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Categories
data visualization
(78)
network analysis
(62)
network generation
(61)
graph analysis
(60)
online data import
(47)
automation
(47)
clustering
(39)
integrated analysis
(37)
utility
(32)
systems biology
(32)
enrichment analysis
(32)
visualization
(29)
data integration
(27)
core app
(25)
annotation
(23)
layout
(22)
pathway database
(18)
ontology analysis
(18)
import
(18)
gene expression
(18)
network comparison
(16)
local data import
(16)
functional analysis
(16)
PPI-network
(15)
interaction database
(15)
Network structure
(14)
scripting
(13)
network dynamics
(13)
GO annotation
(12)
regulatory networks
(11)
Topology
(10)
network inference
(10)
heat map visualization
(10)
export
(10)
pathway
(9)
networks
(9)
network manipulation
(9)
functional module detection
(9)
cancer data analysis
(9)
network partitioning
(8)
gene regulation
(8)
disease
(8)
database
(8)
attribute generation
(8)
animation
(8)
molecular structure
(7)
linked data
(7)
ID mapping
(7)
grouping
(7)
gene-disease association
(7)
Connection sub-graph discovery
(7)
centrality analysis
(7)
3d visualization
(7)
simulation
(6)
Random walk with restart algorithm
(6)
network learning
(6)
microarrays
(6)
cluster visualization
(6)
social network analysis
(5)
shortest paths
(5)
sequence similarity
(5)
SBML
(5)
R
(5)
Protein complex
(5)
Pathway finding
(5)
network alignment
(5)
Gene prioritization
(5)
gene co-expression
(5)
data manipulation
(5)
structural biology
(4)
SPARQL
(4)
signaling
(4)
search
(4)
literature mining
(4)
kegg
(4)
JavaScript
(4)
gene function prediction
(4)
flux analysis
(4)
variant analysis
(3)
set visualization
(3)
set analysis
(3)
python
(3)
protein dynamics
(3)
post-translational modification
(3)
pathway reconstruction
(3)
Pathway analysis
(3)
network repository
(3)
inference
(3)
graph clustering
(3)
genome visualization
(3)
disease-disease association
(3)
Community detection
(3)
Cancer
(3)
Boolean Network
(3)
bayesian networks
(3)
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) 67403 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) 17837 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
(13) 51731 downloads
CyPath2
Pathway Commons (BioPAX L3 database) web service GUI client app
CyPath2
Pathway Commons (BioPAX L3 database) web service GUI client app
(73) 35755 downloads
iRegulon
Detects master regulators and cis-regulatory interactions
iRegulon
Detects master regulators and cis-regulatory interactions
(12) 31622 downloads
ncINetView
ncINetView
(0) 2456 downloads
Pesca3.0
Pesca3.0
(8) 4663 downloads
stringApp
Import and augment Cytoscape networks from STRING
stringApp
Import and augment Cytoscape networks from STRING
(31) 255157 downloads
WikiPathways
WikiPathways web service client and GPML file format importer
WikiPathways
WikiPathways web service client and GPML file format importer
(11) 83199 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) 75818 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) 184260 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) 53004 downloads
CyTargetLinker
Flexible network extension app
CyTargetLinker
Flexible network extension app
(40) 43934 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) 6919 downloads
OmniPath
OmniPath: literature curated human signaling pathways
OmniPath
OmniPath: literature curated human signaling pathways
(17) 12895 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) 29766 downloads
Synapse Client
Access your data on Synapse.org from within Cyoscape
Synapse Client
Access your data on Synapse.org from within Cyoscape
(1) 4971 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) 12514 downloads
Unsupported Plugins for Cytoscape 2.x
APID2NET
Downloads PPI data from APID and performs various analyses and visualizations.
APID2NET
Downloads PPI data from APID and performs various analyses and visualizations.
(13)
bioCycPlugin
Loads any pathway in bioCyc database. Original panel provides useful information for each node.
bioCycPlugin
Loads any pathway in bioCyc database. Original panel provides useful information for each node.
(1)
CABIN
Integrates interaction datasets from various resources to explore and assess the resulting network
CABIN
Integrates interaction datasets from various resources to explore and assess the resulting network
(0)
ConsensusPathDBplugin
Retrieves interaction evidences for given pair of genes or proteins
ConsensusPathDBplugin
Retrieves interaction evidences for given pair of genes or proteins
(4)
CyThesaurus-ID-Mapping
Performs ID mapping using BridgeDb and other public or custom database sources.
