METASOFT 2.0.1 – Meta-analysis Tool

METASOFT 2.0.1

:: DESCRIPTION

METASOFT is a meta-analysis software tool for genome-wide association studies that provides the following methods

Fixed Effects model (FE): Fixed effects model based on inverse-variance-weighted effect size.
Random Effects model (RE): Conventional random effects model based on inverse-variance-weighted effect size. Heterogeneity is estimated using DerSimonian-Laird method.
Han and Eskin’s Random Effects model (RE2): Random effects model that increases power under heterogeneity.
Binary Effects model (BE): Random effects model assuming that the effects either exist or not in the studies.

::DEVELOPER

ZarLab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Mac OsX / Windows
Java

:: DOWNLOAD

METASOFT

:: MORE INFORMATION

Citation

Buhm Han and Eleazar Eskin,
“Random-Effects Model Aimed at Discovering Associations in Meta-Analysis of Genome-wide Association Studies”,
The American Journal of Human Genetics (2011) 88, 586-598.

PreMeta – Exchange of Information between four software packages for Meta-analysis

PreMeta

:: DESCRIPTION

PreMeta is a software program written in C++ that is designed to facilitate the exchange of information between four software packages for meta-analysis of rare-variant associations: MASS, RAREMETAL, MetaSKAT, and seqMeta.

::DEVELOPER

Danyu Lin

:: SCREENSHOTS

N/A

::REQUIREMENTS

Linux

:: DOWNLOAD

PreMeta

:: MORE INFORMATION

Citation

Tang ZZ, Bunn P, Tao R, Liu Z, Lin DY.
PreMeta: a tool to facilitate meta-analysis of rare-variant associations.
BMC Genomics. 2017 Feb 14;18(1):160. doi: 10.1186/s12864-017-3573-1. PMID: 28196472; PMCID: PMC5310051.

MAOS 1.2 – Meta-Analysis with Overlapping Subjects

MAOS 1.2

:: DESCRIPTION

MAOS (Meta-Analysis with Overlapping Subjects) implements valid and efficient statistical methods for meta-analysis of genomewide association studies with overlapping subjects

::DEVELOPER

Danyu Lin

:: SCREENSHOTS

N/A

::REQUIREMENTS

Linux / Windows

:: DOWNLOAD

MAOS

:: MORE INFORMATION

Citation

D. Y. Lin and P. F. Sullivan (2009).
Meta-Analysis of Genome-Wide Association Studies With Overlapping Subjects.
The American Journal of Human Genetics, Volume 85, Issue 6, 862-872,

MASS v7 – Meta-Analysis of Score Statistics

MASS v7

:: DESCRIPTION

The software MASS performs meta-analysis by combining the score statistics from K independent studies.The two approaches are asymptotically equivalent; however, the latter approach is numerically more stable and statistically more accurate, especially for discrete outcomes and unbalanced data (e.g., rare variants in case-control studies) (Lin and Tang, 2011). Another unique feature of MASS is its ability to perform multivariate meta-analysis.

::DEVELOPER

Danyu Lin

:: SCREENSHOTS

N/A

::REQUIREMENTS

Linux

:: DOWNLOAD

MASS

:: MORE INFORMATION

Citation

Lin DY, Tang ZZ. (2011).
A general framework for detecting disease associations with rare variants in sequencing studies.
The American Journal of Human Genetics, 89:354-367.

MetaDE 1.0.5 – Meta-analysis for Differential Expression Analysis

MetaDE 1.0.5

:: DESCRIPTION

MetaDE (Meta-analysis for Differential Expression Analysis)

::DEVELOPER

George C. Tseng

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux/MacOsx
R Package

:: DOWNLOAD

MetaDE

:: MORE INFORMATION

Citation

Jia Li and George C. Tseng. (2010)
An adaptively weighted statistic for detecting differential gene expression when combining multiple transcriptomic studies.
Annals of Applied Statistics 2011, Vol. 5, No. 2A, 994-1019

Shuya Lu, Jia Li, Chi Song, Kui Shen and George C Tseng. (2010)
Biomarker Detection in the Integration of Multiple Multi-class Genomic Studies.
Bioinformatics. 26:333-340.

