Microarray technology has been widely applied in biological and clinical studies for simultaneous monitoring of gene expression in thousands of genes. Gene clustering analysis is found useful for discovering groups of correlated genes potentially co-regulated or associated to…
Desktop app
Web app
Babelomics Babelomics

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…

Desktop app
Affinity Propagation… Affinity Propagation Clustering

APCluster Affinity Propagation Clustering

Allows for determining typical cluster members. APCluster provides leveraged…

Allows for determining typical cluster members. APCluster provides leveraged affinity propagation and an algorithm for exemplar-based agglomerative clustering that can also be used to join clusters…

Desktop app
The Clustering of… The Clustering of Regression Models Method

CORM The Clustering of Regression Models Method

Clusters genes using gene expression data and provides data examples…

Clusters genes using gene expression data and provides data examples illustrating each clustering function in the package. CORM can be applied to cluster gene expression data collected under various…

Desktop app
Bayesian Change Point Bayesian Change Point

BCP Bayesian Change Point

Provides an implementation of the Barry and Hartigan’s product partition…

Provides an implementation of the Barry and Hartigan’s product partition model for the normal errors change point problem using Markov Chain Monte Carlo (MCMC). BCP is sensitive enough to catch…

Desktop app
parcor parcor

parcor

Combines regularized regression methods with the estimation of Graphical…

Combines regularized regression methods with the estimation of Graphical Gaussian models. parcor framework includes various existing methods as well as two new approaches based on ridge regression…

Desktop app
tightClustering tightClustering

tightClustering

Produces tight and stable clusters without forcing all points into clusters.…

Produces tight and stable clusters without forcing all points into clusters. Tight clustering has been developed specifically to avoid the contamination of tightly regulated expression patterns of…

Desktop app
clusterRepro clusterRepro

clusterRepro

A validation procedure for clusters found in datasets independent of the one in…

A validation procedure for clusters found in datasets independent of the one in which they were characterized. An implementation of this algorithm is in a package called ClusterRepro. A cluster…

Desktop app
EXpression Analyzer… EXpression Analyzer and DisplayER

EXPANDER EXpression Analyzer and DisplayER

An integrated software platform for the analysis of microarray gene expression…

An integrated software platform for the analysis of microarray gene expression data. EXPANDER is designed to support all the stages of microarray data analysis, from raw data normalization to…

Desktop app
QUery BICluster QUery BICluster

QUBIC QUery BICluster

An R package that implements a well-cited biclustering algorithm, QUBIC, for…

An R package that implements a well-cited biclustering algorithm, QUBIC, for the interpretation of gene expression profile data. The unique features of QUBIC include: (i) biclustering is integrated…

Desktop app
GeneNT GeneNT

GeneNT

An improved gene clustering approach for inferring gene signaling pathways from…

An improved gene clustering approach for inferring gene signaling pathways from gene microarray data. geneNT has the following features: (i) it tends to group functionally related genes into a tight…

Desktop app
attract attract

attract

Identifies the number of clusters which best separate phenotypic groups.…

Identifies the number of clusters which best separate phenotypic groups. attract is an alternative way to validate the results of a cluster analysis that explicitly takes into account the…

Desktop app
Penalized and… Penalized and Weighted K-means

PWKmeans Penalized and Weighted K-means

A class of loss functions for cluster analysis and applied in high-throughput…

A class of loss functions for cluster analysis and applied in high-throughput genomic and proteomic data. PWKmeans is used to allow a set of scattered objects without being clustered. It allows a…

Desktop app
Profile Analysis… Profile Analysis using Clustering and Kurtosis

PACK Profile Analysis using Clustering and Kurtosis

Finds genes that define either small outlier subgroups or major subdivisions,…

Finds genes that define either small outlier subgroups or major subdivisions, depending on the sign of kurtosis. The method can also be used as a filtering step, prior to supervised analysis, in…

Web app
FuzzyClust FuzzyClust

FuzzyClust

Identifies cluster structures in high-dimensional datasets, such as those…

Identifies cluster structures in high-dimensional datasets, such as those obtained in DNA microarray and quantitative proteomics experiments. FuzzyClust estimates the optimal parameter values by…

