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Meta-analysis software tools | Genome-wide association study

Over the last decade, genome-wide association studies (GWAS) have become the standard tool for gene discovery in human disease research. While debate continues about how to get the most out of these studies and on occasion about how much value these…
META
Desktop

META

A program for the meta analysis of genome-wide association studies. The program…

A program for the meta analysis of genome-wide association studies. The program is designed to synthesizing the evidence from different association studies. Particularly, the program is able to work…

METAL
Desktop

METAL Meta Analysis Helper

Provides a computationally efficient tool for meta-analysis of genome-wide…

Provides a computationally efficient tool for meta-analysis of genome-wide association scans, which is a commonly used approach for improving power complex traits gene mapping studies. METAL provides…

MetABEL
Desktop

MetABEL

Meta-analysis of genome-wide SNP association results. A package for…

Meta-analysis of genome-wide SNP association results. A package for meta-analysis of genome-wide association scans between quantitative or binary traits and SNPs.

GWAR
Web
Desktop

GWAR

Implements robust methods for analysis and meta-analysis of genome-wide…

Implements robust methods for analysis and meta-analysis of genome-wide association studies (GWAS) within the statistical package Stata. GWAR proposes the Cochran-Armitage trend test under a…

MetaSKAT
Desktop

MetaSKAT

A general statistical framework for meta-analysis of gene- or region-based…

A general statistical framework for meta-analysis of gene- or region-based multimarker rare variant association tests in sequencing association studies. MetaSKAT can carry out meta-analysis of SKAT,…

CPAG
Desktop

CPAG Cross-Phenotype Analysis of GWAS

A software tool to look for similarities between 700 traits, build trees with…

A software tool to look for similarities between 700 traits, build trees with informative clusters, and highlight underlying pathways. Clusters are consistent with pre-defined groups and…

PreMeta
Desktop

PreMeta

Facilitates the exchange of information between software packages for…

Facilitates the exchange of information between software packages for meta-analysis of rare-variant associations. PreMeta reformats the output files of study-level summary statistics generated by…

RAREMETAL
Desktop

RAREMETAL

A computationally efficient tool for meta-analysis of rare variants genotyped…

A computationally efficient tool for meta-analysis of rare variants genotyped using sequencing or arrays. RAREMETAL facilitates analyses of individual studies, accommodates a variety of input file…

ETMA
Desktop

ETMA Epistasis Test in Meta-Analysis

A Markov chain Monte Carlo-based method using genotype summary data to obtain…

A Markov chain Monte Carlo-based method using genotype summary data to obtain consistent estimates of epistasis effects in meta-analysis. We defined a series of conditions to generate simulation data…

GWAMA
Desktop

GWAMA Genome-Wide Association Meta-Analysis

Performs meta-analysis of summary statistics generated from genome-wide…

Performs meta-analysis of summary statistics generated from genome-wide association studies of dichotomous phenotypes or quantitative traits. GWAMA can be used for analysing the results of all…

CPBayes
Desktop

CPBayes

Measures the evidence of aggregate-level pleiotropic association and estimates…

Measures the evidence of aggregate-level pleiotropic association and estimates an optimal subset of traits associated with the risk locus. CPBayes uses a unified Bayesian statistical framework based…

METAINTER
Desktop

METAINTER

A tool to perform meta-analysis of summary statistics obtained from a series of…

A tool to perform meta-analysis of summary statistics obtained from a series of related studies. The special feature of METAINTER is the ability to meta-analyze the results of multiple linear and…

MultiMeta
Desktop

MultiMeta

As new methods for multivariate analysis of Genome Wide Association Studies…

As new methods for multivariate analysis of Genome Wide Association Studies (GWAS) become available, it is important to be able to combine results from different cohorts in a meta-analysis. The R…

metaCCA
Desktop

metaCCA

A computational framework for summary statistics-based analysis of a single or…

A computational framework for summary statistics-based analysis of a single or multiple studies that allows multivariate representation of both genotype and phenotype. metaCCA extends the statistical…

QRFCCA
Desktop

QRFCCA Quadratically Regularized Functional Canonical Correlation Analysis

Performs gene-based cross-phenotype association analysis. QRFCCA aims to…

Performs gene-based cross-phenotype association analysis. QRFCCA aims to reduces the dimensions of both genotype and phenotype data while fully retaining the original genotypic and phenotypic…

B-LORE
Desktop

B-LORE Bayesian multiple LOgistic REgression

Allows users to study the effect size of single nucleotide polymorphisms (SNPs)…

Allows users to study the effect size of single nucleotide polymorphisms (SNPs) modeled by a two-component Gaussian mixture. B-LORE is a Bayesian method using multiple logistic regression of the…

metagen
Desktop

metagen

A method for meta-analysis of case-control genetic association studies using…

A method for meta-analysis of case-control genetic association studies using random-effects logistic regression. The main advantages of the proposed methodology is its flexibility and the ease of…

GACT
Desktop
Web

GACT Genome build and Allele definition Conversion Tool

A comprehensive tool with both powerful command-line and user-friendly web…

A comprehensive tool with both powerful command-line and user-friendly web interface versions to predict, and convert both genome builds and allele definitions between multiple GWAS (or deep…

MetaPCA
Desktop

MetaPCA

Implements simultaneous dimension reduction using principal component analysis…

Implements simultaneous dimension reduction using principal component analysis (PCA). This R package contains four methods to find common subspace among multiple studies (datasets): (i) eigenvalue…

rmeta
Desktop

rmeta

Functions for simple fixed and random effects meta-analysis for two-sample…

Functions for simple fixed and random effects meta-analysis for two-sample comparisons and cumulative meta-analyses. rmeta draws standard summary plots, funnel plots, and computes summaries and tests…

MASS
Desktop

MASS Meta-Analysis of Score Statistics

A command-line program to perform meta-analysis of sequencing studies by…

A command-line program to perform meta-analysis of sequencing studies by combining the score statistics from multiple studies. MASS implements three types of multivariate tests that encompass all…

metaphor
Desktop

metaphor

Provides functions for conducting meta-analyses in R. The package includes…

Provides functions for conducting meta-analyses in R. The package includes functions for fitting the meta-analytic fixed- and random-effects models and allows for the inclusion of moderators…

rqt
Desktop

rqt

Offers gene-level genome-wide association study (GWAS) meta-analysis. The rqt…

Offers gene-level genome-wide association study (GWAS) meta-analysis. The rqt package can be easily included into bioinformatics pipeline or used as stand-alone. The workflow of gene-level…

RevMan
Desktop

RevMan Review Manager

A package that does meta-analysis and provides results in tabular format and…

A package that does meta-analysis and provides results in tabular format and graphically. In addition to intervention reviews, the new version includes the ability to write diagnostic test accuracy…

CMA
Desktop

CMA Comprehensive Meta-analysis

A package to do meta-analysis which works in a spreadsheet interface and also…

A package to do meta-analysis which works in a spreadsheet interface and also provides forest plots, which are useful for visualizing between-study heterogeneity. The program combines ease of use…

MetaGAP
Web

MetaGAP Meta-GWAS Accuracy and Power

Infers the statistical power to detect associated single nucleotide…

Infers the statistical power to detect associated single nucleotide polymorphisms (SNPs) and the predictive accuracy of the poly-genic scores (PGS) in a meta-analysis of genome-wide association…

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