CyThesaurus-ID-Mapping
Performs ID mapping using BridgeDb and other public or custom database sources.
(10)
CytoSQL
Retrieves attributes from SQL databases by invoking query command.
CytoSQL
Retrieves attributes from SQL databases by invoking query command.
(0)
Genoscape
Visually integrates gene expression data sets from GenoScript and KEGG pathways into networks.
Genoscape
Visually integrates gene expression data sets from GenoScript and KEGG pathways into networks.
(12)
HOMECAT
Integrate data from multiple species, mapping multiple orthologs
HOMECAT
Integrate data from multiple species, mapping multiple orthologs
(0)
iRefScape
Retrieves interactions associated with input IDs along with interaction details and iRefIndices.
iRefScape
Retrieves interactions associated with input IDs along with interaction details and iRefIndices.
(0)
KNIMEConnector
Imports and exports networks from Konstanz Information Miner (KNIME)
KNIMEConnector
Imports and exports networks from Konstanz Information Miner (KNIME)
(8)
NetAtlas
Integrates gene expression data of multiple tissues from Symatlas into network visualization and analysis.
NetAtlas
Integrates gene expression data of multiple tissues from Symatlas into network visualization and analysis.
(2)
PhosphositePlus Web Service Client Module
Integrates phosphorylation-related information into the network.
PhosphositePlus Web Service Client Module
Integrates phosphorylation-related information into the network.
(2)
PSICQUICUniversalClient
PSICQUIC Web Service Client for importing interactions from public databases
PSICQUICUniversalClient
PSICQUIC Web Service Client for importing interactions from public databases
(16)
ReConn
Loads pathway data from the reactome server and integrates expression data.
ReConn
Loads pathway data from the reactome server and integrates expression data.
(0)
Superpathways-Plugin
Downloads and integrates multiple pathways from Wikipathways.
Superpathways-Plugin
Downloads and integrates multiple pathways from Wikipathways.
(0)
BiNoM
Import/Export of System Biology file formats (BioPAX level 3, SBML, CellDesigner). Analysis and manipulation of biological networks.
BiNoM
Import/Export of System Biology file formats (BioPAX level 3, SBML, CellDesigner). Analysis and manipulation of biological networks.
(17)
BiogridPlugin
Loads interaction data from the Biogrid database into Cytoscape
BiogridPlugin
Loads interaction data from the Biogrid database into Cytoscape
(4)
CARLSBAD
Visualizes and explores chemical pattern bioactivity networks.
CARLSBAD
Visualizes and explores chemical pattern bioactivity networks.
(1)
CySBML
Cytoscape Plugin for SBML
CySBML
Cytoscape Plugin for SBML
(7)
CytoITMprobe
Provides access to the ITM Probe database for querying and importing related network nodes and their attributes.
CytoITMprobe
Provides access to the ITM Probe database for querying and importing related network nodes and their attributes.
(0)
DroID
Imports protein interaction networks from Drosophila Interactions Database (DroID).
DroID
Imports protein interaction networks from Drosophila Interactions Database (DroID).
(3)
GPML-Plugin
Enables import of GPML file via import menu.
GPML-Plugin
Enables import of GPML file via import menu.
(10)
iCTNet
Integrated Complex Traits Network (iCTNet) assembles human disease, tissue, gene and drug-target interactions.
iCTNet
Integrated Complex Traits Network (iCTNet) assembles human disease, tissue, gene and drug-target interactions.
(6)
KGMLReader
File reader and pathway visualizer for KEGG XML (KGML) files
KGMLReader
File reader and pathway visualizer for KEGG XML (KGML) files
(61)
MiMIplugin
Retrieves molecular interactions and interaction attributes from MiMI and displays the interaction networks and attributes.
MiMIplugin
Retrieves molecular interactions and interaction attributes from MiMI and displays the interaction networks and attributes.
(9)
Pathintegrator
Pathintegrator searches for, and integrates in a single network pathways in which a given gene or protein is involved.
Pathintegrator
Pathintegrator searches for, and integrates in a single network pathways in which a given gene or protein is involved.
(11)
PICRClient
PICRClient
(0)
Reactome FIs
Accesses to Reactome Functional interaction (FI) network to perform pathway analyses.
Reactome FIs
Accesses to Reactome Functional interaction (FI) network to perform pathway analyses.
(4)
SFLDLoader
Represents structural protein families and their homologs by graph on Cytoscape.
SFLDLoader
Represents structural protein families and their homologs by graph on Cytoscape.
(0)
