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Classification software tools | Gene expression microarray data analysis

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…
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Babelomics
Desktop
Web

Babelomics

Serves for the functional analysis of gene expression and genomic data.…

Serves for the functional analysis of gene expression and genomic data. Babelomics offers the possibility to explore the effects of alteration in gene expression levels or changes in genes sequences…

Decision Forest
Desktop

Decision Forest

Outperforms decision tree in both training and validation. Decision forest is…

Outperforms decision tree in both training and validation. Decision forest is an ensemble method developed by combining the predictions from multiple independent decision tree models to reach a…

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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…

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EFS
Web
Desktop

EFS Ensemble Feature Selection

Allows binary classification for random clinical trials. EFS is based on the…

Allows binary classification for random clinical trials. EFS is based on the idea of ensemble learning and thus is based on the aggregation of multiple feature selection (FS) methods. It was…

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mRMR
Algorithm

mRMR minimum Redundancy Maximum Relevance

Provides a theoretical analysis of the minimal-redundancy-maximal-relevance…

Provides a theoretical analysis of the minimal-redundancy-maximal-relevance condition. mRMR is a framework allowing users to minimize redundancy, and it uses a series of intuitive measures of…

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ClusterSignific…
Desktop

ClusterSignificance

Allows to determine significant separations in reduced dimensionality data.…

Allows to determine significant separations in reduced dimensionality data. ClusterSignificance contains three stages: (1) principal curve projection, (2) separation classification, and (3) score…

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RefBool
Desktop

RefBool

Provides a computational method for discretization of gene expression data.…

Provides a computational method for discretization of gene expression data. RefBool uses a user-defined gene expression library as a reference for defining each genes state. Each query can be…

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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 can…

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DWFS
Web

DWFS Dragon Wrapper Feature Selection

It allows user to select characteristics for a variety of problems. DWFS is…

It allows user to select characteristics for a variety of problems. DWFS is based on a parallel genetic algorithm. It incorporates various filtering methods that can be applied as a pre-processing…

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ShenEtAl2017
Desktop

ShenEtAl2017

Allows identification of gene pairs associated with biological phenotype or…

Allows identification of gene pairs associated with biological phenotype or clinical outcome. This program is an equivalent model subject to a sum-to-zero constraint on regression coefficients. It…

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optSelect
Desktop

optSelect

Allows evaluation of the classification accuracy of the agents. optSelect is a…

Allows evaluation of the classification accuracy of the agents. optSelect is a multi-stage nested ensemble feature selection algorithm that accounts for function perturbation and data perturbation…

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PROPS
Desktop

PROPS PRObabilistic Pathway Score

Allows individualized pathway-based classification. PROPS creates…

Allows individualized pathway-based classification. PROPS creates individualized features that reflect pathway activity using Gaussian Bayesian networks. It can calculate the log likelihood of each…

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GD-RDA
Desktop

GD-RDA

Produces a geometric version of the diagonalization method for regularized…

Produces a geometric version of the diagonalization method for regularized discriminant analysis (RDA). GD-RDA is a geometric diagonalization method for the regularized discriminant analysis. The…

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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…

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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,…

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fgsPCA
Desktop

fgsPCA Fused and Grouped sparse Principal Component Analysis

Enables incorporation of prior biological information in principal component…

Enables incorporation of prior biological information in principal component analysis (PCA). fgsPCA is a sparse method that allows identification of genes and pathways. It can incorporate prior…

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CAFÉ-Map
Desktop

CAFÉ-Map Context Aware FEature MAPing

Assists users in estimating the relative importance of different features for…

Assists users in estimating the relative importance of different features for individual examples or in different regions of the feature space. CAFÉ-Map is a locally linear classifier with built-in…

GeNNet
Desktop

GeNNet

Unifies scientific workflows with graph databases for selecting relevant genes…

Unifies scientific workflows with graph databases for selecting relevant genes according to the evaluated biological systems. GeNNet is an integrated transcriptome analysis platform that includes…

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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…

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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…

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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…

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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.

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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.

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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…

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Lee2008
Algorithm

Lee2008

Furnishes a method to select and classify gene expressions for microarray data…

Furnishes a method to select and classify gene expressions for microarray data of ovarian cancer. The algorithm first identifies gene markers from the target genes. Then, identified gene are used to…

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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…

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INTERACT
Algorithm

INTERACT

Employs backward elimination to remove features with no or low c-contribution.…

Employs backward elimination to remove features with no or low c-contribution. INTERACT is an algorithm that searches for interacting features. It consists of two major parts: (i) the features are…

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FCBF
Algorithm

FCBF Fast Correlation-Based Filter

Provides a concept of predominant correlation. FCBF is an algorithm that…

Provides a concept of predominant correlation. FCBF is an algorithm that introduce an efficient way of analyzing feature redundancy and design a fast correlation based filter approach. It was…

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CFS
Algorithm

CFS Correlation-based Feature Selection

Measures correlation between nominal characteristics so that numerical…

Measures correlation between nominal characteristics so that numerical characteristics are first discretized. CFS is a fully automatic algorithm that does not require the user to specify any…

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MALA
Desktop

MALA MicroArray Logic Analyzer

Allows microarray gene expression analysis. MALA is based on an alternative…

Allows microarray gene expression analysis. MALA is based on an alternative clustering method and an effective classification approach to distinguish the different experimental samples. It follows…

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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…

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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…

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AUREA
Desktop

AUREA Adaptive Unified Relative Expression Analyzer

Furnishes a set of relative expression analyses. AUREA is an open source…

Furnishes a set of relative expression analyses. AUREA is an open source software that gathers four methods: (i) the The Top-Scoring Pair (TSP), the k-TSP, The Top-Scoring Triplet (TST) and The…

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Relief
Algorithm

Relief

Detects features which are statistically relevant to a target concept. Relief…

Detects features which are statistically relevant to a target concept. Relief is a simple algorithm which relies entirely on a statistical method. This model employs few heuristics, and is less often…

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Information…
Algorithm

Information Gain

Provides an algorithm to feature selection for machine learning that uses a…

Provides an algorithm to feature selection for machine learning that uses a correlation based heuristic to evaluate the merit of features. Information Gain is an approach where the effectiveness of…

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consensusOV
Desktop

consensusOV

Contains a set of functions for subtyping of cancer. consensusOV implements…

Contains a set of functions for subtyping of cancer. consensusOV implements four major subtype classifiers for high-grade serous (HGS) ovarian cancer. In addition, this package implements a consensus…

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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…

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M@CBETH
Web

M@CBETH MicroArray Classification BEnchmarking Tool on Host server

Performs microarray classification by providing prediction classification…

Performs microarray classification by providing prediction classification methods using randomizations of the benchmarking dataset. M@CBETH offers two services: benchmarking and prediction.…

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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.

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MF-GE
Desktop

MF-GE Multiple Filters enhanced Genetic Ensemble system

A hybrid system for feature selection and sample classification of…

A hybrid system for feature selection and sample classification of high-dimensional dataset.

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viRF
Desktop

viRF Variable Importance-weighted Random Forests

Offers a soft manner to select features during the improvement of the…

Offers a soft manner to select features during the improvement of the performance of Random Forests (RF) method. viRF can focus on the most informative features while not completely ignoring…

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PLASMID
Desktop

PLASMID PLasmid Analysis System and Marker IDentification

Distinguishes probes for plasmids or bacteria classification. PLASMID aims to…

Distinguishes probes for plasmids or bacteria classification. PLASMID aims to design both mixed microarrays and expression arrays. It offers an integrated environment including several displaying and…

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