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…
Dcluster
Desktop

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…

ClustEval
Web

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…

rqubic
Desktop

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…

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…

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BicOverlapper
Desktop

BicOverlapper

Allows to visualize complex gene expression analysis results coming from…

Allows to visualize complex gene expression analysis results coming from biclustering algorithms. BicOverlapper visualizes the most relevant aspects of the analysis, including expression data,…

QUBIC
Desktop

QUBIC QUery BICluster

Implements a well-cited biclustering algorithm, QUBIC, for the interpretation…

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 with analyses…

BicPAMS
Desktop

BicPAMS Biclustering based on PAttern Mining Software

Discovers exhaustive and flexible structures of biclusters, with…

Discovers exhaustive and flexible structures of biclusters, with parameterizable coherency and robustness to noise and missings. BicPAMS combines state-of-the-art pattern-based biclustering…

isa2
Desktop

isa2 Iterative Signature Algorithm

A biclustering algorithm that finds modules in an input matrix.

A biclustering algorithm that finds modules in an input matrix.

Mfuzz
Desktop

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).

iBBiG
Desktop

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…

BicAT
Desktop

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.

FABIA
Desktop

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.

Wigwams
Desktop

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.

pyGCluster
Desktop

pyGCluster

A clustering algorithm focusing on noise injection for subsequent cluster…

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

SCUDO
Web

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…

RSAT…
Web

RSAT matrix-clustering

Supports dynamic browsing of motif trees with custom collapse/expansion of…

Supports dynamic browsing of motif trees with custom collapse/expansion of branches. RSAT matrix-clustering also provides multiple ways to inspect the results: motif forest with branch motifs at each…

EXPANDER
Desktop

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…

CnG
Desktop

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…

mAPKL
Desktop

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…

BiVisu
Desktop

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.

XMotifs
Desktop

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…

Bi-Force
Desktop

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…

BHC
Desktop

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…

BicNET
Desktop

BicNET Biclustering NETworks

Enables the efficient unsupervised analysis of largescale network data for the…

Enables the efficient unsupervised analysis of largescale network data for the discovery of coherent modules with parameterizable homogeneity. BicNET is a biclustering algorithm to discover…

xCell
Web

xCell

Performs cell type enrichment analysis from gene expression data for 64 immune…

Performs cell type enrichment analysis from gene expression data for 64 immune and stroma cell types. xCell is a gene signatures-based method learned from thousands of pure cell types from various…

CAMPAIGN
Desktop
goCluster
Desktop

goCluster

Enables scientists to employ annotation information, clustering algorithms and…

Enables scientists to employ annotation information, clustering algorithms and visualization tools in their array data analysis and interpretation strategy. goCluster is a solution that implements a…

APCluster
Desktop

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…

BCP
Desktop

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…

PWKmeans
Desktop

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…

ExpressionView
Desktop

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.

BBC
Desktop

BBC Bayesian BiClustering

Identifies multiple clusters of gene expression data. BBC algorithm outperforms…

Identifies multiple clusters of gene expression data. BBC algorithm outperforms other methods in both robustness and accuracy, using simulated data both from the model and with realistic characters.…

CLIC
Web
VisHiC
Web

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…

ClusTrack
Web

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…

BiC2PAM
Desktop

BiC2PAM BiClustering with Constraints using PAttern Mining

Extends (pattern-based) biclustering algorithms to guarantee the satisfiability…

Extends (pattern-based) biclustering algorithms to guarantee the satisfiability of constraints derived from background knowledge and to effectively explore efficiency gains from their incorporation.…

CORM
Desktop

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…

MDI-GPU
Desktop

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.…

BiGGEsTS
Desktop

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.

