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data visualization
(76)
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(61)
network analysis
(60)
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(59)
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Random walk with restart algorithm
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Graph analysis
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BNMatch2
BNMatch provides a reliable and optimized mapping between networks considering about nodal information and topological similarity
BNMatch2
BNMatch provides a reliable and optimized mapping between networks considering about nodal information and topological similarity
(3) 4412 downloads
CONAN
Analysis of atom interaction networks for structure ensembles of biomolecules
CONAN
Analysis of atom interaction networks for structure ensembles of biomolecules
(1) 2079 downloads
CountTriplets
Counts graph triplets and plots significance profiles
CountTriplets
Counts graph triplets and plots significance profiles
(1) 1908 downloads
CyLinkPredictor
Link Predictor Based on Common Neighbors
CyLinkPredictor
Link Predictor Based on Common Neighbors
(3) 2112 downloads
CytoCopteR
A Cytoscape plug-in for training logic models
CytoCopteR
A Cytoscape plug-in for training logic models
(29) 9097 downloads
CytoMOBAS
Identifies and analyzes disease associated and highly connected subnetworks.
CytoMOBAS
Identifies and analyzes disease associated and highly connected subnetworks.
(0) 2911 downloads
Cytoscape RedisGraph Plugin
Cytoscape RedisGraph Plugin
(1) 2575 downloads
GASOLINE
A Cytoscape App for multiple local alignment of protein-protein interaction (PPI) networks
GASOLINE
A Cytoscape App for multiple local alignment of protein-protein interaction (PPI) networks
(13) 10559 downloads
HGPEC
HGPEC can effectively predict novel disease-gene and disease-disease associations and support network- and rank-based visualization
HGPEC
HGPEC can effectively predict novel disease-gene and disease-disease associations and support network- and rank-based visualization
(2) 3178 downloads
jActiveModules
Finds clusters where member nodes show significant changes in expression levels.
jActiveModules
Finds clusters where member nodes show significant changes in expression levels.
(36) 53050 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.
(30) 171450 downloads
Motif-Discovery
It allows the user to do "Network Motif Discovery" in a fast and friendly way. It uses the G-Tries algorithm which is the fastest one.
Motif-Discovery
It allows the user to do "Network Motif Discovery" in a fast and friendly way. It uses the G-Tries algorithm which is the fastest one.
(12) 10335 downloads
NetMatchStar
An enhanced Cytoscape network querying app
NetMatchStar
An enhanced Cytoscape network querying app
(3) 7038 downloads
Network Coherence Calculator
Calculates the network coherence of differentially expressed genes within a network.
Network Coherence Calculator
Calculates the network coherence of differentially expressed genes within a network.
(2) 1105 downloads
PathExplorer
Finds paths, filters them based on node and edge attributes and saves them.
PathExplorer
Finds paths, filters them based on node and edge attributes and saves them.
(41) 13851 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)
(10) 3021 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)
(8) 2824 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) 97929 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) 9340 downloads
ThematicMap
ThematicMap visualizes the relationships between node attributes. It can help simplify complex networks and highlight hidden relationships.
ThematicMap
ThematicMap visualizes the relationships between node attributes. It can help simplify complex networks and highlight hidden relationships.
(0) 4476 downloads
ZDOG
ZDOG
(0) 1137 downloads
CentiScaPe
Find the most important nodes in a network, calculating centrality parameters for each node.
CentiScaPe
Find the most important nodes in a network, calculating centrality parameters for each node.
(40) 45669 downloads
CoordinatesLayout
Load a graph with a layout that locates its nodes according to predefined 2D coordinates (typically GPS coordinates).
CoordinatesLayout
Load a graph with a layout that locates its nodes according to predefined 2D coordinates (typically GPS coordinates).
(8) 4650 downloads
CycleDetector
Detects Cycles in a Cytoscape network
CycleDetector
Detects Cycles in a Cytoscape network
(0) 3132 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) 33018 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.
(168) 109481 downloads
CytoNCA
Providing calculation, evaluation and visualization analysis for several centralities of weighted and unweighted network.
CytoNCA
Providing calculation, evaluation and visualization analysis for several centralities of weighted and unweighted network.