Desktop app
mAPKL mAPKL

mAPKL

A hybrid gene selection method, which is based on the hypothesis that among the…

A hybrid gene selection method, which is based on the hypothesis that among the statistically significant genes in a ranked list, there should be clusters of genes that share similar biological…

Web app
ClusTrack ClusTrack

ClusTrack

A tool for clustering data sets of coordinates relative to a genome assembly,…

A tool for clustering data sets of coordinates relative to a genome assembly, i.e. genomic tracks. ClusTrack allows fine-tuned clustering analyses to be specified through a web-based interface. We…

Web app
ClustEval ClustEval

ClustEval

A clustering analysis platform to promote streamlined evaluation, comparison…

A clustering analysis platform to promote streamlined evaluation, comparison and reproducibility of clustering results in the future. This allowed us to objectively evaluate the performance of all…

Desktop app
MDI-GPU MDI-GPU

MDI-GPU

An improved implementation of a Bayesian correlated clustering algorithm, that…

An improved implementation of a Bayesian correlated clustering algorithm, that permits integrated clustering to be routinely performed across multiple datasets, each with tens of thousands of items.…

Desktop app
CLUSTERnGO CLUSTERnGO

CnG CLUSTERnGO

A gene expression analysis tool that clusters gene (or protein) expression…

A gene expression analysis tool that clusters gene (or protein) expression profiles, and extracts their GO enrichments. For probabilistic inference, CnG applies a Markov chain Monte Carlo procedure…

Desktop app
Bi-Force Bi-Force

Bi-Force

A software tool implementing a novel heuristic algorithm that efficiently…

A software tool implementing a novel heuristic algorithm that efficiently solves the weighted bicluster editing problem. It is based on the weighted bicluster editing model, to perform biclustering…

Web app
Signature-based… Signature-based ClUstering for DiagnOstic purposes

SCUDO Signature-based ClUstering for DiagnOstic purposes

An online tool for the analysis of gene expression profiles for diagnostic and…

An online tool for the analysis of gene expression profiles for diagnostic and classification purposes. SCUDO is based on a method for the clustering of profiles based on a subject-specific, as…

Web app
VisHiC VisHiC

VisHiC

A public web server for clustering and interpreting gene expression data. The…

A public web server for clustering and interpreting gene expression data. The tool is designed to extract the most significant biological features of a dataset in a single run. The main output is a…

Desktop app
Dcluster Dcluster

Dcluster

This Python package implements the clustering algorithm proposed by Alex…

This Python package implements the clustering algorithm proposed by Alex Rodriguez and Alessandro Laio. It generates the initial rho and delta values for each observation then use these values to…

Desktop app
supraHex supraHex

supraHex

An open-source R/Bioconductor package for tabular omics data analysis using a…

An open-source R/Bioconductor package for tabular omics data analysis using a supra-hexagonal map. A supra-hexagonal map is a giant hexagon on a 2-dimensional grid seamlessly consisting of smaller…

Desktop app
Web app
GeneClust GeneClust

GeneClust

A tool used for exploratory analysis of gene expression microarray data.

A tool used for exploratory analysis of gene expression microarray data.

Desktop app
BicSPAM BicSPAM

BicSPAM

Biclustering algorithms to perform flexible, exhaustive and noise-tolerant…

Biclustering algorithms to perform flexible, exhaustive and noise-tolerant biclustering based on sequential patterns.

Desktop app
BiCluE BiCluE

BiCluE

A bi-clustering software for solving the weighted/unweighted bi-cluster editing…

A bi-clustering software for solving the weighted/unweighted bi-cluster editing problem.

Desktop app
Biclustering Analysis… Biclustering Analysis Toolbox

BicAT Biclustering Analysis Toolbox

A graphical user interface software for the analysis of gene expression data.

A graphical user interface software for the analysis of gene expression data.

Desktop app
BiGGEsTS BiGGEsTS

BiGGEsTS

A free and open source software tool providing an integrated environment for…

A free and open source software tool providing an integrated environment for the biclustering analysis of time series gene expression data.

Desktop app
BiVisu BiVisu

BiVisu

An open-source software tool for detecting and visualizing biclusters embedded…

An open-source software tool for detecting and visualizing biclusters embedded in a gene expression matrix.

