Meta

Available Computational Tools for Meta-Analysis of Microarray Studies



A-MADMAN

http://compgen.bio.unipd.it/bioinfo/amadman/

Bisognin A, A-MADMAN: annotation-based microarray data meta-analysis tool.


BayesPoolMicro

http://www.math.umass.edu/~conlon/research/BayesPoolMicro/

Conlon EM, Bayesian models for pooling microarray studies with multiple sources of replications. BMC Bioinformatics. 2006

http://view.ncbi.nlm.nih.gov/pubmed/16677390


EMA
Servant N, EMA - A R package for Easy Microarray data analysis.


GeneMeta

http://www.bioconductor.org/packages/bioc/html/GeneMeta.html

(-)

PMID: (-)


ICS

http://www.rinst.org/ICS/ICS_Programs.tar.gz.

Rajaram S, A novel meta-analysis method exploiting consistency of high-throughput experiments.

http://www.ncbi.nlm.nih.gov/pubmed/19176547


INMEX

http://www.inmex.ca

Xia J, INMEX--a web-based tool for integrative meta-analysis of expression data.

http://www.ncbi.nlm.nih.gov/pubmed/23766290


MAID

(-)

Borozan I, MAID : an effect size based model for microarray data integration across laboratories and platforms. BMC Bioinformatics. 2008 Jul 10;9:305.

http://view.ncbi.nlm.nih.gov/pubmed/18616827


metaArray

http://www.bioconductor.org/packages/bioc/1.8/html/metaArray.html

Choi H, A latent variable approach for meta-analysis of gene expression data from multiple microarray experiments. BMC Bioinformatics. 2007

http://view.ncbi.nlm.nih.gov/pubmed/17900369

 

metaGEM

http://spiral.imperial.ac.uk/handle/10044/1/4217

Ramasamy A, Key issues in conducting a meta-analysis of gene expression microarray datasets. PLoS Med. 2008

http://view.ncbi.nlm.nih.gov/pubmed/18767902

 

metahdep

http://www.bioconductor.org/packages/bioc/html/metahdep.html

Stevens JR, metahdep: Meta-analysis of hierarchically dependent gene expression studies. Bioinformatics. 2009

http://view.ncbi.nlm.nih.gov/pubmed/19648140


metaMA

http://cran.r-project.org/web/packages/metaMA/index.html

Marot G, Moderated effect size and p-value combinations for microarray meta-analyses. Bioinformatics. 2009

http://view.ncbi.nlm.nih.gov/pubmed/19628502


METRADISC-XL

http://biomath.med.uth.gr/files/METRADISC-XL.exe

Zintzaras E, Meta-analysis for ranked discovery datasets: theoretical framework and empirical demonstration for microarrays. Comput Biol Chem. 2008 

http://view.ncbi.nlm.nih.gov/pubmed/17988949


Meta Threshold Gradient Descent Regularization (MTGDR) 

http://www.cs.uiowa.edu/~jian/MTGDR/main.html

Ma S, Regularized gene selection in cancer microarray meta-analysis. BMC Bioinformatics. 2009 Jan 1;10:1

http://view.ncbi.nlm.nih.gov/pubmed/19118496


MetaOmics

http://www.biostat.pitt.edu/bioinfo/software.htm

http://www.ncbi.nlm.nih.gov/pubmed/22863766


OrderedList

http://www.bioconductor.org/packages/bioc/html/OrderedList.html

Lottaz C, OrderedList--a bioconductor package for detecting similarity in ordered gene lists. Bioinformatics. 2006

http://view.ncbi.nlm.nih.gov/pubmed/16844712

 

RankAggreg

http://cran.r-project.org/web/packages/RankAggreg/index.html

Pihur V, RankAggreg, an R package for weighted rank aggregation. BMC Bioinformatics. 2009

http://view.ncbi.nlm.nih.gov/pubmed/19228411

 

RankProd

http://www.bioconductor.org/packages/2.2/bioc/html/RankProd.html

Hong F, RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis. Bioinformatics. 2006

http://view.ncbi.nlm.nih.gov/pubmed/16982708


Reference:

Forero DA. A survey of available computational tools for meta-analyses of microarray studies.
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