Main logo
?
tutorial arrow
×
Submit new tools
Share tools covering the current topic. Provide easy-to-follow guidelines to improve their usability.
Share new tools with the community
Sign up for free to promote the availability of bioinformatics tools

Single SNP association software tools | Genome-wide association analysis

PLINK
Desktop

PLINK

A free, open-source whole genome association analysis toolset, designed to…

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…

SNPRelate
Desktop

SNPRelate

Offers a way to solve large-scale, numerically intensive genome wide…

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…

GenABEL
Desktop

GenABEL

An R library for genome-wide association (GWA) analysis. GenABEL implements…

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…

snpStats
Web

snpStats

A simple, ready-to-use software which has been designed to analyze…

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…

SCOPA
Desktop

SCOPA Software for COrrelated Phenotype Analysis

A reverse regression model for multiple correlated phenotypes. SCOPA has a…

A reverse regression model for multiple correlated phenotypes. SCOPA has a number of key advantages: (i) the software can accommodate directly typed and imputed single-nucleotide polymorphism (SNPs),…

FaST-LMM
Desktop

FaST-LMM Factored Spectrally Transformed Linear Mixed Models

A linear mixed model (LMM) algorithm for testing sets of genetic markers in the…

A linear mixed model (LMM) algorithm for testing sets of genetic markers in the presence of confounding structure such as arises from ethnic diversity and family relatedness within a cohort. FaST-LMM…

bamlss
Desktop

bamlss

Aims to furnish a computational method to calculate probabilistic…

Aims to furnish a computational method to calculate probabilistic distributional regression models (GAM) in a Bayesian framework. Bamlss gathered several frequently-used algorithms to estimate…

MUGBAS
Desktop

MUGBAS MUlti species Gene-Based Association Suite

A software tool that estimates the p-value of a gene using information on…

A software tool that estimates the p-value of a gene using information on annotation, single marker GWA results and genotype. The software tool is species and annotation independent, fast, highly…

GCP
Algorithm

GCP Group combined p-value

A method for dividing the p-values into multiple groups and combine it at the…

A method for dividing the p-values into multiple groups and combine it at the group level. GCP integrates the significance values at different levels, and the power is improved. GCP can effectively…

gboosting
Desktop

gboosting

A high-dimensional variable selection method for survival analysis by improving…

A high-dimensional variable selection method for survival analysis by improving the existing variable selection methods in several aspects. First, we have developed a computationally feasible…

SWGDT
Desktop

SWGDT Sliding Window-based Genotype Dependence Testing

Tests genotype dependence for genome-wide scan of susceptibility gene. SWGDT…

Tests genotype dependence for genome-wide scan of susceptibility gene. SWGDT utilizes known causal gene information to proceed. It provides an alternative approach for integrating known disease gene…

SurvivalGWAS_SV
Desktop

SurvivalGWAS_SV

Handles large scale genome-wide data and allows for imputed genotypes by…

Handles large scale genome-wide data and allows for imputed genotypes by modelling time to event outcomes under a dosage model. SurvivalGWAS_SV is an analytics software capable of applying a range of…

GWRPV
Desktop

GWRPV Genome-Wide Regression P-Values

Computes the sample probability value (p-value) for the estimated coefficient…

Computes the sample probability value (p-value) for the estimated coefficient from a standard genome-wide univariate regression. GWRPV calculates the skewness and kurtosis of the estimated regression…

eRD-GWAS
Desktop

eRD-GWAS

Permits gene expression level to be tested as an explanatory variable during…

Permits gene expression level to be tested as an explanatory variable during genome-wide association studies (GWAS). eRD-GWAS employs a Bayesian-based statistical method. It utilizes RNA-seq…

SimHap
Desktop

SimHap

A cross-platform integrated graphical analysis tool for conducting…

A cross-platform integrated graphical analysis tool for conducting epidemiological, single SNP and haplotype-based association analysis. SimHap GUI features a workflow interface that guides the user…

SNPassoc
Desktop

SNPassoc

Contains classes and methods to help the analysis of whole genome association…

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…

PBOOST
Desktop

PBOOST

A permutation tool. PBOOST is based on GPU with highly reliable P-value…

A permutation tool. PBOOST is based on GPU with highly reliable P-value estimation. In terms of speed, PBOOST completed 107 permutations for a single SNP pair from the Wellcome Trust Case Control…

