Cytoscape App Store - Gary Bader

Apps

	AutoAnnotate
	Finds clusters and visually annotates them with labels and groups.

	AutoAnnotate
	Finds clusters and visually annotates them with labels and groups.
	(37) 83925 downloads

	clusterMaker2
	Multi-algorithm clustering app for Cytoscape

	clusterMaker2
	Multi-algorithm clustering app for Cytoscape
	(28) 188644 downloads

	CyChat
	Chat with Cytoscape in natural language and get a reproducible Jupyter notebook

	CyChat
	Chat with Cytoscape in natural language and get a reproducible Jupyter notebook
	(8) 184 downloads

	ExpressionCorrelation
	Makes a similarity network where nodes are genes, and edges denote highly correlated genes.

	ExpressionCorrelation
	Makes a similarity network where nodes are genes, and edges denote highly correlated genes.
	(5) 13706 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.
	(32) 261642 downloads

	NetMatchStar
	An enhanced Cytoscape network querying app

	NetMatchStar
	An enhanced Cytoscape network querying app
	(3) 12265 downloads

	SIREN
	Signing of Regulatory Networks

	SIREN
	Signing of Regulatory Networks
	(3) 4471 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) 5716 downloads

	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)

	Cy3D
	Simple 3D Network Renderer App

	Cy3D
	Simple 3D Network Renderer App
	(3) 25515 downloads

	EnrichmentMap
	Visualizes enrichments of pathways as an enrichment map, a network representing overlaps among enriched pathways.

	EnrichmentMap
	Visualizes enrichments of pathways as an enrichment map, a network representing overlaps among enriched pathways.
	(29) 176633 downloads

	HyperModules
	Interaction Network Algorithm to Analyse Gene Mutations and Clinical Data

	HyperModules
	Interaction Network Algorithm to Analyse Gene Mutations and Clinical Data
	(1) 6642 downloads

	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)

	scNetViz
	Single-cell RNASeq analysis in Cytoscape

	scNetViz
	Single-cell RNASeq analysis in Cytoscape
	(1) 22005 downloads

	SocialNetwork
	Summarizes how individuals are connected by building networks where nodes represent authors and edges represent publications.

	SocialNetwork
	Summarizes how individuals are connected by building networks where nodes represent authors and edges represent publications.
	(5) 16592 downloads

	WordCloud
	Summarizes functions of interacting clusters as logos, where sizes of logo represents frequencies of these functions.

	WordCloud
	Summarizes functions of interacting clusters as logos, where sizes of logo represents frequencies of these functions.
	(2) 79144 downloads