Since the release of Cytoscape 2.5 (July 2007), there are 96972 users (distinct IP addresses) downloaded plugins from this site. Total download count is 718512.

 

Plugin Name
version
Total download

Total downlaod

last 30 days

3DScape
0.4
0
 
0.2
0
3DScapeCS
0.6
1640
addParentNeighbors
1.0
1802
AdvancedNetworkMerge
1.12
2125
 
1.10
1755
 
1.05
714
 
1.04
445
AgilentLiteratureSearch
2.78
3547
 
2.77
12783
 
2.76
3414
 
2.71
4429
 
2.70
5727
 
2.69
1461
 
2.68
1587
 
2.55
7674
 
2.54
382
AllegroLayout
1.1
750
 
1.0
157
AllegroMCODE
2.1
1467
 
2.0
125
 
1.0
4185
AlternativeTableImport
1.3
514
 
1.2
263
 
1.1
229
 
1.0
258
APCluster
2.1
1971
APID2NET
1.52
6104
 
1.51
1721
 
1.5
2082
batchTool
1.0
1570
 
0.5
1187
BiNAT
1.0
0
BiNGO
2.44
23445
 
2.42
3610
 
2.31
6056
 
2.3
16027
 
2.1
8995
 
2.0
1052
BiNoM
2.5
867
 
2.4
22
 
2.3
93
 
2.2
256
 
2.1
278
 
2.0
305
 
1.0
2746
bioCycPlugin
0.9
2564
BiogridPlugin
0.2
969
 
0.1
3810
BiomartClient
0.90
2759
 
0.80
6489
BioNetBuilder
2.0
5710
BioQualiPlugin
2.0
1242
 
1.1
1535
 
1.0
1252
BisoGenet
1.41
2673
 
1.40
806
BLAST2SimilarityGraph
1.01
2701
 
1.0
2085
BNMatch
1.1
605
 
1.0
361
BubbleRouter
1.1
3346
 
1.0
2573
CABIN
2.1
2759
CalculateNodeDegree
1.0
1466
CARLSBAD
1.1
388
 
1.0
69
CellFateScout
0.95
117
CentiScaPe
1.21
2559
 
1.2
2088
 
1.1
1560
 
1.0
3615
ChartPlugin
1.1
707
 
1.0
346
ChemViz
1.3
258
 
1.1
1997
ClojureEngine
1.0
340
ClueGO
1.8
1707
 
1.71
626
 
1.7
192
 
1.6
103
 
1.5
313
 
1.4
2749
 
1.31
1321
 
1.3
1587
 
1.2
1888
 
1.1
1560
CluePedia
1.3
670
 
1.21
295
 
1.2
58
 
1.1
44
 
1.0
144
clusterExplorerPlugin
1.01
1776
 
1.0
1701
 
0.9
1774
clusterMaker
1.9
3659
 
1.8
640
 
1.6
2987
 
1.5
797
 
1.11
1630
 
1.10
5093
 
1.1
1828
 
1.0
2406
ClusterONE
0.93
2441
 
0.92
632
 
0.91
1202
 
0.9
858
 
0.1
882
ClusterViz
1.2
2887
 
1.1
1267
 
1.0
1345
ClustnSee
1.0
1202
COMA
1.101
2020
 
1.1
1160
 
1.0
1184
commandTool
0.91
1860
 
0.9
1032
CommFinder
1.1
1404
CommonAttributes
2.0
1945
 
1.3
1321
ConReg
0.1
364
ConsensusPathDBplugin
1.0
1741
ContigScape
1.0
379
coreCommands
0.9
1196
CoryneRegNetLoader
1.101
1589
 
1.1
1196
 
1.0
1047
CyAnimator
0.9
2646
CyClus3D
3.3
1185
 
3.1
626
CyGoose
2.9
946
 
2.8
762
 
2.7
1193
 
2.6
1305
 
2.5
1180
 
2.10
783
CyKEGGParser
1.3
508
 
1.1
225
 
1.0
182
Cyrface
1.0
425
 
0.2
419
CySBGN
1.2
669
 
1.1
158
 
1.0
339
CySBML
1.2
1303
cySBML
0.5
0
CyTableReaderPlugin
0.1
442
CyTargetLinker
2.1
800
 
