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data visualization
(78)
network analysis
(64)
network generation
(63)
graph analysis
(59)
online data import
(47)
automation
(47)
clustering
(38)
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core app
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annotation
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import
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pathway database
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ontology analysis
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gene expression
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interaction database
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export
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pathway
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networks
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disease
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gene regulation
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database
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molecular structure
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linked data
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gene-disease association
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Connection sub-graph discovery
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centrality analysis
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3d visualization
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simulation
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Random walk with restart algorithm
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network learning
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microarrays
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gene co-expression
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cluster visualization
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social network analysis
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shortest paths
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sequence similarity
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SBML
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R
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Protein complex
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Pathway finding
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network alignment
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Gene prioritization
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data manipulation
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structural biology
(4)
SPARQL
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signaling
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search
(4)
literature mining
(4)
kegg
(4)
JavaScript
(4)
gene function prediction
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flux analysis
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bayesian networks
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variant analysis
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subnetwork extraction
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set visualization
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set analysis
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python
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protein dynamics
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post-translational modification
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pathway reconstruction
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Pathway analysis
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non-coding RNA
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network repository
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inference
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graph clustering
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genome visualization
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drug repurposing
(3)
disease module
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disease-disease association
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Cytoscape
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Community detection
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Cancer
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Boolean Network
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Online data import
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AgilentLiteratureSearch
Mines scientific literature to find publications related to search terms and to create interaction networks based on the search result.
AgilentLiteratureSearch
Mines scientific literature to find publications related to search terms and to create interaction networks based on the search result.
(28) 72696 downloads
BridgeDb
Performs ID mapping using BridgeDb and other public or custom database sources.
BridgeDb
Performs ID mapping using BridgeDb and other public or custom database sources.
(20) 21588 downloads
CyKEGGParser
KEGG pathway tuner: accurate, tissue- and protein-protein interaction-specific pathways
CyKEGGParser
KEGG pathway tuner: accurate, tissue- and protein-protein interaction-specific pathways
(14) 65578 downloads
CyPath2
Pathway Commons (BioPAX L3 database) web service GUI client app
CyPath2
Pathway Commons (BioPAX L3 database) web service GUI client app
(73) 43755 downloads
iRegulon
Detects master regulators and cis-regulatory interactions
iRegulon
Detects master regulators and cis-regulatory interactions
(12) 39422 downloads
ncINetView
ncINetView
(0) 3302 downloads
Pesca3.0
Pesca3.0
(9) 6031 downloads
stringApp
Import and augment Cytoscape networks from STRING
stringApp
Import and augment Cytoscape networks from STRING
(34) 389986 downloads
WikiPathways
WikiPathways web service client and GPML file format importer
WikiPathways
WikiPathways web service client and GPML file format importer
(11) 109615 downloads
Bisogenet
Retrieves interactions associated with input IDs. Sophisticated UI gives links to GO, KEGG, etc.
Bisogenet
Retrieves interactions associated with input IDs. Sophisticated UI gives links to GO, KEGG, etc.
(15) 83126 downloads
CluePedia
CluePedia: A ClueGO plugin for pathway insights using integrated experimental and in silico data
CluePedia
CluePedia: A ClueGO plugin for pathway insights using integrated experimental and in silico data
(104) 232914 downloads
CyNDEx-2
Core App: CyNDEx-2 is a user-friendly app for browsing, importing, and exporting networks to an NDEx server.
CyNDEx-2
Core App: CyNDEx-2 is a user-friendly app for browsing, importing, and exporting networks to an NDEx server.
(4) 69551 downloads
CyTargetLinker
Flexible network extension app
CyTargetLinker
Flexible network extension app
(40) 52100 downloads
JGF App
Import / Export OpenBEL Networks. JSON Graph Format Network App handles more restrictive BEL schema.
JGF App
Import / Export OpenBEL Networks. JSON Graph Format Network App handles more restrictive BEL schema.
(1) 9387 downloads
OmniPath
OmniPath: literature curated human signaling pathways
OmniPath
OmniPath: literature curated human signaling pathways
(17) 18996 downloads
Rene
Regulatory Network Enhancing Plugin - ReNE allows users to enhance standard KEGG/Reactome pathways wit
Rene
Regulatory Network Enhancing Plugin - ReNE allows users to enhance standard KEGG/Reactome pathways wit
(12) 41712 downloads
Synapse Client
Access your data on Synapse.org from within Cyoscape
Synapse Client
Access your data on Synapse.org from within Cyoscape
(1) 6647 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
(4) 30080 downloads
