Single SNP association software tools | Genome-wide association study data analysis
Single nucleotide polymorphisms (SNP) are a type of genetic variation that involves mutation of a single pair of bases in the genome between individuals from the same species. They are the most common form of genetic variation with a frequency of one every 1000 base pairs. SNPs are associated with susceptibility to diseases, as well as responses to pathogens, chemicals, drugs, or vaccines. Whole genome sequencing is a powerful tool for genome-wide association study, and SNPs are used to determine association between a genetic variant and a disease or trait.
Contains classes and methods to help the analysis of whole genome association studies. SNPassoc utilizes S4 classes and extends haplo.stats R package to facilitate haplotype analyses. The package is useful to carry out most common analysis when performing whole genome association studies. These analyses include descriptive statistics and exploratory analysis of missing values, calculation of Hardy-Weinberg equilibrium, analysis of association based on generalized linear models (either for quantitative or binary traits), and analysis of multiple SNPs (haplotype and epistasis analysis). Permutation test and related tests (sum statistic and truncated product) are also implemented.
A free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for steps prior to this (e.g. study design and planning, generating genotype or CNV calls from raw data). Through integration with gPLINK and Haploview, there is some support for the subsequent visualization, annotation and storage of results.
A simple, ready-to-use software which has been designed to analyze genetic-epidemiology studies of association using SNPs. Main capabilities include descriptive analysis, test for Hardy-Weinberg equilibrium and linkage disequilibrium. Analysis of association is based on linear or logistic regression according to the response variable (quantitative or binary disease status, respectively). Analysis of single SNPs: multiple inheritance models (co-dominant, dominant, recessive, over-dominant and log-additive), and analysis of interactions (gene-gene or gene-environment). Analysis of multiple SNPs: haplotype frequency estimation, analysis of association of haplotypes with the response, including analysis of interactions.
An R library for genome-wide association (GWA) analysis. GenABEL implements effective storage and handling of GWA data, fast procedures for genetic data quality control, testing of association of single nucleotide polymorphisms with binary or quantitative traits, visualization of results and also provides easy interfaces to standard statistical and graphical procedures implemented in base R and special R libraries for genetic analysis.
Supplies a method to compute exact values of standard test statistics in linear mixed models. GEMMA is a program built on EMMA software. The application fits three types of models: univariate and multivariate linear mixed model as well as Bayesian sparse linear mixed model. In addition, it estimates variance component and chip heritability. This tool provides a mean to make exact calculations for large genome wide association studies (GWAS).
Performs genetic associations. HelixTree combines an unparalleled set of single nucleotide polymorphism (SNP) analysis and genetic association tools, including population- and family-based association studies. This program supplies features for conducting case/control, quantitative trait loci (QTL) and categorical-type analysis or for identifying genetic signals in the presence of confounding factors. This program can also be used as part of the Golden Helix’ SNP and Variation Suite.
Offers a way to solve large-scale, numerically intensive genome wide association studies (GWAS) calculations on multi-core symmetric multiprocessing computer architectures. SNPRelate permits basic calculations of sample and single nucleotide polymorphism (SNP) eigenvectors. It allows principal component analysis (PCA) and identity-by-descent (IBD) relatedness analysis on genomic data structure (GDS) genotype files. The tool permits to accelerate computations on SNP data.