Gene expression profiling based on microarray technology has been applied widely on monitoring global transcriptome changes in biological samples. In cancer research, one of the major microarray applications is to identify genes, or features, whose expression patterns can…
Babelomics
Desktop
Web

Babelomics

A web application for the functional analysis of gene expression and genomic…

A web application for the functional analysis of gene expression and genomic data. Babelomics offers user-friendly access to a full range of methods that cover: (i) primary data analysis, (ii) a…

WilcoxCV
Desktop

WilcoxCV

Provides functions to perform fast variable selection based on the Wilcoxon…

Provides functions to perform fast variable selection based on the Wilcoxon rank sum test in the cross-validation or Monte-Carlo cross-validation settings, for use in microarray-based binary…

varSelRF
Desktop

varSelRF

Implements a validated method for gene selection including bootstrap estimates…

Implements a validated method for gene selection including bootstrap estimates of classification error rate. varSelRF is a variable selection from random forests using both backwards variable…

GeneSrF
Web

GeneSrF

Implements a validated method for gene selection including bootstrap estimates…

Implements a validated method for gene selection including bootstrap estimates of classification error rate. GeneSrF is a web-based tool for applied biomedical researchers, specially for exploratory…

CMA
Desktop

CMA Classification for MicroArrays

Classifies construction and evaluation of microarrays data implementing most…

Classifies construction and evaluation of microarrays data implementing most usual approaches. CMA offers an interface to a total of more than twenty different classifiers, seven univariate and…

SCRDA
Desktop

SCRDA Shrunken Centroids Regularized Discriminant Analysis

Generalizes the idea of the “nearest shrunken centroids” (NSC) into the…

Generalizes the idea of the “nearest shrunken centroids” (NSC) into the classical discriminant analysis. The SCRDA method is specially designed for classification problems in high dimension low…

Tspair
Desktop

Tspair Top Scoring Pairs

A package which can be used to quickly identify and assess TSP (Top Scoring…

A package which can be used to quickly identify and assess TSP (Top Scoring Pairs) classifiers for gene expression data. Tspair can rapidly calculate the TSP for typical gene expression datasets,…

Ktspair
Desktop

Ktspair k-Top Scoring Pairs for Microarray Classification

A package which computes the k-TSP (k-Top Scoring Pairs). Ktspair uses pairs of…

A package which computes the k-TSP (k-Top Scoring Pairs). Ktspair uses pairs of genes to perform a classification which compares the relative ordering of the gene expressions within each profile. It…

SwitchBox
Desktop

SwitchBox

An R package for kTSP (k–Top Scoring Pairs). SwitchBox selects the gene pairs…

An R package for kTSP (k–Top Scoring Pairs). SwitchBox selects the gene pairs for the kTSP decision rule. The package has a method for calculating sample-specific scores based on the pairs, which…

S-CART
Desktop

S-CART sequential classification-and-regression-tree

Variables selection in the binary classification setting and compares it…

Variables selection in the binary classification setting and compares it against the more sophisticated procedures using simulated and real biological data. S-CART outperforms stochastic search…

geneClassifiers
Desktop

geneClassifiers

Aims for easy accessible application of classifiers which have been published…

Aims for easy accessible application of classifiers which have been published in literature using an ExpressionSet as input. geneClassifiers provides a method for running gene classifiers generating…

kernelPLS
Desktop

kernelPLS

A feature selection method based on the partial least squares (PLS) and theory…

A feature selection method based on the partial least squares (PLS) and theory of Reproducing Kernel Hilbert Space. kernelPLS makes use of the relationship between PLS and linear discriminant…

FiGS
Web

FiGS Filter-based Gene Selection

A web-based workbench where user can conveniently compare the classification…

A web-based workbench where user can conveniently compare the classification performances of many different filter-based gene selection procedures.

MF-GE
Desktop
SET
Desktop

SET Signature Evaluation Tool

A Java tool to evaluate and visualize the sample discrimination abilities of…

A Java tool to evaluate and visualize the sample discrimination abilities of gene expression signatures.

geneCommittee
Web

geneCommittee

A web-based interactive tool for routinely evaluating the discriminative…

A web-based interactive tool for routinely evaluating the discriminative classification power of custom hypothesis in the form of biologically relevant gene sets.

M@CBETH
Web
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