The proliferation of public data repositories creates a need for meta-analysis methods to efficiently evaluate, integrate and validate related datasets produced by independent groups. Source text: Hong and Breitling, 2008.

Desktop app
RankProd RankProd

RankProd

Provides a simple, yet powerful meta-analysis tool for detecting differentially…

Provides a simple, yet powerful meta-analysis tool for detecting differentially expressed genes between two experimental conditions. RankProd overcomes the heterogeneity among multiple datasets and…

Desktop app
Annotation-based… Annotation-based MicroArray DataMeta ANalysis tool

A-MADMAN Annotation-based MicroArray DataMeta ANalysis tool

An annotation-based package for meta-analysis of data from public repositories.…

An annotation-based package for meta-analysis of data from public repositories. A-MADMAN allows the batch retrieval from Gene Expression Omnibus and the local organization of raw data files and of…

Desktop app
Meta-Analysis Package… Meta-Analysis Package for R

metafor Meta-Analysis Package for R

A comprehensive collection of functions for conducting meta-analyses in R. The…

A comprehensive collection of functions for conducting meta-analyses in R. The metafor package includes functions to calculate various effect sizes or outcome measures, fit fixed, random, and…

Web app
ExAtlas ExAtlas

ExAtlas

A web app for meta-analysis and visualization of gene expression data. ExAtlas…

A web app for meta-analysis and visualization of gene expression data. ExAtlas offers a set of computational and management tools for meta-analysis of data stored in the GEO database: (1) standard…

Desktop app
Meta-Analysis of… Meta-Analysis of MicroArray data

MAMA Meta-Analysis of MicroArray data

A data-mining platform that allows users to simultaneously and conveniently…

A data-mining platform that allows users to simultaneously and conveniently analyze multiple microarray datasets. MAMA collects microarray experiments in a centralized repository, but it will focus…

Desktop app
meta-analysis for… meta-analysis for MicroArrays

metaMA meta-analysis for MicroArrays

Combines either p-values or moderated effect sizes from different studies to…

Combines either p-values or moderated effect sizes from different studies to find differentially expressed genes. metaMA can compute empirical Bayes statistics from Limma analysis with only one group…

Web app
joint NMF… joint NMF transcriptomics data Meta-Analysis…

jNMFMA joint NMF transcriptomics data Meta-Analysis method

A computational method for transcriptomics data meta-analysis for detection of…

A computational method for transcriptomics data meta-analysis for detection of DEGs. jNMFMA jointly factorizes multiple transcriptomics data matrices into a low-dimensional metagene space. The joint…

Desktop app
metaAnalyzeAll metaAnalyzeAll

metaAnalyzeAll

A method to perform a meta-analysis using the elastic net, a powerful and…

A method to perform a meta-analysis using the elastic net, a powerful and versatile approach for classification and regression. This approach both addresses the limitations of previous methods and…

Web app
Gemma Gemma

Gemma

A database, analysis software system and web site for genomics data re-use and…

A database, analysis software system and web site for genomics data re-use and meta-analysis. Currently, Gemma contains analyzed data from over 3300 expression profiling studies, yielding hundreds of…

Desktop app
MetaDE MetaDE

MetaDE

Implements 12 major meta-analysis methods for differential expression analysis.

Implements 12 major meta-analysis methods for differential expression analysis.

Desktop app
MetaOmics MetaOmics

MetaOmics

A suite of three R packages MetaQC, MetaDE and MetaPath, for quality control,…

A suite of three R packages MetaQC, MetaDE and MetaPath, for quality control, differentially expressed gene identification and enriched pathway detection for microarray meta-analysis.

Desktop app
MetaQC MetaQC

MetaQC

Quality control and diagnosis for microarray meta-analysis.

Quality control and diagnosis for microarray meta-analysis.

Desktop app
YuGene YuGene

YuGene

A simple method for comparison of gene expression generated across different…

A simple method for comparison of gene expression generated across different experiments, and on different platforms; that does not require global renormalization, and is not restricted to comparison…

Desktop app
OrderedList OrderedList

OrderedList

A package for meta-analysis based on ordered gene lists like those resulting…

A package for meta-analysis based on ordered gene lists like those resulting from differential gene expression analysis. OrderedList quantifies the similarity between gene lists. The significance of…

Desktop app
RankAggreg RankAggreg

RankAggreg

This package performs aggregation of ordered lists based on the ranks using…

This package performs aggregation of ordered lists based on the ranks using several different algorithms: Borda count, Cross-Entropy Monte Carlo algorithm, Genetic algorithm, and a brute force…

Desktop app
Meta-Analysis of… Meta-Analysis of Affymetrix Microarray Data…

MAAMD Meta-Analysis of Affymetrix Microarray Data analysis

A workflow to facilitate and standardize Meta-Analysis of Affymetrix Microarray…

A workflow to facilitate and standardize Meta-Analysis of Affymetrix Microarray Data analysis in Kepler.

Web app
Multi Experiment… Multi Experiment Matrix

MEM Multi Experiment Matrix

A web resource for gene expression similarity searches across many datasets.…

A web resource for gene expression similarity searches across many datasets. Unique features include automatic detection, characterization and visualization of datasets that includes the strongest…

Desktop app
IQRray IQRray

IQRray

Method in identification of poor quality arrays in dataset composed of arrays…

Method in identification of poor quality arrays in dataset composed of arrays from many independent experiments.

Desktop app
categoryCompare categoryCompare

categoryCompare

A package that calculates significant annotations (categories) in each of two…

A package that calculates significant annotations (categories) in each of two (or more) feature (i.e. gene) lists, determines the overlap between the annotations, and returns graphical and tabular…

Desktop app
GeneMeta GeneMeta

GeneMeta

A collection of meta-analysis tools for analysing high throughput experimental…

A collection of meta-analysis tools for analysing high throughput experimental data.

Desktop app
MergeMaid MergeMaid

MergeMaid

A package and associated object definitions to merge and visualize multiple…

A package and associated object definitions to merge and visualize multiple gene expression datasets. MergeMaid uses arbitrary character IDs and generates objects that can efficiently support a…

Desktop app
metahdep metahdep

metahdep

A package that contains tools for combining the results of multiple gene…

A package that contains tools for combining the results of multiple gene expression studies. metahdep accounts for both sampling and hierarchical dependence among studies, as well as fundamental…

Desktop app
metaArray metaArray

metaArray

A general probabilistic framework for combining high-throughput genomic data…

A general probabilistic framework for combining high-throughput genomic data from several related microarray experiments using mixture models. A key feature of the model is the use of latent…

Web app
Desktop app
ShinyMDE ShinyMDE

ShinyMDE

A meta-analysis tool to integrate different gene expression data for…

A meta-analysis tool to integrate different gene expression data for differentially expressed gene detection in an easy and efficient way. ShinyMDE handles processed and raw data generated from most…

Web app
INtegrative… Deprecated INtegrative Meta-analysis of EXpression data

INMEX INtegrative Meta-analysis of EXpression data

Assists researchers in conducting two common types of analyses - meta-analysis…

Assists researchers in conducting two common types of analyses - meta-analysis of multiple gene expression datasets ( meta-analysis) or joint analysis of a gene expression dataset and a metabolomic…

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