Cytoscape Plugin Porting

	A	B	C	D	F	G
1	rdf	Description	Compatibility	Working on Port

2	addParentNeighbors	For a selected node in child network, adds neighboring nodes from a parent network .				=ported!
3	AgilentLiteratureSearch	Mines scientific literatures to find ones related to search term and to create interaction network based on the search result.	2.8	Allan Kuchinsky, Agilent		=port in process
4	AllegroMCODE	Very fast clustering based on MCODE algorithm.
5	APCluster	Uses affinity propagation described in Frey BJ and Duec D (2007) to perform clustering.
6	APID2NET	Downloads PPI data from http://bioinfow.dep.usal.es/apid/ and performs various analyses including protein motif, GO, hub identification, etc. through the original GUI. Equipped with impressing "rainbow" coloring of nodes.			Fxvcxd
7	BiLayout	Finds a bipartite network for two sets of user-selected nodes and performs layout.
8	BiNGO	Calculates overrepresented GO terms in the network and display them as a network of significant GO terms.		Mike Smoot
9	bioCycPlugin	Loads any pathway in bioCyc database. Original panel provides useful information for each node.		Scooter Morris
10	BiogridPlugin	Loads Biogrid tab file onto Cytoscape.
11	BiomartClient	Retrieves attributes associated with given gene or protein
12	BioNetBuilder	Through the wizard, user can easily construct networks from public databases. User can also create interologs.
13	BioQualiPlugin	Performs consistency check of regulatory network and expression data.
14	Bisogenet	Retrieves interactions associated with input IDs. Sophisticated UI gives links to GO, KEGG, etc.
15	BLAST2similarityGraph	Visualizes BLAST similarity as graph.
16	BridgeDb	Performs ID mapping using BridgeDb and other public or custom database sources.
17	CABIN	Integrates interaction datasets from different resources to explore the integrated network and to perform confidence analysis for interactions. User can give weight to each interaction set which will be used for the level of confidence.
18	CalculatenodeDegree	Simply calcuates degree for selected single node.
19	CentiScaPe	Calculates topological characteristic values (ex. Centralities) for each node.		Giovanni Scardoni
20	ChemViz	Visualizes chemical structure of each compound in chemical network with original interface.
21	ClojureEngine	Provides Clojure API.
22	ClueGO	Creates and visualizes a functionally organized GO term network or pathway from given interaction network.	2.8	Bernhard Mlecnik Gabriela Bindea
23	clusterExplorerPlugin	Explores a given similarity graph.
24	clusterMaker	Clusters densely connected nodes and node attributes (i.e. expression data) in a given network. Results of these two types of clustering can be analysed in the integrated interface.	2.8	Scooter Morris
25	ClusterONE	Finds overlapping protein complexes in a protein interaction network. Clusters are visualized by original interface with their p-values.
26	ClusterViz	Clustering based on FAG-EC, EAGLE or MCODE. Found cluster can be subjected to GO enrichment analysis.	2.8	Gang Chen
27	commandTool	Provides simple command-line interface to Cytoscape.
28	CommFinder	Clustering based on QCUT, HQCUT, MCL, MCODE.
29	Commonattributes	Find attributes shared between selected nodes.
30	ConsensusPathDBplugin	Retrieves interaction evidences for given pair of genes or proteins
31	CyAnimator	Creates animation based on added frames of network views.		Scooter Morris
32	CyClus3D	Clusters a given network based on three-node motifs. Accepts multiple types of interactions. Cluster ID is given to edge attributes, "EdgeCluster".
33	CyGoose	Provides Gaggle Boss, which routes data from one application to another.
34	CyOog
35	cytoHubba	Predicts and explores important nodes and subnetworks in a given network by several topological algorithms.
36	Cytoprophet
37	CytoSaddleSum	Finds enriched function based on sum-of-weight scores.
38	CytoscapeRPC	Allows user to query and modify networks through an XML-RPC connection.
39	CytoSEED	Enables users to view, manipulate and analyze metabolic models created by the Model SEED. The reactions are organized into a set of maps based on each reaction's membership in KEGG pathways.
40	CytoSQL	Retrieves attributes from SQL databases by invoking query command.
41	DisGeNET	Queries and analyzes networks of diseases and their associated genes.
42	DomainGraph	Visualizes domain-domain interactions which connect pairs of interacting proteins.
43	DroID	Retrieves interactions associated with input IDs. Detailed information associated with interactiong proteins can also be obtained.
44	dynamicXpr	Dynamically change colors of nodes like a movie according to their expression level across many conditions.	dormant project
45	edgeLengthPlugin	Calculate edge length in the main network view window, and stores them as edge attributes "length".
46	edgeLister	Records selected edges and provides some functionality for them (ex. hiding recorded edges)
47	EnhancedSearch	Performs keyword search. Wildcards, logical operators, etc. are allowed.	in core
48	EnrichmentMap	Visualizes enrichment of specific functions (GO terms) by interactions between functions.
49	ExprEssence	Searches for differentially altered links in a given network using multiple set of expression data.
50	ExpressionCorrelation	Makes a similarity network where nodes are genes, and edges denote highly correlated genes.
51	FERN	Performs stochastic simulation of chemical reaction networks.
52	FluxViz	Visualizes fluxes as visual effect to edges on Cytoscape network.
53	FM3	Performs one of the fastest multilevel force directed Layouts called FM3 Layout introduced by Hachul S et al 2005.