2.0
688
 
1.0
849
CyThesaurus-ID-Mapping
1.31
2736
 
1.30
183
 
1.20
780
 
1.11
888
 
1.10
447
 
1.04
681
 
1.03
516
 
1.02
12
 
1.01
58
 
1.0
12
CytoCopteR
1.2
255
 
1.1
364
 
1.0
372
CytoHiCPlugin
1.1
362
 
1.0
421
cytoHubba
1.6
3025
 
1.5
783
 
1.4
723
 
1.3
380
 
1.2
604
 
1.1
1717
 
1.0
1297
CytoITMprobe
1.5
524
 
1.4
300
CytoKavosh
1.1
1407
 
1.0
415
Cytomcl
1.1
1623
 
1.1
1278
 
1.0
933
 
1.0
0
Cytoprophet
1.0
3241
CytoSaddleSum
1.5
819
 
1.4
401
CytoscapeRPC
1.8
4001
 
1.7
712
 
1.6
728
 
1.5
438
 
1.4
430
 
1.3
626
 
1.2
667
 
1.1
450
 
1.0
690
CytoSEED
1.1
513
 
1.0
126
CytoSeVis
1.0
562
CytoSQL
1.0
1323
 
0.9
810
DisGeNET
1.02
0
DisplayNetworkFromFlatFile
1.0
1134
DomainGraph
3.01
1666
 
2.01
1752
 
2.0
746
DroID
1.0
2062
DualLayout
0.01
1168
DvD
1.0
238
dynamicXpr
1.3
2993
 
1.2
1864
edgeLengthPlugin
1.1
1768
 
1.0
1336
edgeLister
1.2
1209
 
1.1
1511
EnhancedSearch
1.2
3334
 
1.1
3439
 
1.0
1533
EnrichmentMap
1.3
909
 
1.2
4702
 
1.1
1010
 
1.0
800
ENViz
1.1
541
 
1.0
307
ExprEssence
1.20
1414
ExpressionCorrelation
1.01
4666
 
1.0
1392
FluxViz
0.12
912
 
0.09
577
FM3
1.1
1686
FNodeAtt
0.9
312
FunNetViz
1.0
1219
GALANT
1.0
0
GASOLINE
1.0
382
GeneMANIA
3.2
2679
 
3.1
418
 
3.0
204
 
2.5
1177
 
2.4
739
 
2.3
426
 
2.2
921
 
2.1
790
 
2.0
739
 
1.0
719
GenomeSpaceLibsPlugin
0.1
185
GenomeSpacePlugin
0.1
500
Genoscape
1.2
2502
 
1.11
1122
 
1.1
929
GESTODifferent
1.0
0
GFD-Net
1.0
414
GIANT
1.0
0
GoogleChartFunctions
1.1
2362
GPEC
1.1
915
GPML-Plugin
1.4
1433
 
1.3
1563
 
1.2
1195
 
1.1
929
 
1.0
676
 
0.9
753
 
0.8
1032
 
0.7
664
 
0.6
692
 
0.5
572
 
0.4
749
 
0.3
1199
 
0.2
1042
 
0.1
1061
GraMoFoNe
0.12
557
GraphletCounter
1.2
1337
 
1.0
753
GraphMLReader
0.11
3157
GroovyEngine
1.0
316
GroovyScriptingEngine
0.11
800
GroupTool
1.3
1317
 
1.2
1722
 
1.1
1261
 
1.0
1550
HiderSlider
1.0
2275
HOMECAT
1.2
357
 
1.1
106
 
1.0
182
HyperEdgeEditor
2.68
1113
 
2.66
1154
 
2.65
761
 
2.62
1703
 
2.61
1446
 
2.60
1100
 
2.56
593
 
2.53
395
iCTNet
0.1
856
IDSwitcher
1.0
772
IgraphPlugin
0.1
925
IntActWSClient
0.66
2282
Interference
1.0
919
iRefScape
1.18
1673
 
