Cluster Analysis
- VI-Cut – find a Clustering that best matches Imperfectly-known Cluster Hints
- Coral – Visualization for Comparing Clusterings
- WCD 0.6.3 – DNA Sequence Clustering tool
- BCLUST – Assess Reliability of Gene Clusters from Expression Data
- LEB – Localize and Extract Biclusters
- BHC 1.1.0 – Bayesian Hierarchical Clustering for R
- ChAT – Unsupervised algorithm to Search Combinatorial Chromatin Signatures.
- SpaCEM3 2.0 – Spatial Clustering with EM and Markov Model
- clusterMaker 1.10 – Creat and Visualize Cytoscape Clusters
- EDISA 1.0 – Extracting Biclusters from multiple Time-series of Gene Expression Profiles
- ClusterDis – Calculate Distances of STRUCTURE Clusters
- EXPANDER 6.06 – Gene Expression Analysis & Visualization
- CLEAN 1.2.9 – CLustering Enrichment ANalysis
- GIMM 3.8 – Gaussian Infinite Mixture Models for Cluster Analysis of Genomics Data
- FABIA 2.5.0 – Factor Analysis for Bicluster Acquisition
- BRB-ArrayTools 4.3.0 Beta2 – Visualization & Analysis of DNA Microarray Gene Expression Data
- RAP – Association Analysis Approach to Biclustering
- TriCluster / MicroCluster – Microarray Gene Expression Clustering
- CLOSET r78 – CLoud Open SequencE clusTering
- PaCE – Parallel software for Clustering DNA sequences
- pClust 1.0 – Parallel Identification of Dense Protein Clusters
- pvclust 1.2-2 – Hierarchical Clustering with P-values
- CAPIU 0.2 – Clustering using A Priori Information via Unsupervised decision trees
- BALBOA – Extension of Bicluster Analysis to allow for the Functional Classification of ORFs
- dChip 2011.12 – Analysis & Visualization of Gene Expression & SNP Microarrays
- MACML 1.1.2 – Model Averaging Clustering by Maximum Likelihood
- CAFS 1.0 – Cluster of Functional Shifts
- Bimax – Systematic Comparison and Evaluation of Biclustering Methods for Gene Expression Data
- BicAT 2.22 – Biclustering Analysis Toolbox
- Bibit – Biclustering Algorithm for Extracting Bit-Patterns from Binary Datasets
- WebGimm – Cluster Analysis Server
- MSBE 1.0.5 – Analysis of Gene Expression data using a new bi-clustering method
- generate_oriented_clusters – Single-linkage Clustering of Chromosomal Locations
- LCD – Local Coherence Detection
- SCG 20110716 – Self Consistency Grouping
- HappieClust 1.6.1 – Fast Approximate Hierarchical Clustering using Similarity Heuristics
- GEMS 1.5 – Biclustering Analysis of Expression data
- Genesis 1.7.6 / GenesisServer 1.1.0 – Cluster Analysis of Microarray data
- BiVisu 1.3 – Bicluster Visualization
- APCluster 1.2.1 – Affinity Propagation Clustering
- Trixy – Cluster of various types of Gene Expression data
- OCG 1.0 – Create Overlapping Class system
- MCL 12-135 / MCL-edge – Cluster Algorithm for Graphs
- J-Express 2012 – Analysis and Visualization of Microarray Data
- DySC 20120601 – Software for Greedy Clustering of 16S rRNA Reads
- ESPRIT-Tree – Hierarchical Clustering Analysis of Massive Sequence data
- SLP – Single-Linkage Preclustering for improved OTU clustering
- GICL 0.01 – Cluster & Assembly of a large EST/mRNA dataset
- TGICL 2.1 – TGI Clustering Tools
- ClusterViz 0.2 – Cluster Visualisation
- FreClu – Efficient Frequency-based De novo Short Read Clustering
- MITree – Clusterin Algorithm based on a Straightforward Geometric principle
- DISCLOSE 1.0.0 – DISsection of CLusters Obtained by SEries of transcriptome data
- FIVA 1.0.0 – Functional Information Viewer and Analyzer
- FunCluster 1.07 – Functional Analysis of Gene Expression data
- CLENCH 2.0 – Calculate Cluster Enrichment using the Gene Ontology
