RedeR: Interactive visualization and manipulation of nested networks

RedeR is an R-based package combined with a stand-alone Java application for interactive visualization and manipulation of modular structures, nested networks and multiple levels of hierarchical associations.

AuthorMauro Castro, Xin Wang, Florian Markowetz
Date of publicationNone
MaintainerMauro Castro <mauro.a.castro@gmail.com>
LicenseGPL (>= 2)
Version1.22.0
http://genomebiology.com/2012/13/4/R29

View on Bioconductor

Man pages

addEdgeBetweenContainers: Add edges between containers.

addEdges: Add edges to RedeR graphs.

addGraph: Add graphs to RedeR application.

addLegend: Add graph legends to RedeR application.

addNodes: Add nodes to RedeR graphs.

addSeries: Add series to RedeR application.

addSubgraph: Add subgraphs to RedeR application.

addSubgraph.list: Add a list of subgraphs to RedeR application.

att: Map and set edge and vertex attributes to RedeR application.

calld: Call RedeR app from R.

cea: Co-expression analysis.

deleteEdges: Remove edges from RedeR graphs.

deleteNodes: Remove nodes from RedeR graphs.

deleteSelectedEdges: Delete selected edges in RedeR graphs.

deleteSelectedNodes: Delete selected nodes in RedeR graphs.

deSelectEdges: Unmark selected edges.

deSelectGraph: Unmark selected graph objects.

deSelectNodes: Unmark selected nodes.

duplicateGraph: Duplicate graphs in RedeR application.

exitd: Exit RedeR R-to-Java interface.

getContainerComponets: Get container components.

getEdgeIDs: Get edge IDs.

getEdges: Get edges.

getGraph: Get RedeR graph.

getNodeIDs: Get node IDs.

getNodes: Get nodes.

getSourceEdgeIDs: Get source-edge IDs.

getTargetEdgeIDs: Get target-edge IDs.

gtoy.rm: Random graphs and modules.

isDynamicsActive: Inquires about RedeR current state.

mergeNodes: Merge nodes.

mergeOutEdges: Merge out-edges between connected containers and transfers...

nesthc: Nest hclust objects to containers.

nestNodes: Nest nodes to containers.

ping: Test RedeR R-to-Java interface.

RedeR.data: Pre-processed dataset for RedeR case study.

RedeR-package: RedeR: bridging the gap between network analysis and...

RedPort: The constructor for the RedPort class.

RedPort-class: Class "RedPort"

relax: relax

resetd: Reset RedeR app.

selectAllEdges: Select all edges.

selectAllNodes: selectAllNodes

selectEdges: selectEdges

selectGraph: Select graph.

selectNodes: Select nodes.

setArrowDirection: Set arrow direction.

subg: Subgraph of a graph.

updateContainerSize: Update container size.

updateGraph: Update RedeR graphs.

version: Version

Functions

addEdgeBetweenContainers Man page
addEdgeBetweenContainers,RedPort-method Man page
addEdges Man page
addEdges,RedPort-method Man page
addGraph Man page
addGraph,RedPort-method Man page
addLegend.color Man page
addLegend.color,RedPort-method Man page
addLegend.shape Man page
addLegend.shape,RedPort-method Man page
addLegend.size Man page
addLegend.size,RedPort-method Man page
addNodes Man page
addNodes,RedPort-method Man page
addSeries Man page
addSeries,RedPort-method Man page
addSubgraph Man page
addSubgraph.list Man page
addSubgraph.list,RedPort-method Man page
addSubgraph,RedPort-method Man page
att.mape Man page
att.mapv Man page
att.sete Man page
att.setv Man page
calld Man page
calld,RedPort-method Man page
Carroll2006 Man page
cea Man page
deleteEdges Man page
deleteEdges,RedPort-method Man page
deleteNodes Man page
deleteNodes,RedPort-method Man page
deleteSelectedEdges Man page
deleteSelectedEdges,RedPort-method Man page
deleteSelectedNodes Man page
deleteSelectedNodes,RedPort-method Man page
deSelectEdges Man page
deSelectEdges,RedPort-method Man page
deSelectGraph Man page
deSelectGraph,RedPort-method Man page
deSelectNodes Man page
deSelectNodes,RedPort-method Man page
duplicateGraph Man page
duplicateGraph,RedPort-method Man page
ER.deg Man page
ER.limma Man page
exitd Man page
exitd,RedPort-method Man page
getContainerComponets Man page
getContainerComponets,RedPort-method Man page
getEdgeIDs Man page
getEdgeIDs,RedPort-method Man page
getEdges Man page
getEdges,RedPort-method Man page
getGraph Man page
getGraph,RedPort-method Man page
getNodeIDs Man page
getNodeIDs,RedPort-method Man page
getNodes Man page
getNodes,RedPort-method Man page
getSourceEdgeIDs Man page
getSourceEdgeIDs,RedPort-method Man page
getTargetEdgeIDs Man page
getTargetEdgeIDs,RedPort-method Man page
gtoy.rm Man page
hs.inter Man page
isDynamicsActive Man page
isDynamicsActive,RedPort-method Man page
mergeNodes Man page
mergeNodes,RedPort-method Man page
mergeOutEdges Man page
mergeOutEdges,RedPort-method Man page
nesthc Man page
nesthc,RedPort-method Man page
nestNodes Man page
nestNodes,RedPort-method Man page
ping Man page
ping,RedPort-method Man page
RedeR Man page
RedeR-package Man page
RedPort Man page
RedPort-class Man page
relax Man page
relax,RedPort-method Man page
resetd Man page
resetd,RedPort-method Man page
selectAllEdges Man page
selectAllEdges,RedPort-method Man page
selectAllNodes Man page
selectAllNodes,RedPort-method Man page
selectEdges Man page
selectEdges,RedPort-method Man page
selectGraph Man page
selectGraph,RedPort-method Man page
selectNodes Man page
selectNodes,RedPort-method Man page
setArrowDirection Man page
setArrowDirection,RedPort-method Man page
subg Man page
updateContainerSize Man page
updateContainerSize,RedPort-method Man page
updateGraph Man page
updateGraph,RedPort-method Man page
version Man page
version,RedPort-method Man page