1.17
226
 
1.16
299
 
0.90
710
 
0.89
399
 
0.88
238
 
0.87
255
 
0.86
262
 
0.82
334
iRegulon
1.3
64
 
1.2
75
 
1.1
280
 
1.0
27
jActiveModules
2.23
8751
 
2.22
1472
 
2.21
1471
 
2.2
5461
JavaScriptEngine
1.0
952
 
0.11
1062
KeyPathwayMiner
4.0
385
 
3.0
1749
 
2.1
544
 
2.0
347
 
1.0
505
KGMLReader
0.151
2273
 
0.15
1855
 
0.11
409
 
0.10
1203
 
0.06
1498
KNIMEConnector
1.1
817
 
1.0
705
LayoutSaverPlugin
1.0
1128
Mark
2
0
mcl-new
1.1
533
MCODE
1.32
9514
 
1.31
6305
 
1.3
6602
 
1.2
2851
MetaNetter
2.1
2428
MetaNodePlugin2
1.6
1758
 
1.5
1301
 
1.2
1702
 
1.1
1275
 
1.01
1378
 
1.0
1255
MetScape
2.33
1912
 
2.32
1238
 
2.31
1226
 
2.3
489
 
2.21
186
 
2.2
17
 
2.11
373
 
2.0
252
 
1.01
1736
 
1.0
1089
 
0.8
1520
MiMIplugin
3.11
5754
 
3.1
1000
 
3.01
4003
 
3.0
1579
 
2.2
1752
 
2.1
1536
 
2.0
1491
MINE
1.5
1761
 
1.0
878
MiSink
2.04
1706
 
2.03
1152
 
2.00
1412
ModuLand
1.5
0
 
1.4
0
MONET
2.1
1312
 
2.01
895
 
1.1
1893
Mosaic
1.1
1105
 
1.0
1349
MostHighlyConnectedSubgraphPlugin
1.0
506
MultiColoredNodes
2.540
1468
 
2.533
174
 
2.500
768
 
2.432
315
MultilevelLayoutPlugin
0.6
1913
 
0.41
1781
 
0.4
307
NamedSelection
1.5
1245
 
1.2
1777
 
1.1
1321
 
1.0
2221
NatureProtocolsWorkflow
1.0
3177
NCBIClient
0.92
2746
 
0.70
7161
NCBIEntrezGeneUserInterface
0.52
11219
NDBReaderPlugin
0.1
552
NeighborHighlight
1.0
4368
NeMo
1.4
3460
 
1.3
1184
NetAtlas
1.2
893
 
1.1
1372
NetCirChro
1.0
532
NetDS
3.0
1054
NetLink
0.1
2227
netMatch
2.2
1867
 
2.1
2339
NetTwo
0.1
483
NetworkEvolution
2.1
1042
NetworkPrioritizer
1.01
0
NOA
1.1
1222
 
1.0
342
nodeCharts
0.94
2753
 
0.92
689
 
0.91
667
 
0.91
18
OrthoNets
1.0
1183
OWLPlugin
1.0
1031
PanGIA
1.1
1429
 
1.0
590
Pathintegrator
1.0
1594
PerturbationAnalyzer
1.2
1393
 
1.1
415
 
1.0
657
 
0.2
502
 
0.1
643
PhosphositePlus Web Service Client Module
1.0
0
PhyloTree
0.1
1655
PICRClient
0.2
1767
PINA4MS
1.1
165
 
1.0
200
PiNGO
1.11
3540
 
1.10
836
 
1.00
1278
PinnacleZ
1.1
1880
 
1.0
1263
PSICQUICUniversalClient
0.31
1684
 
0.25
3254
PythonScriptingEngine
2.53
482
 
0.21
1631
RandomNetworks
1.0
5130
Reactome FIs
1.1
0
 
1.0beta
0
 
1.0
0
RemainingDegreeDistribution
1.0
858
ReOrientPlugin
1.0
1792
 
0.3
969
RINalyzer
1.3
0
RubyScriptingEngine
1.7
165
 
1.0
424
 
0.21
736
ScriptEngineManager
1.0
1124
 
0.08
1730
SessionForWeb
3.2
1069
 
3.1
1380
 
3.0
1087
SFLDLoader
1.3
1500
 
1.2
1248
 
1.0
1394
ShortestPath Plugin
1.1
5791
SimBoolNet
1.0
344
SimTrek
1.0
668
SLiMScape
1.6
573
 
1.5
144
 
1.2
132
 
1.0
127
SPNConverter
1.0
312
STOP
1.0
557
StringWSClient
1.2
4443
 
1.1
1518
 
1.0
1045
structureViz
1.9
1697
 
1.3
2109
 
1.2
1368
 
1.0
1736
SubnetworkCreator
1.2
737
 
1.1
466
 
1.0
1176
Superpathways-Plugin
1.2
1408
 
1.0
1091
TransClust
1.01
1522
 
1.0
1681
VennDiagramGenerator
1.4
2614
 
1.02
1584
 
1.0
1276
VennDiagrams
0.5
941
 
0.3
1230
Viacomplex for Cytoscape
1.0
0
VistaClaraPlugin
1.05
3357
 
1.02
1844
 
1.01
2310
 
1.0
1460
 
0.20
180
WordCloud
1.0
1759
 
1.0
0