54	FunNetViz	Integrates and visualizes co-expression network with biological role of transcripts (e.g., GO terms). Centrality measures are equipped.
55	GeneMANIA	Generates interaction networks from public databases based on user's list of genes. Also provides annotation and putative function for those genes.	2.6.4-3.0	Jason Montojo (Gary Bader's lab)
56	Genoscape
57	GoogleChartFunctions	Creates image from attribute values (URL) using the Google Chart API.
58	GPML-Plugin	Enables import of GPML file via import menu.	2.8	Alex Pico, Thomas Kelder
59	GraphletCounter	Calculates "graphlet" (small connected non-isomorphic subgraph) degree distribution.
60	GraphMLReader	Loads interactions or pathways in GraphML format.	In Core
61	GroovyEngine	Provides scripting interface of Groovy.
62	GroovyScriptingEngine	Provides scripting interface of Groovy.
63	GroupTool	Enables user to defines groups of nodes. For each group, basic information such as number of nodes will be displayed on the panel.	in core	Scooter Morris
64	HiderSlider	Provides user sliders which can hide nodes whose continuous attribute is below threshold specied by sliders.
65	HyperEdgeEditor	Enables one to create hyper-edge by Cytoscape editor.
66	IgraphPlugin	Brings some functionality of Igraph such as layouts into Cytoscape. Mac only.
67	IntActWSClient	Retrieves interactions associated with input IDs.	Removed. Replaced by PSICQUIC
68	Interference	Evaluates the topological effects of single or multiple nodes removal from a network using the effect to Radiality, Closeness, Betweenness, Centroid Value and Eccentricity.
69	iRefScape	Retrieves interactions associated with input IDs. Detailed information for each interaction as well as link to iRefIndex is provided.
70	jActiveModules	Finds clusters where member nodes show significant changes in expression levels.		Mike Smoot
71	JavaScriptEngine	Provides Java Script API.	Part of JVM
72	KeyPathwayMiner	Detects highly-connected sub-networks where most genes show similar expression behavior.
73	KGMLReader	Opens KEGG pathways
74	mcl-new	Clusters given network. Subnetwork is indicated by set of nodes, and they are shown by selecting subnetwork number.
75	MCODE	Clusters a given network based on vertex weighting by local neighborhood density and outward traversal from a locally dense seed protein to isolate the dense regions.	2.8	Christian Lopes (Gary Bader's lab)
76	MetaNetter	Infers of metabolic networks based on high resolution metabolomic data.
77	MetanodePlugin2	Enables user to define "meta-node", a group of nodes. Meta-nodes can have hierarchy.	in core	Scooter Morris
78	MetScape	Loads human or mouse metabolic network. Sophisticated GUI is provided which allows user to perform various tasks including gene expression analysis along the pathways.
79	MiMIplugin	Retrieves interactions associated with input IDs. User can add own annotations to genes which can be viewed by different users.
80	MINE	Clusters a given network based on agglomerative clustering algorithm very similar to MCODE, but it uses a modified vertex weighting strategy and can factor in a measure of network modularity. Adjustment of only few parameters are necessary.	2.8
81	MiSink	Provides network interface to MiSink-enabled Web sites, including DIP.
82	MONET	Predicts gene regulatory network from biological annotations and expression data.
83	Mosaic	Systematically partition the given graph, and layout and color nodes based on GO terms.	2.8
84	NamedSelection	Assign name to selected nodes, and after unselection, enables user to re-select the nodes according to the name.
85	NCBIClient	Imports various data from NCBI database.
86	NCBIEntrezgeneUserInterface	Imports various data from NCBI database.	in core
87	NeighborHighlight	Highlights the current node and all its neighboring nodes and edges when the user hovers the mouse over it.
88	NeMo	Identifies densely connected and biopartite network modules based on combination of a unique neighbour-sharing score with hierarchical agglomerative clustering.
89	NetAtlas	Integrates gene expression data of multiple tissues (ex. from Symatlas) into pre-loaded network. genes showing characteristic expression in specified tissues can be filtered and colored.
90	NetCirChro	Visualizes interaction network on circular genome. Original GUI with some network analysis functions (shortest path, degree distribution, etc.) are equipped.
91	NetMatch	Finds user defined network motifs in a given network. network motif can be created and edited using original GUI.
92	NetworkAnalyzer	Computes basic properties of whole network (degree distribution, clustering coefficients, centrality, etc.)	in core
93	NetworkEvolution	Allows interactive comparative analysis of networks across different species.
94	nodeCharts	Paints bar, line or pie graphs onto nodes.	in core
95	OmicsAnalyzer	Integrates omics data such as expression data, proteome data, etc. onto the network to visualize such data by graph on the network.
96	OrthoNets	Enables simultaneous comparison of interaction network of two species. protein domain information can be visualized.
97	PanGIA	Performs integrated analysis and visualization of PPIs and genetic interactions to infer functional modules and interactions that connect these modules.		Mike Smoot
98	Pathintegrator	Integrates pathways in which given proteins are associated.
99	PerturbationAnalyzer
100	PhosphositePlus Web Service Client Module	Integrates phosphorylation-related information into the network.