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Summary statistics software tools | Genome-wide association analysis

Imputation of individual level genotypes at untyped markers using an external reference panel of genotyped or sequenced individuals has become standard practice in genetic association studies. Direct imputation of summary statistics can also be…
LDSC
Desktop

LDSC LD SCore regression

Provides a method for partitioning heritability from genome-wide association…

Provides a method for partitioning heritability from genome-wide association studies (GWAS) summary statistics while accounting for linked markers. LD SCore regression identified strong enrichment…

SMR
Desktop

SMR Summary-data-based Mendelian Randomization

Identifies associations between gene expression and complex traits using…

Identifies associations between gene expression and complex traits using summary data from genome-wide association studies (GWAS) and expression quantitative trait locus (eQTL). Then, a heterogeneity…

pulver
Desktop

pulver

Allows user to calculate p-values for interaction terms in huge numbers of…

Allows user to calculate p-values for interaction terms in huge numbers of linear regressions in a practical amount of time. pulver can be used as a screening tool for scenarios where the number of…

biMM
Desktop

biMM

Estimates variance parameters of a bivariate lineax mixed model (LMM) in the…

Estimates variance parameters of a bivariate lineax mixed model (LMM) in the following context arising in genetics research. BiMM is a computationally efficient implementation of a bivariate linear…

JEPEGMIX
Desktop

JEPEGMIX

Allows gene-level joint analysis of expression Quantitative Trait Loci (eQTLs)…

Allows gene-level joint analysis of expression Quantitative Trait Loci (eQTLs) in cosmopolitan cohorts. JEPEGMIX is a summary statistics based tool that (i) imputes eQTLs statistics, (ii) infers…

USAT
Algorithm

USAT Unified Score-Based Association Test

Permits association analysis using multiple traits and a single marker for…

Permits association analysis using multiple traits and a single marker for unrelated individuals. USAT combines the MANOVA and the small subunit (SSU) approach to maximize power. It can compute…

RiVIERA-MT
Desktop
GWASH
Desktop

GWASH GWAS heritability

Allows estimation of genome-wide association studies (GWAS). GWASH is an…

Allows estimation of genome-wide association studies (GWAS). GWASH is an estimator that consists in a modification of the Dicker estimator.

IGESS
Desktop

IGESS

Integrates individual level genotype data and summary statistics for…

Integrates individual level genotype data and summary statistics for exploration of genetic architecture of complex phenotypes. The IGESS algorithm is based on variational inference and is developed…

Adapt-Mix
Desktop

Adapt-Mix

Combines information across all available reference panels to produce estimates…

Combines information across all available reference panels to produce estimates of local genetic correlation structure for summary statistics-based methods in arbitrary populations. Adapt-Mix can be…

DISTMIX
Desktop

DISTMIX

A very fast software tool for directly imputing summary statistics of untyped…

A very fast software tool for directly imputing summary statistics of untyped makers from cosmopolitan cohorts without using subject-level genotype data. DISTMIX uses a relevant reference panel to…

DISSCO
Desktop

DISSCO Direct Imputation of Summary Statistics allowing COvariates

A JAVA application for direct imputation of summary statistics allowing for…

A JAVA application for direct imputation of summary statistics allowing for covariates. The proof-of-concept simulations and applications to two real data sets demonstrate the value of DISSCO,…

attack
Desktop

attack

Identifies specific individuals from limited published associations from the…

Identifies specific individuals from limited published associations from the Wellcome Trust Case Control Consortium (WTCCC) dataset. For GWAS results computed over 25 randomly-selected loci, attack…

JEPEG
Desktop

JEPEG

A software tool which uses only GWAS summary statistics to i) impute the…

A software tool which uses only GWAS summary statistics to i) impute the summary statistics at unmeasured eQTLs and ii) test for the joint effect of all measured and imputed eQTLs in a gene. Applied…

HESS
Desktop

HESS Heritability Estimation from Summary Statistics

Estimates the amount of variance in trait explained by typed single nucleotide…

Estimates the amount of variance in trait explained by typed single nucleotide polymorphisms (SNPs) at each single locus on the genome from genome-wide association study (GWAS) summary statistics,…

ImpG-Summary
Desktop

ImpG-Summary

A software tool for Gaussian imputation from summary association statistics, a…

A software tool for Gaussian imputation from summary association statistics, a type of data that is becoming widely available. This approach accounts for the limited sample size of the reference…

DIST
Desktop

DIST Direct Imputation of summary Statistics

Imputes the summary statistics of untyped variants without first imputing their…

Imputes the summary statistics of untyped variants without first imputing their subject-level genotypes. This is achieved by (i) using the conditional expectation formula for multivariate normal…

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