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Unclassified tools | Gene expression microarray data analysis

Onto-Design
Web

Onto-Design

Allows the user to select genes that represent given functional categories.…

Allows the user to select genes that represent given functional categories. Onto-Design permits to create customized array representing some chosen biological processes. It provides the means to…

L2L
Dataset

L2L

Provides lists of differentially expressed genes. L2L was constructed by…

Provides lists of differentially expressed genes. L2L was constructed by compiling data from published mammalian microarray studies. It contains a set of lists for each of the three organizing…

BiTrinA
Desktop

BiTrinA

Integrates different multiscale algorithms for binarization and for…

Integrates different multiscale algorithms for binarization and for trinarization of one-dimensional data with methods for quality assessment and visualization of the results. By identifying…

massiR
Desktop

massiR

Provides a method for researchers to predict the sex of samples in microarray…

Provides a method for researchers to predict the sex of samples in microarray datasets.

CIBERSORT
Web
quantroSim
Desktop

quantroSim

An R-package to simulate gene expression and DNA methylation data. The…

An R-package to simulate gene expression and DNA methylation data. The R-package quantroSim is the supporting data simulation package for the quantro R/Bioconductor package which can be used to…

MGFM
Web
Desktop

MGFM Marker Gene Finder in Microarray data

Predicts tissue/cell type marker genes using microarray gene expression data.…

Predicts tissue/cell type marker genes using microarray gene expression data. The main advantages of MGFM are i) a short running time of some seconds per analysis. This is achieved by sorting the…

spkTools
Desktop

spkTools

Enables cross-platform comparisons, and proposes a comprehensive procedure for…

Enables cross-platform comparisons, and proposes a comprehensive procedure for assessments based on spike-in experiments. spkTools is implemented as a user friendly Bioconductor package. It contains…

qpgraph
Desktop

qpgraph

Estimates gene and eQTL networks from high-throughput expression and genotyping…

Estimates gene and eQTL networks from high-throughput expression and genotyping assays. qpgraph is based in the so-called q-order limited partial correlation graphs, qp-graphs, which is specifically…

CAFE
Desktop

CAFE

Follows the expression based karyotyping workflow (e-karyotyping) and greatly…

Follows the expression based karyotyping workflow (e-karyotyping) and greatly simplifies and speeds up the detection analysis of chromosomal aberrations from expression DNA microarrays.

MaLTE
Desktop

MaLTE Machine Learning of Transcript Expression

An alternative approach to gene expression estimation that uses a machine…

An alternative approach to gene expression estimation that uses a machine learning approach. MaLTE relies on a gold standard (such as RNA-Seq) to infer gene expression models that make better use of…

DetectiV
Desktop

DetectiV

Offers powerful yet simple visualization, normalization and significance…

Offers powerful yet simple visualization, normalization and significance testing tools. DetectiV uses simple and well established visualization and statistical techniques to analyze data from…

eXPatGen
Web

eXPatGen

A simulator of gene expression patterns in order to evaluate different analysis…

A simulator of gene expression patterns in order to evaluate different analysis methods, such as clustering and principle component analysis (PCA).

AtMIAMExpress
Desktop

AtMIAMExpress

Uses as submission tool for Microarray experiments. AtMIAMExpress is an…

Uses as submission tool for Microarray experiments. AtMIAMExpress is an open-source Web-based software application for the submission of Arabidopsis-based microarray data to ArrayExpress. It was…

pcaMethods
Desktop

pcaMethods principal component analysisMethods

A compliant library for computing principal component analysis on incomplete…

A compliant library for computing principal component analysis on incomplete data sets. pcaMethods combines an expectation maximization approach with a probabilistic model. It also offers methods for…

MASQOT-GUI
Desktop

MASQOT-GUI

An open-source, platform-independent software pipeline for two-channel…

An open-source, platform-independent software pipeline for two-channel microarray spot quality control. MASQOT-GUI hosts a set of independent applications for gridding, segmentation, quantification,…

UNDO
Desktop

UNDO UNsupervised DecOnvolution

An R package that can be used to automatically detect cell-specific marker…

An R package that can be used to automatically detect cell-specific marker genes (MGs) located on the scatter radii of mixed gene expressions, estimate cellular proportions in each sample and…

GiGA
Desktop

GiGA Graph-based iterative Group Analysis

A fast and flexible delimitation of the most interesting areas in a microarray…

A fast and flexible delimitation of the most interesting areas in a microarray experiment. GiGA identifies all relevant physiological processes, puts them into context, summarizes them in an…

G T A T C G C T A
TReNA
Desktop

TReNA

Permits to reconstruct transcriptional regulatory networks. TReNA uses gene…

Permits to reconstruct transcriptional regulatory networks. TReNA uses gene expression, priors, machine learning to process. It is particularly useful in species for which genome-wide transcription…

MiningABs
Desktop

MiningABs

A meta-analysis method able to efficiently identify associated biomarkers (ABs)…

A meta-analysis method able to efficiently identify associated biomarkers (ABs) from different independently performed array-based datasets. MiningABs quantifies the similarity between paired probe…

phylochipanalys…
Desktop

phylochipanalyser

A Windows-program for the analysis of experiments with hierarchical probe-sets.…

A Windows-program for the analysis of experiments with hierarchical probe-sets. PhylochipAnalyzer operates in two modes: first, the hierarchy of probes is defined interactively; second, the intensity…

KegArray
Desktop

KegArray

Provides an environment for analyzing both transcriptome data (gene expression…

Provides an environment for analyzing both transcriptome data (gene expression profiles) and metabolome data (compound profiles). KegArray is a Java application that enables users to easily map those…

MVIAeval
Web

MVIAeval

Allows researchers to easily conduct a comprehensive and objective performance…

Allows researchers to easily conduct a comprehensive and objective performance evaluation of their newly developed missing value imputation algorithm for microarray data or any data which can be…

MADGene
Web

MADGene

Allows the user to convert id lists in order to unify heterogeneous gene sets.…

Allows the user to convert id lists in order to unify heterogeneous gene sets. MADGene is a software environment comprising a web-based database and a java application. This database creates bridges…

MAGE-ML
Desktop

MAGE-ML Microarray Gene Expression Markup Language

Retrieves data from different microarray databases using MAGE-ML and for…

Retrieves data from different microarray databases using MAGE-ML and for combining microarray data with breast cancer image analysis and clinical data for correlation studies. MAGE-ML provides the…

DeMix
Desktop

DeMix

A statistical method for deconvolving mixed cancer transcriptomes which…

A statistical method for deconvolving mixed cancer transcriptomes which addresses the aforementioned issues in array-based expression data. DeMix can be applied to ongoing biomarker-based clinical…

HCNet
Dataset

HCNet Heart and Calcium functional Network

A collection of functional gene modules calculated from the microarray data…

A collection of functional gene modules calculated from the microarray data compendium available from the GEO database. HCNet is a specialized database designed to assist experimentalists for cardiac…

Sample Sizes
Web

Sample Sizes

A tool to compute the number of samples needed to detect expression changes for…

A tool to compute the number of samples needed to detect expression changes for a microarray experiment.

MADAM
Desktop

MADAM MicroArray DAta Manager

Guides users through the microarray process from RNA procurement to data…

Guides users through the microarray process from RNA procurement to data analysis, offering intelligent forms to simplify the tracking of experimental parameters and results.

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