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 studies really provide, it is clear that many of the strongest results have come from large-scale mega-consortia and/or meta-analyses that combine data from up to dozens of studies and tens of thousands of subjects.
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 different genetic models (multiplicative, additive, dominant, recessive). It incorporates error trapping facilities to identify strand alignment errors and allele flipping, and performs tests of heterogeneity of effects between studies.
Provides functions for simple fixed and random effects meta-analysis for two-sample comparisons and cumulative meta-analyses. rmeta is a package that draws standard summary plots, funnel plots, and computes summaries and tests for association and heterogeneity. It offers commands to realize meta-analysis of antibacterial catheter coating, or to access cumulative meta-analysis of binary data.
Allows genome-wide association study analysis. METASOFT is a meta-analysis software designed for performing a range of basic and advanced meta-analytic methods. The software provides several methods: Fixed Effects model (FE), Random Effects model (RE), Han and Eskin's Random Effects model (RE2) and Binary Effects model (BE). It also includes the following estimates: summary effect size estimates, heterogeneity estimates and M-values.
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 with a wide array of computational options and sophisticated graphics.
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 reviews, methodology reviews and overviews of reviews.
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 variables (study-level covariates) in these models. The package provides various plot functions (for example, for forest, funnel, and radial plots) and functions for assessing the model fit, for obtaining case diagnostics, and for tests of publication bias.
Allows user to handle files recorded under the GCTx format, which is especially suited to manage data matrices paired accompanied by metadata annotations. cmap gathers an assortment of open source software, available in four different languages, providing the ability to interact with the features supplied by the Connectivity map resources. These programs aim to ease their integration in existing frameworks.