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) 6757 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) 65688 downloads

	copycatLayout
	Clone a network view layout by mapping node column values

	copycatLayout
	Clone a network view layout by mapping node column values
	(1) 4178 downloads

	cyBrowser
	Core App: Add HTML Browser to Cytoscape

	cyBrowser
	Core App: Add HTML Browser to Cytoscape
	(0) 6143 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) 38662 downloads

	layoutSaver
	Map node positions from one network to another

	layoutSaver
	Map node positions from one network to another
	(1) 2363 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) 1544 downloads

	scNetViz
	Single-cell RNASeq analysis in Cytoscape

	scNetViz
	Single-cell RNASeq analysis in Cytoscape
	(1) 632 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) 5535 downloads

	boundaryLayout
	A Force-Directed Network Layout with Custom Boundary Constraints

	boundaryLayout
	A Force-Directed Network Layout with Custom Boundary Constraints
	(2) 2710 downloads

	cdtReader
	Read Cluster 3 output files into Cytoscape

	cdtReader
	Read Cluster 3 output files into Cytoscape
	(0) 2011 downloads

	chemViz2
	Cheminformatics App for Cytoscape

	chemViz2
	Cheminformatics App for Cytoscape
	(6) 10518 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) 22197 downloads

	cyPlot
	A utility to display data plots

	cyPlot
	A utility to display data plots
	(1) 668 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)

	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) 809 downloads

	Omics Visualizer
	Import & Visualize several data for the same node

	Omics Visualizer
	Import & Visualize several data for the same node
	(5) 1988 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) 4627 downloads

	setsApp
	Save and manipulate sets of nodes and edges

	setsApp
	Save and manipulate sets of nodes and edges
	(3) 10527 downloads

	stringApp
	Import and augment Cytoscape networks from STRING

	stringApp
	Import and augment Cytoscape networks from STRING
	(18) 68156 downloads

	structureViz2
	App to visualize macromolecular structures in a network context

	structureViz2
	App to visualize macromolecular structures in a network context
	(2) 7841 downloads