parcor
Desktop

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…

clusterRepro
Desktop

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…

BicAT
Desktop

BicAT Biclustering Analysis Toolbox

Finds the hidden order-preserving submatrices in the random matrix. BicAT…

Finds the hidden order-preserving submatrices in the random matrix. BicAT recovers the hidden order-preserving submatrices with a very high success rate. It offers a graphical user interface (GUI)…

tightClustering
Desktop

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…

biclust
Desktop

biclust

Provides several algorithms to find biclusters in two-dimensional data. biclust…

Provides several algorithms to find biclusters in two-dimensional data. biclust provides methods for data preprocessing (normalization and discretisation), visualisation, and validation of bicluster…

Plaid
Desktop

Plaid

Provides several algorithms to find biclusters in two-dimensional data. Plaid…

Provides several algorithms to find biclusters in two-dimensional data. Plaid is based on speedy individual differences clustering and uses binary least squares to update the cluster membership…

LAS
Desktop

LAS Large Average Submatrices

Finds large average submatrices within a given real-valued data matrix. LAS…

Finds large average submatrices within a given real-valued data matrix. LAS operates in an iterative-residual fashion, and is driven by a Bonferroni-based significance score that effectively trades…

CPB
Desktop

CPB Correlated Patterns Biclustering

Discovers genes that function in a common biological process. CPB is a two-step…

Discovers genes that function in a common biological process. CPB is a two-step Pearson correlation based biclustering approach to mine genes that are co-regulated with a given reference gene. The…

BicARE
Desktop

BicARE

Biclustering Analysis and Results Exploration.

Biclustering Analysis and Results Exploration.

eisa
Desktop

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…

GeneNT
Desktop

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…

attract
Desktop

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…

PACK
Desktop

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…

FuzzyClust
Web

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…

Furby
Desktop

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…

BicSPAM
Desktop

BicSPAM

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

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

CTen
Web

CTen Cell Type enrichment

Determines if the observed gene regulation is the result of changes in the…

Determines if the observed gene regulation is the result of changes in the cellular make up of the sample. CTen can distinguish between active gene transcription and apparent gene expression…

BicPAM
Desktop

BicPAM

Integrates existing principles made available by state-of-the-art pattern-based…

Integrates existing principles made available by state-of-the-art pattern-based approaches with two new contributions. BicPAM is an efficient attempt to exhaustively mine non-constant types of…

Co-clustering
Desktop

Co-clustering

Identifies potential local patterns, characterized by coherent groups of genes…

Identifies potential local patterns, characterized by coherent groups of genes and conditions. Co-clustering employs an alternating minimization scheme and generates coclusters in a…

supraHex
Desktop

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…

BiCluE
Desktop

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.

Hierarchical…
Desktop

Hierarchical Density-Based Spatial Clustering of Applications with Noise

Provides a clustering hierarchy from which a simplified tree of significant…

Provides a clustering hierarchy from which a simplified tree of significant clusters can be constructed. HDBSCAN performs Density-Based Spatial Clustering of Applications with Noise over varying…

DeBi
Desktop

DeBi Differentially Expressed Biclusters

Discovers maximum size homogeneous biclusters in which each gene is strongly…

Discovers maximum size homogeneous biclusters in which each gene is strongly associated with a subset of samples. DeBi is based on a well known data mining approach called frequent item set. The…

BiBit
Desktop

BiBit

Extracts Bit-Patterns from binary datasets. BiBit will apply a cumulative…

Extracts Bit-Patterns from binary datasets. BiBit will apply a cumulative binarization process and will generate 11 different versions of the same dataset. The Bibit algorithm source code is…

GeneClust
Desktop
Web

GeneClust

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

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

BiBench
Desktop

BiBench

A Python library designed to simplify biclustering tasks.

A Python library designed to simplify biclustering tasks.

COALESCE
Web
ArrayMiner
Desktop

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.

Cluster
Desktop

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.

Biosphere
Web

Biosphere

Allows different algorithms to be used to cluster gene expression datasets…

Allows different algorithms to be used to cluster gene expression datasets uploaded by individual users via the Web. Biosphere is a web server application that allows the users to do the following:…

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