Package: RCy3 2.25.0

Alex Pico

RCy3: Functions to Access and Control Cytoscape

Vizualize, analyze and explore networks using Cytoscape via R. Anything you can do using the graphical user interface of Cytoscape, you can now do with a single RCy3 function.

Authors:Alex Pico [aut, cre], Tanja Muetze [aut], Paul Shannon [aut], Ruth Isserlin [ctb], Shraddha Pai [ctb], Julia Gustavsen [ctb], Georgi Kolishovski [ctb], Yihang Xin [ctb]

RCy3_2.25.0.tar.gz
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RCy3.pdf |RCy3.html✨
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NEWS

Peer review:

Bug tracker:https://github.com/cytoscape/rcy3/issues

On BioConductor:RCy3-2.25.0(bioc 3.20)RCy3-2.24.0(bioc 3.19)

bioconductor-package

416 exports 3.60 score 42 dependencies 15 dependents 22 mentions

Last updated 2 months agofrom:47b2922d86

Exports:addAnnotationBoundedTextaddAnnotationImageaddAnnotationShapeaddAnnotationTextaddCyEdgesaddCyNodesAddToGroupanalyzeNetworkapplyFilterbundleEdgescheckNotebookIsRunningcheckRunningRemoteclearEdgeBendsclearEdgePropertyBypassclearNetworkCenterBypassclearNetworkPropertyBypassclearNetworkZoomBypassclearNodeOpacityBypassclearNodePropertyBypassclearSelectioncloneNetworkcloseSessioncollapseGroupcommandEchocommandOpenDialogcommandPausecommandQuitcommandRunFilecommandsAPIcommandsGETcommandsHelpcommandSleepcommandsPOSTcommandsRuncopyVisualStylecreateColumnFiltercreateCompositeFiltercreateCytoscapejsFromNetworkcreateDegreeFiltercreateGraphFromNetworkcreateGroupcreateGroupByColumncreateIgraphFromNetworkcreateNetworkFromCytoscapejscreateNetworkFromDataFramescreateNetworkFromGraphcreateNetworkFromIgraphcreateSubnetworkcreateViewcreateVisualStylecybrowserClosecybrowserDialogcybrowserHidecybrowserListcybrowserSendcybrowserShowcybrowserVersioncyrestAPIcyrestDELETEcyrestGETcyrestPOSTcyrestPUTcytoscapeApiVersionscytoscapeFreeMemorycytoscapeMemoryStatuscytoscapeNumberOfCorescytoscapePingcytoscapeVersionInfodeleteAllNetworksdeleteAllVisualStyledeleteAnnotationdeleteDuplicateEdgesdeleteGroupdeleteNetworkdeleteSelectedEdgesdeleteSelectedNodesdeleteSelfLoopsdeleteStyleMappingdeleteTableColumndeleteVisualStylediffusionAdvanceddiffusionBasicdisableAppdockPaneldoInitializeSandboxdoRequestRemotedoSetSandboxenableAppexpandGroupexportFiltersexportImageexportJPGexportNetworkexportNetworkToNDExexportPDFexportPNGexportPSexportSVGexportVisualStylesfindRemoteCytoscapefitContentfloatPanelgetAbsSandboxPathgetAllEdgesgetAllNodesgetAllStyleMappingsgetAnnotationListgetAppInformationgetAppStatusgetAppUpdatesgetArrowShapesgetAvailableAppsgetBackgroundColorDefaultgetBrowserClientChannelgetBrowserClientJsgetCollectionListgetCollectionNamegetCollectionNetworksgetCollectionSuidgetCurrentSandboxgetCurrentSandboxNamegetCurrentSandboxPathgetCurrentStylegetDefaultSandboxgetDefaultSandboxPathgetDisabledAppsgetEdgeColorgetEdgeCountgetEdgeInfogetEdgeLineStylegetEdgeLineWidthgetEdgePropertygetEdgeSelectionColorDefaultgetEdgeTargetArrowShapegetFilterListgetFirstNeighborsgetGroupInfogetInstalledAppsgetJupyterBridgeURLgetLayoutNameMappinggetLayoutNamesgetLayoutPropertyNamesgetLayoutPropertyTypegetLayoutPropertyValuegetLineStylesgetNetworkCentergetNetworkCountgetNetworkListgetNetworkNamegetNetworkNDExIdgetNetworkPropertygetNetworkSuidgetNetworkViewsgetNetworkViewSuidgetNetworkZoomgetNodeColorgetNodeCountgetNodeHeightgetNodeLabelPositiongetNodeLabelPositionDefaultgetNodePositiongetNodePropertygetNodeSelectionColorDefaultgetNodeShapesgetNodeSizegetNodeWidthgetNotebookIsRunninggetSandboxReinitializegetSelectedEdgeCountgetSelectedEdgesgetSelectedNodeCountgetSelectedNodesgetStyleDependenciesgetStyleMappinggetTableColumnNamesgetTableColumnsgetTableColumnTypesgetTableValuegetUninstalledAppsgetVisualPropertyDefaultgetVisualPropertyNamesgetVisualStyleJSONgetVisualStyleNamesgroupAnnotationhideAllPanelshideEdgeshideNodeshidePanelhideSelectedEdgeshideSelectedNodesimportFileFromUrlimportFiltersimportNetworkFromFileimportNetworkFromNDEximportVisualStylesinstallAppinvertEdgeSelectioninvertNodeSelectionlayoutCopycatlayoutNetworklistGroupsloadTableDatalockNodeDimensionsmakeSimpleGraphmakeSimpleIgraphmapTableColumnmapVisualPropertymatchArrowColorToEdgemergeNetworksnotebookExportShowImagenotebookShowImageopenAppStoreopenSessionpaletteColorBrewerAccentpaletteColorBrewerBluespaletteColorBrewerBrBGpaletteColorBrewerBuGnpaletteColorBrewerBuPupaletteColorBrewerDark2paletteColorBrewerGnBupaletteColorBrewerGreenspaletteColorBrewerGreyspaletteColorBrewerOrangespaletteColorBrewerOrRdpaletteColorBrewerPairedpaletteColorBrewerPastel1paletteColorBrewerPastel2paletteColorBrewerPiYGpaletteColorBrewerPRGnpaletteColorBrewerPuBupaletteColorBrewerPuBuGnpaletteColorBrewerPuOrpaletteColorBrewerPuRdpaletteColorBrewerPurplespaletteColorBrewerRdBupaletteColorBrewerRdPupaletteColorBrewerRdYlBupaletteColorBrewerRedspaletteColorBrewerSet1paletteColorBrewerSet2paletteColorBrewerSet3paletteColorBrewerYlGnpaletteColorBrewerYlGnBupaletteColorBrewerYlOrBrpaletteColorBrewerYlOrRdpaletteColorRandompaletteColorVirdisRemoveFromGroupremoveNodeCustomGraphicsrenameNetworkrenameTableColumnresetDefaultSandboxrotateLayoutrunningRemoteChecksandboxGetFileInfosandboxGetFromsandboxInitializersandboxRemovesandboxRemoveFilesandboxSendTosandboxSetsandboxUrlTosaveSessionscaleLayoutselectAllselectAllEdgesselectAllNodesselectEdgesselectEdgesAdjacentToNodesselectEdgesAdjacentToSelectedNodesselectEdgesConnectingSelectedNodesselectFirstNeighborsselectNodesselectNodesConnectedBySelectedEdgessetBackgroundColorDefaultsetCatchupFilterSecssetCatchupNetworkSecssetCurrentNetworksetCurrentSandboxsetCurrentViewsetDefaultSandboxsetDefaultSandboxPathsetEdgeColorBypasssetEdgeColorDefaultsetEdgeColorMappingsetEdgeFontFaceBypasssetEdgeFontFaceDefaultsetEdgeFontFaceMappingsetEdgeFontSizeBypasssetEdgeFontSizeDefaultsetEdgeFontSizeMappingsetEdgeLabelBypasssetEdgeLabelColorBypasssetEdgeLabelColorDefaultsetEdgeLabelColorMappingsetEdgeLabelDefaultsetEdgeLabelMappingsetEdgeLabelOpacityBypasssetEdgeLabelOpacityDefaultsetEdgeLabelOpacityMappingsetEdgeLineStyleBypasssetEdgeLineStyleDefaultsetEdgeLineStyleMappingsetEdgeLineWidthBypasssetEdgeLineWidthDefaultsetEdgeLineWidthMappingsetEdgeOpacityBypasssetEdgeOpacityDefaultsetEdgeOpacityMappingsetEdgePropertyBypasssetEdgeSelectionColorDefaultsetEdgeSourceArrowColorBypasssetEdgeSourceArrowColorDefaultsetEdgeSourceArrowColorMappingsetEdgeSourceArrowMappingsetEdgeSourceArrowShapeBypasssetEdgeSourceArrowShapeDefaultsetEdgeSourceArrowShapeMappingsetEdgeTargetArrowColorBypasssetEdgeTargetArrowColorDefaultsetEdgeTargetArrowColorMappingsetEdgeTargetArrowMappingsetEdgeTargetArrowShapeBypasssetEdgeTargetArrowShapeDefaultsetEdgeTargetArrowShapeMappingsetEdgeTooltipBypasssetEdgeTooltipDefaultsetEdgeTooltipMappingsetLayoutPropertiessetModelPropagationSecssetNetworkCenterBypasssetNetworkPropertyBypasssetNetworkZoomBypasssetNodeBorderColorBypasssetNodeBorderColorDefaultsetNodeBorderColorMappingsetNodeBorderOpacityBypasssetNodeBorderOpacityDefaultsetNodeBorderOpacityMappingsetNodeBorderWidthBypasssetNodeBorderWidthDefaultsetNodeBorderWidthMappingsetNodeColorBypasssetNodeColorDefaultsetNodeColorMappingsetNodeComboOpacityMappingsetNodeCustomBarChartsetNodeCustomBoxChartsetNodeCustomHeatMapChartsetNodeCustomLinearGradientsetNodeCustomLineChartsetNodeCustomPieChartsetNodeCustomPositionsetNodeCustomRadialGradientsetNodeCustomRingChartsetNodeFillOpacityBypasssetNodeFillOpacityDefaultsetNodeFillOpacityMappingsetNodeFontFaceBypasssetNodeFontFaceDefaultsetNodeFontFaceMappingsetNodeFontSizeBypasssetNodeFontSizeDefaultsetNodeFontSizeMappingsetNodeHeightBypasssetNodeHeightDefaultsetNodeHeightMappingsetNodeLabelBypasssetNodeLabelColorBypasssetNodeLabelColorDefaultsetNodeLabelColorMappingsetNodeLabelDefaultsetNodeLabelMappingsetNodeLabelOpacityBypasssetNodeLabelOpacityDefaultsetNodeLabelOpacityMappingsetNodeLabelPositionBypasssetNodeLabelPositionDefaultsetNodeOpacityBypasssetNodePositionBypasssetNodePropertyBypasssetNodeSelectionColorDefaultsetNodeShapeBypasssetNodeShapeDefaultsetNodeShapeMappingsetNodeSizeBypasssetNodeSizeDefaultsetNodeSizeMappingsetNodeTooltipBypasssetNodeTooltipDefaultsetNodeTooltipMappingsetNodeWidthBypasssetNodeWidthDefaultsetNodeWidthMappingsetNotebookIsRunningsetSandboxReinitializesetStyleDependenciessetVisualPropertyDefaultsetVisualStylespoofResponsesyncNodeCustomGraphicsSizetoggleGraphicsDetailsungroupAnnotationunhideAllunhideEdgesunhideNodesuninstallAppUpdateAnnotationBoundedTextupdateAnnotationImageupdateAnnotationShapeupdateAnnotationTextupdateAppupdateGroupAnnotationupdateNetworkInNDExupdateStyleDefaultsupdateStyleMapping

Dependencies:askpassbackportsbase64encbase64urlBiocGenericsbitopscaToolsclicrayoncurldigestevaluatefansifastmapfsgluegplotsgraphgtoolshtmltoolshttrIRdisplayIRkerneljsonliteKernSmoothlifecyclemimeopensslpbdZMQpillarR6RColorBrewerRCurlreprRJSONIOrlangstringisysutf8uuidvctrsXML