Desktop app
Iterative Signature… Iterative Signature Algorithm

isa2 Iterative Signature Algorithm

A biclustering algorithm that finds modules in an input matrix.

A biclustering algorithm that finds modules in an input matrix.

Desktop app
XMotifs XMotifs

XMotifs

Searches for rows with constant values over a set of columns, and aims to find…

Searches for rows with constant values over a set of columns, and aims to find conserved genes expression motifs (xMOTIFs) which defined as a subset of genes (rows) that is simultaneously conserved…

Desktop app
Bayesian Hierarchical… Bayesian Hierarchical Clustering

BHC Bayesian Hierarchical Clustering

The method performs bottom-up hierarchical clustering, using a Dirichlet…

The method performs bottom-up hierarchical clustering, using a Dirichlet Process (infinite mixture) to model uncertainty in the data and Bayesian model selection to decide at each step which clusters…

Desktop app
Wigwams Wigwams

Wigwams

A computational tool for analysing multiple gene expression time series data…

A computational tool for analysing multiple gene expression time series data sets for the same organism.

Desktop app
Mfuzz Mfuzz

Mfuzz

Package for noise-robust soft clustering of gene expression time-series data…

Package for noise-robust soft clustering of gene expression time-series data (including a graphical user interface).

Desktop app
BiBench BiBench

BiBench

A Python library designed to simplify biclustering tasks.

A Python library designed to simplify biclustering tasks.

Desktop app
BicARE BicARE

BicARE

Biclustering Analysis and Results Exploration.

Biclustering Analysis and Results Exploration.

Web app
Combinatorial… Combinatorial Algorithm for Expression and…
Desktop app
Expression data… Expression data analysis via the Iterative…

eisa Expression data analysis via the Iterative Signature Algorithm

A package based on an Iterative Signature Algorithm (ISA) which is a…

A package based on an Iterative Signature Algorithm (ISA) which is a biclustering method; it finds correlated blocks (transcription modules) in gene expression (or other tabular) data. The ISA is…

Desktop app
ExpressionView ExpressionView

ExpressionView

An R package that provides an interactive environment to explore biclusters…

An R package that provides an interactive environment to explore biclusters identified in gene expression data.

Desktop app
Factor Analysis for… Factor Analysis for Bicluster Acquisition

FABIA Factor Analysis for Bicluster Acquisition

A model-based technique for biclustering that is clustering rows and columns…

A model-based technique for biclustering that is clustering rows and columns simultaneously.

Desktop app
Iterative Binary… Iterative Binary Biclustering of Genesets

iBBiG Iterative Binary Biclustering of Genesets

A package based on a bi-clustering algorithm to perform meta-GSA that addresses…

A package based on a bi-clustering algorithm to perform meta-GSA that addresses the shortcomings of ‘ranked list’ meta-GSA approaches. iBBiG scales well when applied to hundreds of datasets, is…

Desktop app
rqubic rqubic

rqubic

Solves the biclustering problem in a more general form, compared to existing…

Solves the biclustering problem in a more general form, compared to existing algorithms, through employing a combination of qualitative (or semi-quantitative) measures of gene expression data and a…

Desktop app
ArrayMiner ArrayMiner

ArrayMiner

A set of analysis tools using advanced algorithms to reveal the true structure…

A set of analysis tools using advanced algorithms to reveal the true structure of your gene expression data.

Desktop app
Cluster Cluster

Cluster

Performs a variety of types of cluster analysis and other types of processing…

Performs a variety of types of cluster analysis and other types of processing on large microarray datasets.

Desktop app
pyGCluster pyGCluster

pyGCluster

A clustering algorithm focusing on noise injection for subsequent cluster…

A clustering algorithm focusing on noise injection for subsequent cluster validation.

Desktop app
Furby Furby

Furby

An interactive visualization tool for exploring and analyzing fuzzy…

An interactive visualization tool for exploring and analyzing fuzzy biclustering results. First, the technique provides an overview of a biclustering result, showing the actual data that forms the…

Web app
Clustering analysis… Clustering analysis of Large microarray data with…
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