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.

Author
Mauro Castro, Xin Wang, Florian Markowetz
Date of publication
None
Maintainer
Mauro Castro <mauro.a.castro@gmail.com>
License
GPL (>= 2)
Version
1.22.0
URLs

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

Files in this package

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