Cluster Analysis聚类分析软件

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GuidedClustering 0.9 – Combined analysis of a Microarray and Experimental data
Kolmogorov – Compression-based Classification of Biological Sequences and Structures
GenClust 2.0 – Clustering Gene Expression data
ValWorkBench 1.0 – Java library for Cluster Validation
HAC – Hierarchical Agglomerative Clustering for a large-scale Network data
Genesis 1.7.7 / GenesisServer 1.1.0 – Cluster Analysis of Microarray data
VISDA 1.0 – Visualization, and Discovery for Cluster Analysis of Genomic data
LRC – Logistic Regression Model and Clustering Approach
KegArray 1.2.4 – Microarray Data Analysis & Cluster
CLAG 2.18.1 – Unsupervised Non Hierarchical Clustering algorithm
Hammock 1.02 – Hidden Markov Model-based Peptide Clustering algorithm
FreeView & FreeOView – Gene Expression Dendrogram Viewer & Optimizer
Furby 3.1.3beta1 – Fuzzy Force-Directed Bicluster Visualization
TransClust – A Feature-rich Clustering tool for Biomedical Data sets
Bi-Force v2 – Large-scale Bicluster Editing and its application to Gene Expression data Biclustering
BiCluE – Weighted Bi-cluster Editing of Biomedical Data
k-link – EST Clustering Algorithm
DCAFP – Density-based Clustering Approach with Functional Preferences
MOCSVM 2 – Multiobjective Clustering with Support Vector Machine
DGEclust 20150129 – Hierarchical non-parametric Bayesian Clustering of Digital Expression data
SCUDO – Signature-based Clustering of Expression Profiles
TimeClust 1.3 – Clustering tool for Gene Expression Time Series
CLIC – Clustering Large Microarray
bio-MOSAIC – Multiple Orthologous Sequence Analysis and Integration by Cluster optimization
GDHC – Nonlinear Hierarchical Clustering
PFClust – Novel Parameter Free Clustering algorithm
SNN-Cliq 1.0 – Clustering method for High Dimensional Dataset
BCCA / ACCA / DCCA – Bi-Correlation / Average Correlation / Divisive Correlation Clustering Algorithm
MBCluster.Seq 1.0 – Model-Based Clustering for RNA-seq Data
Starcode 1.0 – All Pairs Search and Sequence Clustering
ELaSTIC 1.70 – Rapid Identification and Clustering of Similar Sequences
SCBD – Sequence Clustering based HIV Incident/Chronic Identification
HTSCluster 2.0.4 – Clustering High Throughput Sequencing (HTS) data
piClust – Find piRNA Clusters and Transcripts from small RNA-seq data
Bicluster – Seed-based Biclustering of Gene Expression Data
geneRxCluster 1.2.0 – Detect Differential Clustering of Genomic Sites
Mfuzz 2.27.0 – Soft Clustering of Microarray data
APCluster 1.4.1 – Affinity Propagation Clustering
FABIA 2.12.0 – Factor Analysis for Bicluster Acquisition
SiLiX 1.2.9 – Ultra-fast Sequence Clustering from Similarity Networks
RPMM 1.20 – Recursively Partitioned Mixture Model for Beta and Gaussian Mixtures
Cluster 3.0 2014.10.07 – Enhanced Version of Cluster
CLOSET r78 – CLoud Open SequencE clusTering
pvclust 1.3-2 – Hierarchical Clustering with P-values
MACML 1.1.2 – Model Averaging Clustering by Maximum Likelihood
MCL 14-137 / MCL-edge – Cluster Algorithm for Graphs
MACCU 0.7 – Multi-Array Correlation Computation Utility
PermutMatrix 1.9.3 – Microarray Data Cluster & Seriation Analysis
AptaCluster / AptaGUI – Efficient Clustering of HT-SELEX Aptamer Pools
MUFOLD_CL – Protein Structural Model Clustering
JustClust – Analysing Biological Data with Cluster Analysis
SCPS 0.9.8 – Spectral Clustering of Protein Sequences
Bibit – Biclustering Algorithm for Extracting Bit-Patterns from Binary Datasets
GenomeCluster 20140824 – Clusters of Genome Elements
MCAM v9 – Multiple Clustering Analysis Methodology
QCanvas 1.2.1 – Fast Clustering and Visualization of data
wDCB – Weighted Constrained Bi-Clustering
AutoSOME 2.0 – Clustering method for Identifying Gene Expression Modules
kClust – Clustering of Large Protein Sequence Databases
UIcluster 3.0.5 – Parallel Clustering of EST (Gene) Sequences
tlcluster 1.0 – Clustering on Fasta Formatted Sequences
TBC 1.0 – Taxonomy-Based Clustering
CAPIU 0.2 – Clustering using A Priori Information via Unsupervised decision trees
M-pick – Modularity-based Clustering method for OTU picking
CAGEScan-Clustering – Create CAGEscan Clusters from CAGE paired-end reads
RECLU 1.0 – Clustering pipeline with multiple scales for Capped Analysis of Gene Expression (CAGE) datasets
SS-CoSBI – Finding Combinatorial Histone Code by Semi-supervised Biclustering
CoSBI – Identify Combinatorial Chromatin Modification Patterns across Genomic Loci
NCIS – Network-Assisted Co-clustering Algorithm to Discover Cancer Subtypes based on Gene Expression
SPICi – Fast Biological Network Clustering Algorithm
SP/SS Clustering – Superparamagnetic Clustering and Sequential Superparamagnetic Clustering
