Submit an App
Submit a 3.0 App
Guide to 3.0 App Development
Sign In
All Apps
Categories
collections
(4)
data visualization
(75)
network generation
(60)
network analysis
(59)
graph analysis
(58)
online data import
(47)
automation
(43)
integrated analysis
(38)
clustering
(37)
systems biology
(33)
utility
(31)
enrichment analysis
(30)
visualization
(29)
data integration
(27)
layout
(21)
annotation
(21)
core app
(20)
ontology analysis
(18)
import
(18)
pathway database
(17)
network comparison
(17)
local data import
(16)
gene expression
(16)
functional analysis
(16)
interaction database
(14)
scripting
(13)
PPI-network
(13)
Network structure
(12)
network dynamics
(12)
GO annotation
(12)
regulatory networks
(11)
network inference
(10)
Topology
(9)
network manipulation
(9)
heat map visualization
(9)
export
(9)
pathway
(8)
networks
(8)
gene regulation
(8)
functional module detection
(8)
disease
(8)
database
(8)
cancer data analysis
(8)
attribute generation
(8)
animation
(8)
molecular structure
(7)
linked data
(7)
ID mapping
(7)
simulation
(6)
Random walk with restart algorithm
(6)
network partitioning
(6)
network learning
(6)
microarrays
(6)
grouping
(6)
gene-disease association
(6)
Connection sub-graph discovery
(6)
centrality analysis
(6)
social network analysis
(5)
shortest paths
(5)
sequence similarity
(5)
R
(5)
Protein complex
(5)
Pathway finding
(5)
network alignment
(5)
Gene prioritization
(5)
data manipulation
(5)
3d visualization
(5)
structural biology
(4)
SPARQL
(4)
signaling
(4)
literature mining
(4)
kegg
(4)
JavaScript
(4)
gene function prediction
(4)
gene co-expression
(4)
disease-disease association
(4)
cluster visualization
(4)
variant analysis
(3)
set visualization
(3)
set analysis
(3)
search
(3)
SBML
(3)
protein dynamics
(3)
pathway reconstruction
(3)
network repository
(3)
inference
(3)
genome visualization
(3)
flux analysis
(3)
bayesian networks
(3)
Pathway database
Search for posts about pathway database →
Ask a question about pathway database →
CyKEGGParser
KEGG pathway tuner: accurate, tissue- and protein-protein interaction-specific pathways
CyKEGGParser
KEGG pathway tuner: accurate, tissue- and protein-protein interaction-specific pathways
(12) 36185 downloads
cyTransFinder
Signal Transduction Pathway Finder
cyTransFinder
Signal Transduction Pathway Finder
(3) 12517 downloads
KEGGscape
File reader and pathway visualizer for KEGG XML (KGML) files
KEGGscape
File reader and pathway visualizer for KEGG XML (KGML) files
(2) 55932 downloads
OmniPath
OmniPath: literature curated human signaling pathways
OmniPath
OmniPath: literature curated human signaling pathways
(16) 5172 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) 66984 downloads
WikiPathways
WikiPathways web service client and GPML file format importer
WikiPathways
WikiPathways web service client and GPML file format importer
(11) 51830 downloads
CyPath2
Pathway Commons (BioPAX L3 database) web service GUI client app
CyPath2
Pathway Commons (BioPAX L3 database) web service GUI client app
(73) 28205 downloads
ENViz
Enrichment analysis and visualization - integrated analysis of multiple sample matched data sets in the context of systematic annotation
ENViz
Enrichment analysis and visualization - integrated analysis of multiple sample matched data sets in the context of systematic annotation
(13) 25007 downloads
MetScape
Maps human, mouse and rat metabolomics and gene expression data to human metabolic networks and enables pathway and correlation analysis.
MetScape
Maps human, mouse and rat metabolomics and gene expression data to human metabolic networks and enables pathway and correlation analysis.
(23) 37715 downloads
Pathway Scoring Application
Evaluates the biological activity of genes and processes in pathways
Pathway Scoring Application
Evaluates the biological activity of genes and processes in pathways
(2) 7662 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) 19692 downloads
Unsupported Plugins for Cytoscape 2.x
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)
KGMLReader
File reader and pathway visualizer for KEGG XML (KGML) files
KGMLReader
File reader and pathway visualizer for KEGG XML (KGML) files
(61)
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)
GPML-Plugin
Enables import of GPML file via import menu.
GPML-Plugin
Enables import of GPML file via import menu.
(10)
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)
Superpathways-Plugin
Downloads and integrates multiple pathways from Wikipathways.
Superpathways-Plugin
Downloads and integrates multiple pathways from Wikipathways.
(0)