Files

RedeR/.Rinstignore
RedeR/DESCRIPTION
RedeR/NAMESPACE
RedeR/R
RedeR/R/AllClasses.R RedeR/R/AllGenerics.R RedeR/R/AllMethods.R RedeR/R/RedPort.R RedeR/R/Supplements.R RedeR/R/zzz.R
RedeR/build
RedeR/build/vignette.rds
RedeR/data
RedeR/data/Carroll2006.RData
RedeR/data/ER.deg.RData
RedeR/data/ER.limma.RData
RedeR/data/datalist
RedeR/data/hs.inter.RData
RedeR/inst
RedeR/inst/CITATION
RedeR/inst/NEWS.Rd
RedeR/inst/doc
RedeR/inst/doc/RedeR.R
RedeR/inst/doc/RedeR.Rnw
RedeR/inst/doc/RedeR.pdf
RedeR/inst/java
RedeR/inst/java/reder_v2.jar
RedeR/inst/script
RedeR/inst/script/script_case_st.r
RedeR/man
RedeR/man/RedPort-class.Rd RedeR/man/RedPort.Rd RedeR/man/RedeR-package.Rd RedeR/man/RedeR.data.Rd RedeR/man/addEdgeBetweenContainers.Rd RedeR/man/addEdges.Rd RedeR/man/addGraph.Rd RedeR/man/addLegend.Rd RedeR/man/addNodes.Rd RedeR/man/addSeries.Rd RedeR/man/addSubgraph.Rd RedeR/man/addSubgraph.list.Rd RedeR/man/att.Rd RedeR/man/calld.Rd RedeR/man/cea.Rd RedeR/man/deSelectEdges.Rd RedeR/man/deSelectGraph.Rd RedeR/man/deSelectNodes.Rd RedeR/man/deleteEdges.Rd RedeR/man/deleteNodes.Rd RedeR/man/deleteSelectedEdges.Rd RedeR/man/deleteSelectedNodes.Rd RedeR/man/duplicateGraph.Rd RedeR/man/exitd.Rd RedeR/man/getContainerComponets.Rd RedeR/man/getEdgeIDs.Rd RedeR/man/getEdges.Rd RedeR/man/getGraph.Rd RedeR/man/getNodeIDs.Rd RedeR/man/getNodes.Rd RedeR/man/getSourceEdgeIDs.Rd RedeR/man/getTargetEdgeIDs.Rd RedeR/man/gtoy.rm.Rd RedeR/man/isDynamicsActive.Rd RedeR/man/mergeNodes.Rd RedeR/man/mergeOutEdges.Rd RedeR/man/nestNodes.Rd RedeR/man/nesthc.Rd RedeR/man/ping.Rd RedeR/man/relax.Rd RedeR/man/resetd.Rd RedeR/man/selectAllEdges.Rd RedeR/man/selectAllNodes.Rd RedeR/man/selectEdges.Rd RedeR/man/selectGraph.Rd RedeR/man/selectNodes.Rd RedeR/man/setArrowDirection.Rd RedeR/man/subg.Rd RedeR/man/updateContainerSize.Rd RedeR/man/updateGraph.Rd RedeR/man/version.Rd
RedeR/vignettes
RedeR/vignettes/RedeR.Rnw
RedeR/vignettes/bib.bib
RedeR/vignettes/fig1.pdf
RedeR/vignettes/fig2.pdf
RedeR/vignettes/fig3.pdf
RedeR/vignettes/fig4.pdf
RedeR/vignettes/fig5a.pdf
RedeR/vignettes/fig5b.pdf
RedeR/vignettes/fig5c.pdf
RedeR/vignettes/fig6.pdf
RedeR/vignettes/fig7.pdf

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