Cytoscape App Store - John "Scooter" Morris

Apps

	addParentNeighbors
	For a selected node in child network, adds neighboring nodes from a parent network .

	addParentNeighbors
	For a selected node in child network, adds neighboring nodes from a parent network .
	(0)

	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)

	cddApp
	Integration between Cytoscape the the NCBI Conserved Domain Database

	cddApp
	Integration between Cytoscape the the NCBI Conserved Domain Database
	(0) 8339 downloads

	ChemViz
	Visualizes chemical structure of each compound in chemical network with original interface.

	ChemViz
	Visualizes chemical structure of each compound in chemical network with original interface.
	(8)

	clusterExplorerPlugin
	Explores a given similarity graph.

	clusterExplorerPlugin
	Explores a given similarity graph.
	(2)

	clusterMaker2
	Multi-algorithm clustering app for Cytoscape

	clusterMaker2
	Multi-algorithm clustering app for Cytoscape
	(22) 82980 downloads

	copycatLayout
	Clone a network view layout by mapping node column values

	copycatLayout
	Clone a network view layout by mapping node column values
	(1) 5551 downloads

	cyBrowser
	Core App: Add HTML Browser to Cytoscape

	cyBrowser
	Core App: Add HTML Browser to Cytoscape
	(0) 18307 downloads

	dynamicXpr
	Dynamically change colors of nodes like a movie according to their expression level across many conditions.

	dynamicXpr
	Dynamically change colors of nodes like a movie according to their expression level across many conditions.
	(2)

	enhancedGraphics
	A passthrough mapper for charts and gradients

	enhancedGraphics
	A passthrough mapper for charts and gradients
	(11) 68229 downloads

	IntAct App
	BETA: Build molecular interaction networks from IntAct database. Access all details in one click.

	IntAct App
	BETA: Build molecular interaction networks from IntAct database. Access all details in one click.
	(0) 1239 downloads

	Legend Creator
	A way to add legends of discrete and continuous mappings to your graph

	Legend Creator
	A way to add legends of discrete and continuous mappings to your graph
	(2) 8333 downloads

	NamedSelection
	Assign name to selected nodes, and after unselection, enables user to re-select the nodes according to the name.

	NamedSelection
	Assign name to selected nodes, and after unselection, enables user to re-select the nodes according to the name.
	(0)

	nodeCharts
	Paints bar, line or pie graphs onto nodes.

	nodeCharts
	Paints bar, line or pie graphs onto nodes.
	(2)

	polyLayout
	Simple n-partide layout algorithm that organizes categories along sides of regular polygons

	polyLayout
	Simple n-partide layout algorithm that organizes categories along sides of regular polygons
	(1) 2320 downloads

	scNetViz
	Single-cell RNASeq analysis in Cytoscape

	scNetViz
	Single-cell RNASeq analysis in Cytoscape
	(1) 2816 downloads

	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)

	structureViz
	Enables user to traverse from biological networks to detailed view of their structures.

	structureViz
	Enables user to traverse from biological networks to detailed view of their structures.
	(4)

	aMatReader
	App to read adjacency matrix (.mat, .adj) files

	aMatReader
	App to read adjacency matrix (.mat, .adj) files
	(1) 7644 downloads

	boundaryLayout
	A Force-Directed Network Layout with Custom Boundary Constraints

	boundaryLayout
	A Force-Directed Network Layout with Custom Boundary Constraints
	(2) 5253 downloads

	cdtReader
	Read Cluster 3 output files into Cytoscape

	cdtReader
	Read Cluster 3 output files into Cytoscape
	(0) 2629 downloads

	chemViz2
	Cheminformatics App for Cytoscape

	chemViz2
	Cheminformatics App for Cytoscape
	(6) 12764 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)

	commandTool
	Provides simple command-line interface to Cytoscape.

	commandTool
	Provides simple command-line interface to Cytoscape.
	(0)

	CyAnimator
	Simple key-frame animation for Cytoscape

	CyAnimator
	Simple key-frame animation for Cytoscape
	(5) 28777 downloads

	cyPlot
	A utility to display data plots

	cyPlot
	A utility to display data plots
	(1) 2307 downloads

	edgeLengthPlugin
	Calculate edge length in the main network view window, and stores them as edge attributes "length".

	edgeLengthPlugin
	Calculate edge length in the main network view window, and stores them as edge attributes "length".
	(0)

	GroupTool
	Enables user to define groups of nodes and display information about groups.

	GroupTool
	Enables user to define groups of nodes and display information about groups.
	(0)

	layoutSaver
	Map node positions from one network to another

	layoutSaver
	Map node positions from one network to another
	(1) 3041 downloads

	MetanodePlugin2
	Enables user to define a group of nodes as a "meta node". Meta nodes can have hierarchy and can be expanded and collapsed.

	MetanodePlugin2
	Enables user to define a group of nodes as a "meta node". Meta nodes can have hierarchy and can be expanded and collapsed.
	(0)

	netIMP
	Visualize IMP pathway models

	netIMP
	Visualize IMP pathway models
	(0) 1047 downloads

	Omics Visualizer
	Import & Visualize several data for the same node

	Omics Visualizer
	Import & Visualize several data for the same node
	(5) 5485 downloads

	RINalyzer
	Provides a number of important methods for analyzing and visualizing residue interaction networks (RINs).

	RINalyzer
	Provides a number of important methods for analyzing and visualizing residue interaction networks (RINs).
	(9) 5446 downloads

	setsApp
	Save and manipulate sets of nodes and edges

	setsApp
	Save and manipulate sets of nodes and edges
	(3) 12593 downloads

	stringApp
	Import and augment Cytoscape networks from STRING

	stringApp
	Import and augment Cytoscape networks from STRING
	(21) 107309 downloads

	structureViz2
	App to visualize macromolecular structures in a network context

	structureViz2
	App to visualize macromolecular structures in a network context
	(3) 9448 downloads