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Clustering
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AutoAnnotate
Finds clusters and visually annotates them with labels and groups.
AutoAnnotate
Finds clusters and visually annotates them with labels and groups.
(37) 24784 downloads
clusterMaker2
Multi-algorithm clustering app for Cytoscape
clusterMaker2
Multi-algorithm clustering app for Cytoscape
(22) 71173 downloads
ClusterViz
Clustering based on FAG-EC, EAGLE or MCODE. Found cluster can be subjected to GO enrichment analysis.
ClusterViz
Clustering based on FAG-EC, EAGLE or MCODE. Found cluster can be subjected to GO enrichment analysis.
(13) 12358 downloads
CytoCluster
a Cytoscape app for analysis and visualization of clusters from network
CytoCluster
a Cytoscape app for analysis and visualization of clusters from network
(12) 21921 downloads
CytoMOBAS
Identifies and analyzes disease associated and highly connected subnetworks.
CytoMOBAS
Identifies and analyzes disease associated and highly connected subnetworks.
(0) 1581 downloads
EClerize
EClerize
(2) 1004 downloads
Mass Spec Collection
Collection of apps to facilitate network analysis of mass spectrometry data. By installing this app, you will be installing a set of apps.
Mass Spec Collection
Collection of apps to facilitate network analysis of mass spectrometry data. By installing this app, you will be installing a set of apps.
(1) 8750 downloads
ModuLand 2.0
Modularization method family offering modular hierarchies and adjustable overlaps
ModuLand 2.0
Modularization method family offering modular hierarchies and adjustable overlaps
(2) 6319 downloads
Omics Analysis Collection
Collection of apps to facilitate network analysis of omic data. By installing this app, you will be installing a set of apps.
Omics Analysis Collection
Collection of apps to facilitate network analysis of omic data. By installing this app, you will be installing a set of apps.
(1) 13124 downloads
PEPPER
Find meaningful pathways / complexes connecting a protein set members within a PPI-network using multi-objective optimization
PEPPER
Find meaningful pathways / complexes connecting a protein set members within a PPI-network using multi-objective optimization
(40) 18842 downloads
ReactomeFIPlugIn
Explore Reactome pathways and search for diseases related pathways and network patterns using the Reactome functional interaction network
ReactomeFIPlugIn
Explore Reactome pathways and search for diseases related pathways and network patterns using the Reactome functional interaction network
(21) 63780 downloads
TiCoNE
Time Course Network Enricher is an interactive clustering method for time-series data
TiCoNE
Time Course Network Enricher is an interactive clustering method for time-series data
(68) 29298 downloads
cdtReader
Read Cluster 3 output files into Cytoscape
cdtReader
Read Cluster 3 output files into Cytoscape
(0) 2604 downloads
ClusterONE
Finds overlapping protein complexes in a protein interaction network.
ClusterONE
Finds overlapping protein complexes in a protein interaction network.
(34) 20186 downloads
CyCommunityDetection
Integrates multiscale community detection and functional enrichment for network analysis.
CyCommunityDetection
Integrates multiscale community detection and functional enrichment for network analysis.
(1) 953 downloads
cytoHubba
Predicts and explores important nodes and subnetworks in a given network by several topological algorithms.
cytoHubba
Predicts and explores important nodes and subnetworks in a given network by several topological algorithms.
(132) 24724 downloads
DyNetViewer
Construction, analysis, and visualization of dynamic networks in Cytoscape 3.0
DyNetViewer
Construction, analysis, and visualization of dynamic networks in Cytoscape 3.0
(4) 6482 downloads
GIANT
a Cytoscape plugin for network cartography
GIANT
a Cytoscape plugin for network cartography
(1) 4093 downloads
MCODE
Clusters a given network based on topology to find densely connected regions.
MCODE
Clusters a given network based on topology to find densely connected regions.
(28) 75124 downloads
NCMine
Finds functional modules in gene networks by Near-Clique Mining
NCMine
Finds functional modules in gene networks by Near-Clique Mining
(3) 2432 downloads
PEmeasure
Compute links weights and assess the reliability of the links in a network (e.g. protein-protein interactions)
PEmeasure
Compute links weights and assess the reliability of the links in a network (e.g. protein-protein interactions)
(9) 1964 downloads
PEWCC
Detect dense sub-network (e.g. protein/gene complexes) in network (e.g. PPI/gene network)
PEWCC
Detect dense sub-network (e.g. protein/gene complexes) in network (e.g. PPI/gene network)
(7) 1854 downloads
SCODE
This is the Cytoscape app implementation for Protein Complex Identification by Supervised Graph Clustering
SCODE
This is the Cytoscape app implementation for Protein Complex Identification by Supervised Graph Clustering
(0) 6010 downloads
Unsupported Plugins for Cytoscape 2.x
APCluster
Uses affinity propagation described in Frey BJ and Duec D (2007) to perform clustering.
APCluster
Uses affinity propagation described in Frey BJ and Duec D (2007) to perform clustering.
(5)
clusterMaker
Clusters densely connected nodes and node attributes in a given network.
clusterMaker
Clusters densely connected nodes and node attributes in a given network.
(22)
CommFinder
Clustering based on QCUT, HQCUT, MCL, MCODE.
CommFinder
Clustering based on QCUT, HQCUT, MCL, MCODE.
(5)
CytoKavosh
Allows network motifs discovery
CytoKavosh
Allows network motifs discovery
(4)
MINE
Clusters a network based on network topology using a modified agglomerative clustering algorithm very similar to MCODE.
MINE
Clusters a network based on network topology using a modified agglomerative clustering algorithm very similar to MCODE.
(4)
NeMo
Identifies densely connected and biopartite network modules.
NeMo
Identifies densely connected and biopartite network modules.
(3)
clusterExplorerPlugin
Explores a given similarity graph.
clusterExplorerPlugin
Explores a given similarity graph.
(2)
ClustnSee
Identification, visualization and analysis of clusters from large networks
ClustnSee
Identification, visualization and analysis of clusters from large networks
(14)
CyClus3D
Clusters a network based on three-node motifs.
CyClus3D
Clusters a network based on three-node motifs.
(1)
CytoSeVis
Visualizes networks by semantic similarities.
CytoSeVis
Visualizes networks by semantic similarities.
(0)
ModuLand
Modularization method family offering modular hierarchies and adjustable overlaps
ModuLand
Modularization method family offering modular hierarchies and adjustable overlaps
(10)
TransClust
Clusters a given similarity graph.
TransClust
Clusters a given similarity graph.
(12)