(9) 76123 downloads
DyNet
Compare two or more networks and identify the most 'rewired' nodes.
DyNet
Compare two or more networks and identify the most 'rewired' nodes.
(6) 11347 downloads
GNC
Gene Network Coherence with direct and indirect relationships
GNC
Gene Network Coherence with direct and indirect relationships
(57) 6069 downloads
ISMAGS
Enumerate all instances of a motif in a graph, making optimal use of the motif's symmetries.
ISMAGS
Enumerate all instances of a motif in a graph, making optimal use of the motif's symmetries.
(1) 9012 downloads
Jesse
Calculate the graphlet degrees of all nodes within a graph
Jesse
Calculate the graphlet degrees of all nodes within a graph
(1) 2832 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) 8516 downloads
NCMine
Finds functional modules in gene networks by Near-Clique Mining
NCMine
Finds functional modules in gene networks by Near-Clique Mining
(3) 3648 downloads
NetworkAnalyzer
Calculates topological properties of a network (degree distribution, clustering coefficients, centrality, etc.)
NetworkAnalyzer
Calculates topological properties of a network (degree distribution, clustering coefficients, centrality, etc.)
(11) 56935 downloads
OCSANA+
Optimal Control and Simulation of Signaling Networks from Network Analysis
OCSANA+
Optimal Control and Simulation of Signaling Networks from Network Analysis
(25) 1663 downloads
PathLinker
Reconstructs signaling pathways from protein interaction networks
PathLinker
Reconstructs signaling pathways from protein interaction networks
(14) 20753 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
(44) 23103 downloads
PSFC
Pathway Signal Flow Calculator: Calculates pathway activity based on gene expression/metabolite abundance and pathway topology.
PSFC
Pathway Signal Flow Calculator: Calculates pathway activity based on gene expression/metabolite abundance and pathway topology.
(1) 14829 downloads
RWRMTN
a tool for predicting disease-associated microRNAs based on a microRNA-target gene network
RWRMTN
a tool for predicting disease-associated microRNAs based on a microRNA-target gene network
(4) 2162 downloads
SenseNet
Analysis of atom interaction networks for structure ensembles of biomolecules
SenseNet
Analysis of atom interaction networks for structure ensembles of biomolecules
(1) 1956 downloads
XlinkCyNET
Generate residue-to-residue connections provided by XL-MS in protein interaction networks
XlinkCyNET
Generate residue-to-residue connections provided by XL-MS in protein interaction networks
(3) 9758 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)
Interference
Evaluates the topological effects of node removal like Radiality, Closeness, Betweenness, Centroid Value and Eccentricity.
Interference
Evaluates the topological effects of node removal like Radiality, Closeness, Betweenness, Centroid Value and Eccentricity.
(12)
ModuLand
Modularization method family offering modular hierarchies and adjustable overlaps
ModuLand
Modularization method family offering modular hierarchies and adjustable overlaps
(10)
NetDS
Network Dynamics and Structure Analysis
NetDS
Network Dynamics and Structure Analysis
(1)
Randomnetworks
Generates random network or randomizes already loaded network.
Randomnetworks
Generates random network or randomizes already loaded network.
(12)
ShortestPath
Finds shortest pathway between two selected nodes.
ShortestPath
Finds shortest pathway between two selected nodes.
(3)
CalculatenodeDegree
Simply calcuates degree for selected node.
CalculatenodeDegree
Simply calcuates degree for selected node.
(0)
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)
GraphletCounter
Calculates "graphlet" (small connected non-isomorphic subgraph) degree distribution.
GraphletCounter
Calculates "graphlet" (small connected non-isomorphic subgraph) degree distribution.
(1)
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)
NetMatch
Finds user defined network motifs in a given network. network motif can be created and edited using original GUI.
NetMatch
Finds user defined network motifs in a given network. network motif can be created and edited using original GUI.
(2)
RemainingDegreeDistribution
Calculates remaining degree (excess degree) distribution.
RemainingDegreeDistribution
Calculates remaining degree (excess degree) distribution.
(1)
SubnetworkCreator
Create subnetworks for disconnected graphs.
SubnetworkCreator
Create subnetworks for disconnected graphs.
(2)