Gemma 1.27.4 – Analyze Genomics data using Meta-analysis

Gemma 1.27.4

:: DESCRIPTION

Gemma is an open-source database and software system for the meta-analysis of gene expression data.

::DEVELOPER

Pavlidis lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX
Web Server

:: DOWNLOAD

Gemma

:: MORE INFORMATION

Citation

Bioinformatics. 2009 Jun 15;25(12):1543-9. Epub 2009 Apr 17.
Application and evaluation of automated semantic annotation of gene expression experiments.
French L, Lane S, Law T, Xu L, Pavlidis P.

RegionalP 1.0 – Region-based meta-analysis of Genome-wide Association Studies in genetically Diverse Populations

RegionalP 1.0

:: DESCRIPTION

RegionalP works by quantifying the degree of over-representation of associated SNPs in a pre-defined genomic region, given a specific definition of statistical significance.

::DEVELOPER

Saw Swee Hock School of Public Health

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C++ Compiler

:: DOWNLOAD

RegionalP

:: MORE INFORMATION

Citation

Eur J Hum Genet. 2012 Apr;20(4):469-75. doi: 10.1038/ejhg.2011.219. Epub 2011 Nov 30.
A statistical method for region-based meta-analysis of genome-wide association studies in genetically diverse populations.
Wang X, Liu X, Sim X, Xu H, Khor CC, Ong RT, Tay WT, Suo C, Poh WT, Ng DP, Liu J, Aung T, Chia KS, Wong TY, Tai ES, Teo YY.

OpenMEE 2016 – Ecological and Evolutionary Meta-analysis

OpenMEE 2016

:: DESCRIPTION

OpenMEE is a user-friendly, open-source program for carrying out meta-analysis in ecology and evolution. The aim is to make newly developed statistical approaches easily accessible to all. These statistics include: multi-factor meta-analysis, meta-regression, and phylogenetic meta-analysis.

::DEVELOPER

The Center for Evidence-Based Medicine (CEBM) @ Brown

:: SCREENSHOTS

:: REQUIREMENTS

Windows / MacOsX

:: DOWNLOAD

OpenMEE

:: MORE INFORMATION

phyloMeta 1.3 – Phylogenetic Comparative Analyses with Meta-analysis

phyloMeta 1.3

:: DESCRIPTION

PhyloMeta is a program for integrating a phylogeny (in NEWICK format) into traditional meta-analysis. All the familiar statistics of meta-analysis are calculated (e.g., pooled effect sizes with 95%CI and homogeneity tests) and paired with the phylogenetically-independent equivalents to these statistics.

::DEVELOPER

The Lajeunesse Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows

:: DOWNLOAD

phyloMeta

:: MORE INFORMATION

Citation

phyloMeta: a program for phylogenetic comparative analyses with meta-analysis.
Lajeunesse MJ.
Bioinformatics. 2011 Sep 15;27(18):2603-4. doi: 10.1093/bioinformatics/btr438

MetaSKAT 0.81 – Meta-analysis for multiple markers

MetaSKAT 0.81

:: DESCRIPTION

MetaSKAT is a R package for multiple marker meta-analysis across studies. It can carry out meta-analysis of SKAT, SKAT-O and burden tests with individual level genotype data or gene level summary statistics.

::DEVELOPER

Xihong Lin’s Group, Harvard School of Public Health

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
R Package

:: DOWNLOAD

MetaSKAT

:: MORE INFORMATION

Citation

Lee, S., Teslovich, T.M., Boehnke, M. and Lin, X. (2013)
General framework for meta-analysis of rare variants in sequencing association studies
Am J Hum Genet. 2013 Jul 11;93(1):42-53. doi: 10.1016/j.ajhg.2013.05.010