- MACCU 0.60a – Multi-Array Correlation Computation Utility
- Mosclust 1.0 – Discovery of Significant Structures in Bio-molecular data
- Clusterv 1.1 – Cluster Validation
- TimeClust 1.3 – Clustering tool for Gene Expression Time Series
- PROCSE 2.0 – Probabilistic Clustering of Sequences
- EnsemblQDB – Ensembl Query-based Biclustering
- PATTERN CLUSTERING 20060220 – Cluster a set of DNA patterns
- Excavator 2.0 – Gene Expression Data Clustering
- COMUSA – Combining Multiple Clusterings Using Similarity Graph
- relax_bicluster – Bicluster based the Probabilistic Relaxation Labeling Framework
- CLUTO 2.1.2a / gCLUTO 1.0 – Software for Clustering High-Dimensional Datasets
- COGRIM – Clustering of Genes into Regulons using Integrated Modeling
- Spark 1.1.0 – Interactive Cluster Visualization Tool
- ISA 1.0.0 – Iterative Signature Algorithm
- ExpressionView 1.00 – Explore Biclusters Identified in Gene Expression data
- TreeView 1.66 – Cluster Results Visualization Software
- QDB 1.1 – Query Driven Biclustering
- Pathway – Heritable Clustering Algorithms
- ClusterProject 1.0 – Computer Software for Clustering Analysis
- VISDA – Visualization, and Discovery for Cluster Analysis of Genomic data
- Cleaner 1.03 – Assembly of Informative, Transcript-specific Probe-clusters
- NNN 1.01 – Nearest Neighbor Networks Clustering
- HiDimViewer – Visualization tool for High-dimensional Datasets
- WCluster – Weighted Hierarchical Clustering
- CFinder 2.0.5 – Cluster data represented by Large Graphs
- SICER 1.1 – Identification of Enriched Domains from Histone modification ChIP-Seq data
- Local Clustering – Find Timeshifted and/or Inverted Relationships in Gene Expression data
- CROP 1.33 – Clustering 16S rRNA For OTU Prediction
- Modk-Prototypes – Clusters Biological Samples
- QUBIC 1.0 – Biclustering Tool for Microarray Data
- ClusterJudge – Score the Results from any Clustering Algorithm
- CurveSOM – Curve-based Custering of Time Course Expression data
- KegArray 1.2.3 – Microarray Data Analysis & Cluster
- LAS – Finding Large Average Submatricies in High Dimensional Data
- LUMIWCLUSTER 1.0 – Implement Weighted Model based Clustering
- CLUSPECT 1.0 – Supervised spectral clustering
- CompClust 1.2 – Explore and Quantify Relationships between Clustering Results
- Network Motif Clustering Toolbox 2.0 – Cluster Topological Network Motif
- MatrixClust 20080804 – Fuzzy Clustering of a Symmetric Matrix
- GaneSh – Cluster Expression Data by Gibbs sampling procedure
- OSCAR 6.1.1 – Open Source Cluster Application Resources
- Diametrical Clustering – Identify Anti-correlated Gene Clusters
- Java Treeview 1.1.6r2 – Gene Expression Visualization Tool
- psi-square 1.2 – Search the Space of Gene Vectors
- CRC 1.1 – Dirichlet Process Model-based Cluster
- EFC – Evolutionary Fuzzy Clustering
- OC 2.1a – Cluster Analysis Program
- VIZARD 1.2 – Affymetrix GeneChip® Data Analysis & Visualization
- PermutMatrix 1.9.3 – Microarray Data Cluster & Seriation Analysis
- MAGIC Tool 2.1 – MicroArray Genome Imaging & Clustering Tool
- Venn Mapper 1.01 – Compare Heterologous Microarray Data Sets
- ArrayMiner 5.3 – Microarray Gene Expression Data Analysis
- Samster 2.0 – SAM to Cluster
- AACK 1.0 – Add Annotation
- CAGED 1.1 – Cluster Analysis of Gene Expression Dynamics
- Cluster 3.0 2010.12.27 – Enhanced Version of Cluster
- AMIADA 2.0.7 – Analysis of Microarray Data
- FreeView & FreeOView – Gene Expression Dendrogram Viewer & Optimizer
- MAExplorer 0.96.34.01 – MicroArray Explorer Tool
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