical methods assume that all subjects are unrelated and that haplotypes are ambiguous (due to unknown linkage phase of the genetic markers). The main functions are: haplo.em, haplo.glm, haplo.score, haplo.power, and seqhap.
Performs genetic association analysis. UNPHASED is an application that permits users to analyze nuclear families and unrelated subjects, discrete or quantitative traits. It also provides global association tests, tests of individual haplotypes and permutation tests that allows for multiple testing. This method supports non-genetic covariates including parent-of-origin.
Provides haplotype analysis in unrelated individuals that can treat quantitative, binary, survival and polychotomous phenotype analyses. THESIAS is a multiple-imputation algorithm that never assigns haplotype to individuals. It is based on the Stochastic Expectation Maximisation (SEM) algorithm, a method that has the advantage over the standard EM algorithm of being more robust to problems of lack of convergence and convergence to local minima.
An R package that performs Logistic Bayesian Lasso for finding association of SNP haplotypes and environmental factors with a trait in a case-control setting. Bayesian lasso is used to find the posterior distributions of logistic regression coefficients, which are then used to calculate Bayes Factor to test for association.
Provides an assortment of methods to establish and fit a wide range of models. BhGLM offers an R package which is developed to handle about six different types of models including Bayesian hierarchical, negative binomial, or Cox survival models. The application includes features to compute measures to evaluate a given model as well as utilities which serves to numerically and graphically summarize it.