Desktop app
qpgraph qpgraph

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…

Desktop app
spkTools spkTools

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…

Desktop app
principal component… principal component analysisMethods

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…

Web app
Desktop app
Marker Gene Finder in… Marker Gene Finder in Microarray data

MGFM Marker Gene Finder in Microarray data

A useful tool to predict tissue/cell type marker genes using microarray gene…

A useful tool to predict 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…

Desktop app
Graph-based iterative… Graph-based iterative Group Analysis

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…

Desktop app
Machine Learning of… Machine Learning of Transcript Expression

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…

Desktop app
MiningABs MiningABs

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…

Desktop app
MASQOT-GUI MASQOT-GUI

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,…

Desktop app
BiTrinA BiTrinA

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…

Desktop app
phylochipanalyser phylochipanalyser

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…

Desktop app
DeMix DeMix

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…

Desktop app
quantroSim quantroSim

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…

Desktop app
UNsupervised… UNsupervised DecOnvolution

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…

Web app
Sample Sizes Sample Sizes

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.

Desktop app
massiR massiR

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.

Desktop app
CAFE CAFE

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.

Web app
eXPatGen eXPatGen

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).

Web app
MVIAeval Deprecated MVIAeval

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…

Desktop app
Microarray Gene… Deprecated Microarray Gene Expression Markup Language

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…

Heart and Calcium… Deprecated Heart and Calcium functional Network

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…

Desktop app
MicroArray DAta… MicroArray DAta Manager

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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