SurvivalGWAS_Po…
Desktop

SurvivalGWAS_Power

Calculates the power to detect single nucleotide polymorphism (SNP) association…

Calculates the power to detect single nucleotide polymorphism (SNP) association with a time to event outcome over a range of study design scenarios. SurvivalGWAS_Power enables analyses under a Cox…

Sherlock
Web

Sherlock

A computational algorithm to search for gene-disease associations from GWASs,…

A computational algorithm to search for gene-disease associations from GWASs, taking advantage of independent eQTL data. Sherlock is applicable to any complex phenotype. It is readily generalizable…

covmodfdr
Desktop

covmodfdr covariate-modulated local false discovery rate

A Bayesian approach to incorporate a set of important covariates into the fdr…

A Bayesian approach to incorporate a set of important covariates into the fdr under a heteroscedastic model, where the probability of non-null status and the distribution of the test statistic under…

PC-Select
Desktop

PC-Select

A hybrid approach that includes the principal components (PCs) of the genotype…

A hybrid approach that includes the principal components (PCs) of the genotype matrix as fixed effects in FaST-LMM Select. PC-Select leverages the advantages of the FaST-LMM Select framework while…

MarkerSet
Desktop

MarkerSet

Finds the best possible markers for further linkage analysis. MarkerSet employs…

Finds the best possible markers for further linkage analysis. MarkerSet employs already available information about markers informativity, expressed in number of heterozygous animals out of all the…

CGEN
Desktop

CGEN Clinical GENetics

Provides a module for logistic regression analyses of single-nucleotide…

Provides a module for logistic regression analyses of single-nucleotide polymorphism (SNP) data. CGEN is a Bioconductor package for analysis of case-control studies in genetic epidemiology. It is…

Puma
Desktop

Puma Penalized Unified Multiple-locus Association

Comprises a family of statistical methods designed to identify weak…

Comprises a family of statistical methods designed to identify weak associations in genome-wide association studies that are not detectable by conventional analytical methods. Puma uses a regularized…

Bmagwa
Desktop

Bmagwa Bayesian Model Averaging in Genome-wide Association Studies

Implements a method for computing posterior association probabilities of…

Implements a method for computing posterior association probabilities of single-nucleotide polymorphisms (SNP) (and other quantities) in genome-wide association studies (GWAS) using Bayesian variable…

GENOVA
Desktop

GENOVA GENe OVerlap Analysis

Tests the hypothesis that variants nominally associated with a phenotype may be…

Tests the hypothesis that variants nominally associated with a phenotype may be more likely to overlap genes than those not associated with a phenotype. For each clump, GENOVA determines whether it…

JAG
Desktop

JAG

A free open source tool to run gene-set analysis in GWAS data. JAG uses raw…

A free open source tool to run gene-set analysis in GWAS data. JAG uses raw data as input and includes bot self-contained and competitive tests.

LuoEtAl2011
Algorithm

LuoEtAl2011

Provides a method for resequencing data. The algorithm proposed is based on a…

Provides a method for resequencing data. The algorithm proposed is based on a genome continuum model and functional principal components. Beside, this algorithm was developed to test the phenotypic…

WuEtAl2010
Desktop

WuEtAl2010

Analyzes genome-wide interaction by using haplotype-based odds-ratio. The…

Analyzes genome-wide interaction by using haplotype-based odds-ratio. The software allows users to perform a method that evaluates interaction between two linked or unlinked loci. It also can be used…

LuoEtAl2010
Desktop

LuoEtAl2010

Offers a gene and pathway based genome wide association study (GWAS). The…

Offers a gene and pathway based genome wide association study (GWAS). The software aims to provides a general framework for complex diseases and novel statistics for testing association between…

PERMORY
Desktop

PERMORY

A free, open-source software, designed to perform efficient permutation tests…

A free, open-source software, designed to perform efficient permutation tests for large-scale genetic data sets. Using 10,000 permutations, a data set of several thousand individuals genotyped for…

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.