Tag: Meta-analysis

SecureMA 0.2 – Secure Meta-analysis for Genetic Association Studies

SecureMA 0.2

:: DESCRIPTION

SecureMA is a secure framework for performing multi-site genetic association studies across large consortia, without violating privacy/confidentiality of individual participants or substudy sites. It aims at addressing various attacks on genomic privacy, and provides comprehensive protection over genomic data without impeding scientific endeavor.

::DEVELOPER

Wei Xie (XieConnect@gmail.com)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 SecureMA

:: MORE INFORMATION

Citation

SecureMA: protecting participant privacy in genetic association meta-analysis.
Xie W, Kantarcioglu M, Bush WS, Crawford D, Denny JC, Heatherly R, Malin BA.
Bioinformatics. 2014 Aug 21. pii: btu561.

YAMAS 2014 – Meta-analysis of Genome Wide Association Studies

YAMAS 2014

:: DESCRIPTION

YAMAS (Yet Another Meta-Analysis Software) is a software for meta-analysis of genome wide association studies.

::DEVELOPER

YAMAS team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 YAMAS

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012 Sep 12;13:231. doi: 10.1186/1471-2105-13-231.
Quick, “imputation-free” meta-analysis with proxy-SNPs.
Meesters C1, Leber M, Herold C, Angisch M, Mattheisen M, Drichel D, Lacour A, Becker T.

NetworkAnalyst 1.0 – Statistical, Visual & Network-based approaches for Gene Expression Meta analysis

NetworkAnalyst 1.0

:: DESCRIPTION

NetworkAnalyst is designed to support integrative analysis of gene expression data through statistical, visual and network-based approaches.

::DEVELOPER

the Hancock Lab at The University of British Columnbia.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

NetworkAnalyst for statistical, visual and network-based meta-analysis of gene expression data.
Xia J, Gill EE, Hancock RE.
Nat Protoc. 2015 Jun;10(6):823-44. doi: 10.1038/nprot.2015.052. Epub 2015 May 7.

metaArray 1.66.0 – Integration of Microarray Data for Meta-analysis

metaArray 1.66.0

:: DESCRIPTION

metaArray is a general probabilistic framework for combining high-throughput genomic data from several related microarray experiments using mixture models.

::DEVELOPER

metaArray team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX/ WIndows
  • R package
  • BioCOnductor

:: DOWNLOAD

  metaArray

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2007 Sep 27;8:364.
A latent variable approach for meta-analysis of gene expression data from multiple microarray experiments.
Choi H1, Shen R, Chinnaiyan AM, Ghosh D.

metaRNASeq 1.0.5 – Meta-analysis of RNA-seq data

metaRNASeq 1.0.5

:: DESCRIPTION

metaRNASeq implements two p-value combination techniques (inverse normal and Fisher methods). It also provides a vignette explaining how to combine data from multiple RNA-seq experiments.

::DEVELOPER

Guillemette Marot <guillemette.marot at inria.fr>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • R

:: DOWNLOAD

 metaRNASeq

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2014 Mar 29;15:91. doi: 10.1186/1471-2105-15-91.
Differential meta-analysis of RNA-seq data from multiple studies.
Rau A1, Marot G, Jaffrézic F.

ExAtlas – Meta-analysis of Gene Expression data

ExAtlas

:: DESCRIPTION

ExAtlas is an on-line software tool for meta-analysis and visualization of gene expression data.

::DEVELOPER

Laboratory of Genetics, National Institute on Aging,  NIH

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

ExAtlas: An interactive online tool for meta-analysis of gene expression data.
Sharov AA, Schlessinger D, Ko MS.
J Bioinform Comput Biol. 2015 Jun 9:1550019.

MetaPath 1.0 – Meta-analysis for Pathway Analysis

MetaPath 1.0

:: DESCRIPTION

MetaPath (Meta-analysis for Pathway Analysis) performs the meta-analysis for pathway enrichment analysis

::DEVELOPER

George C. Tseng 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 MetaPath

:: MORE INFORMATION

Citation

Kui Shen and George C. Tseng. (2010)
Meta-analysis for pathway enrichment analysis when combining multiple microarray studies.
Bioinformatics. 26:1316-1323.

META 1.7 – Carryout Meta-analysis of Genetic Studies

META 1.7

:: DESCRIPTION

META is 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 seamlessly with the output of SNPTEST [1] . This program was used in the meta analysis of the genome-wide association studies of smoking.

::DEVELOPER

Jonathan Marchini

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 META

:: MORE INFORMATION

Citation

J. Z. Liu, et al (2010)
Meta-analysis and imputation refines the association of 15q25 with smoling quantity.
Nature Genetics, 42, 436-440
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AnnotCompute – Annotation-based Exploration and Meta-analysis of Genomics Experiments

AnnotCompute

:: DESCRIPTION

AnnotCompute is an information discovery platform for repositories of functional genomics experiments such as ArrayExpress.

::DEVELOPER

the Computational Biology and Informatics Laboratory at the University of Pennsylvania

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation:

Database (Oxford). 2011 Dec 21;2011:bar045. doi: 10.1093/database/bar045.
AnnotCompute: annotation-based exploration and meta-analysis of genomics experiments.
Zheng J, Stoyanovich J, Manduchi E, Liu J, Stoeckert CJ Jr.

GWAtoolbox 2.2.4-7 – Quality Control and Handling of Genome-wide Association Studies Meta-analysis data

GWAtoolbox 2.2.4-7

:: DESCRIPTION

GWAtoolbox is an R-package for fast quality control and data handling of multiple data files obtained from genome-wide association studies (GWAS).

::DEVELOPER

the Center of Biomedicine (CBM) at EURAC research.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/windows/MacOsX
  • R package

:: DOWNLOAD

 GWAtoolbox

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Feb 1;28(3):444-5. doi: 10.1093/bioinformatics/btr679.
GWAtoolbox: an R package for fast quality control and handling of genome-wide association studies meta-analysis data.
Fuchsberger C, Taliun D, Pramstaller PP, Pattaro C; CKDGen consortium.