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Meta-analysis software tools | Gene expression microarray data analysis

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) A comparison of…
RankProd
Desktop

RankProd

Allows detection of differentially expressed features in molecular profiling…

Allows detection of differentially expressed features in molecular profiling experiments. RankProd is a non-parametric method that provides a robust and reliable implementation of the Rank Product…

Onto-Compare
Web

Onto-Compare

Allows efficient comparisons of any sets of commercial or custom arrays.…

Allows efficient comparisons of any sets of commercial or custom arrays. Onto-Compare permits to users to determine quickly which array, or set of arrays, covers best the hypotheses studied. It…

MetaKTSP
Desktop

MetaKTSP

Allows to work about omics data meta-analysis of differentially expressed gene…

Allows to work about omics data meta-analysis of differentially expressed gene detection, pathway, prediction, clustering, classification and network analyses. MetaKTSP contains several approaches…

OrderedList
Desktop

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…

metaMA
Desktop

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…

MEM
Web

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…

RankAggreg
Desktop

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…

metaArray
Desktop

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…

metahdep
Desktop

metahdep

Contains tools for combining the results of multiple gene expression studies.…

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 covariate…

MINT
Desktop

MINT Multivariate INTegrative method

Accounts for unwanted systematic variation and identifies predictive gene…

Accounts for unwanted systematic variation and identifies predictive gene signatures with greater reproducibility and accuracy. MINT led to superior classification and prediction accuracy compared to…

CellMontage
Dataset

CellMontage

Allows users to access gene expression profiles. CellMontage permits users to…

Allows users to access gene expression profiles. CellMontage permits users to access expression data in a content-based manner. Query profiles are searched against a database to find profiles with…

metaAnalyzeAll
Desktop

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…

MetaQC
Desktop

MetaQC

Quality control and diagnosis for microarray meta-analysis.

Quality control and diagnosis for microarray meta-analysis.

ShinyMDE
Web
Desktop

ShinyMDE

Integrates different gene expression data for differentially expressed gene…

Integrates different gene expression data for differentially expressed gene detection in an easy and efficient way. ShinyMDE handles processed and raw data generated from most widely used data…

MergeMaid
Desktop

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…

MAAMD
Desktop

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.

MetaSignature
Dataset

MetaSignature

Provides several data about gene expression microarrays across diseases.…

Provides several data about gene expression microarrays across diseases. MetaSignature allows users to identify consistent gene expression signatures in a specific disease state. It enables…

jNMFMA
Web

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…

IQRray
Desktop

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.

YuGene
Desktop

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…

A-MADMAN
Desktop

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…

NMF
Desktop

NMF Non-negative Matrix Factorization

Provides a framework to perform Non-negative Matrix Factorization (NMF). NMF…

Provides a framework to perform Non-negative Matrix Factorization (NMF). NMF implements a set of already published algorithms and seeding methods. This method permits to test, develop and plug…

metafor
Desktop

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…

ExAtlas
Web

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…

MetaDE
Desktop

MetaDE

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

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

categoryCompare
Desktop

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…

GeneMeta
Desktop

GeneMeta

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

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

Gemma
Web

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…

MetaOmics
Desktop

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.

MetaSparseKmean…
Desktop

MetaSparseKmeans

Represents a meta-analysis software which combines multiple transcriptomic…

Represents a meta-analysis software which combines multiple transcriptomic studies for disease subtype discovery. MetaSparseKmeans allows especially to visualize gene expression matrix.

MAMA
Desktop

MAMA Meta-Analysis of MicroArray data

Allows users to simultaneously and conveniently analyze multiple microarray…

Allows users to simultaneously and conveniently analyze multiple microarray datasets. MAMA collects microarray experiments in a centralized repository, but it will focus on high-level analyses of…

INMEX
Web

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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