rsgcc 1.0.6 – Gini methodology-based correlation and Clustering analysis of Microarray and RNA-Seq Gene Expression data
EFC – Evolutionary Fuzzy Clustering
ESPRIT-Tree 1.2 – Hierarchical Clustering Analysis of Massive Sequence data
clusterMaker2 0.9.3 – Creat and Visualize Cytoscape Clusters
CFinder 2.0.6 – Cluster data represented by Large Graphs
hclust 1.0 – Clustering Expression data with Hopfield Networks
BCLUST – Assess Reliability of Gene Clusters from Expression Data
MSClust 20130708 – Clustering 16S rRNA sequences into OTUs
LUMIWCLUSTER 1.0.2 – Implement Weighted Model based Clustering
OC 2.1a – Cluster Analysis Program
McKmeans 0.42 – Multi-core algorithm for Clustering extremely large datasets
HiFiX 1.0.5 – High-quality Sequence Clustering
iNJclust – Genotypic data Clustering software
KAUSTNMF – Non-negative Matrix Factorization by Maximizing Correntropy for Cancer Clustering
QDB 1.1 – Query Driven Biclustering
EnsemblQDB – Ensembl Query-based Biclustering
CrunchClust V43 – Clustering software for 454 Sequence
SEED 1.5.1 – Clustering Next Generation Sequences
ClutrFree 1.4 – Cluster Viewer Package
LCS-HIT 0.5.3 – Sequecence Clustering tool
Gclust 3.5.5z3 – Genome-wide Clustering
DomClust – Hierarchical Clustering for Orthologous Domain Classification
CAGT r132 – Clustering AGgregation Tool
fuzzyClustering – K-partite Graph Clustering algorithm that allows for Overlapping (Fuzzy) Clusters
iCluster 2.1.0 / iClusterPlus 0.99.4 – Integrative Clustering of Multiple Genomic Data Types
BiGGEsTS 1.0.5 – Biclustering Analysis of Time Series Gene Expression Data
OSCAR 6.1.1 – Open Source Cluster Application Resources
GWproxy – Clustering Metagenome Short Reads using Weighted Proteins
Java Treeview 1.1.6r4 – Gene Expression Visualization Tool
CLEAN 1.3.1 – CLustering Enrichment ANalysis
ClusterA 1004 – Calculating Silhouette scores for Assessment of SNP Genotype Clusters
Excavator 2.0 – Gene Expression Data Clustering
CLCL 1.0 – CLique CLustering
Treebic 1.11 – Hierarchical Generative Biclustering for MicroRNA Expression Analysis
Secator/DPC – Sequence Clustering from a Multiple Alignment
ClusterLustre 1.2 – Consensus Clustering
SCHype 1.0 – Spectral Clustering in Hypergraphs
Network Motif Clustering Toolbox 2.0 – Cluster Topological Network Motif
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
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
EDISA 1.0 – Extracting Biclusters from multiple Time-series of Gene Expression Profiles
GIMM 3.8 – Gaussian Infinite Mixture Models for Cluster Analysis of Genomics Data
RAP – Association Analysis Approach to Biclustering
TriCluster / MicroCluster – Microarray Gene Expression Clustering
PaCE – Parallel software for Clustering DNA sequences
pClust 1.0 – Parallel Identification of Dense Protein Clusters
BALBOA – Extension of Bicluster Analysis to allow for the Functional Classification of ORFs
dChip 2011.12 – Analysis & Visualization of Gene Expression & SNP Microarrays
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
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
BiVisu 1.3 – Bicluster Visualization
Trixy – Cluster of various types of Gene Expression data
OCG 1.0 – Create Overlapping Class system
J-Express 2012 – Analysis and Visualization of Microarray Data
DySC 20120601 – Software for Greedy Clustering of 16S rRNA Reads
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
FunCluster 1.07 – Functional Analysis of Gene Expression data
CLENCH 2.0 – Calculate Cluster Enrichment using the Gene Ontology
Mosclust 1.0 – Discovery of Significant Structures in Bio-molecular data
Clusterv 1.1 – Cluster Validation
PATTERN CLUSTERING 20060220 – Cluster a set of DNA patterns
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
Pathway – Heritable Clustering Algorithms
ClusterProject 1.0 – Computer Software for Clustering Analysis
Cleaner 1.03 – Assembly of Informative, Transcript-specific Probe-clusters
NNN 1.01 – Nearest Neighbor Networks Clustering
HiDimViewer – Visualization tool for High-dimensional Datasets
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
LAS – Finding Large Average Submatricies in High Dimensional Data
CLUSPECT 1.0 – Supervised spectral clustering
CompClust 1.2 – Explore and Quantify Relationships between Clustering Results
MatrixClust 20080804 – Fuzzy Clustering of a Symmetric Matrix
GaneSh – Cluster Expression Data by Gibbs sampling procedure
Diametrical Clustering – Identify Anti-correlated Gene Clusters
psi-square 1.2 – Search the Space of Gene Vectors
CRC 1.1 – Dirichlet Process Model-based Cluster
VIZARD 1.2 – Affymetrix GeneChip® Data Analysis & Visualization
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
AMIADA 2.0.7 – Analysis of Microarray Data
MAExplorer 0.96.34.01 – MicroArray Explorer Tool