Package: RedeR 3.3.0

Mauro Castro

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 nested networks. Graph, node, and edge attributes can be configured using either graphical or command-line methods, following igraph syntax rules.

Authors:Xin Wang [ctb], Florian Markowetz [ctb], Mauro Castro [aut, cre]

RedeR_3.3.0.tar.gz
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RedeR.pdf |RedeR.html✨
RedeR/json (API)
NEWS

# Install 'RedeR' in R:
install.packages('RedeR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • ER.limma - Pre-processed dataset for RedeR case studies.
  • hs.inter - Pre-processed igraph object for RedeR case studies.

On BioConductor:RedeR-3.3.0(bioc 3.21)RedeR-3.2.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

guigraphandnetworknetworknetworkenrichmentnetworkinferencesoftwaresystemsbiology

6.95 score 7 packages 107 scripts 540 downloads 21 mentions 60 exports 19 dependencies

Last updated 2 months agofrom:7abfaa7d01. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 17 2024
R-4.5-winNOTEDec 17 2024
R-4.5-linuxNOTEDec 17 2024
R-4.4-winNOTEDec 17 2024
R-4.4-macNOTEDec 17 2024
R-4.3-winOKDec 17 2024
R-4.3-macOKDec 17 2024

Exports:addEdgeBetweenContainersaddEdgesaddGraphaddGraphToRedeRaddLegend.coloraddLegend.shapeaddLegend.sizeaddLegendToRedeRaddNodesatt.addeatt.addvatt.mapeatt.mapvatt.seteatt.setvcalldceadeleteEdgesdeleteNodesdeleteSelectedEdgesdeleteSelectedNodesdeSelectEdgesdeSelectGraphdeSelectNodesexitdexitRedeRgetContainerComponetsgetEdgeIDsgetEdgesgetGraphgetGraphFromRedeRgetNodeIDsgetNodesgetSourceEdgeIDsgetTargetEdgeIDsgtoy.rmmergeNodesmergeOutEdgesnesthcnestNodespingpingRedeRRedPortrelaxrelaxRedeRresetdresetRedeRselectAllEdgesselectAllNodesselectEdgesselectGraphselectNodessetArrowDirectionstartRedeRsubgupdateContainerSizeupdateCoordXYupdateGraphupdateLayoutFromRedeRversion

Dependencies:clicolorspacecpp11farverglueigraphlabelinglatticelifecyclemagrittrMatrixmunsellpkgconfigR6RColorBrewerrlangscalesvctrsviridisLite

RedeR: bridging network analysis and visualization

Sysbiolab - Bioinformatics and Systems Biology Laboratory.

Rendered fromRedeR.Rmdusingknitr::rmarkdownon Dec 17 2024.

Last update: 2024-02-02
Started: 2017-10-12

Readme and manuals

Help Manual

Help pageTopics
addEdgesaddEdges addEdges,character-method addEdges,data.frame-method
Adding 'igraph' objects to RedeRaddGraph addGraph,RedPort-method
Adding 'igraph' objects to RedeRaddGraphToRedeR
Adding graph legends to the RedeR appaddLegendToRedeR
addNodesaddNodes addNodes,character-method
Call RedeR app from Rcalld calld,RedPort-method
deleteEdgesdeleteEdges deleteEdges,character-method deleteEdges,data.frame-method
deleteNodesdeleteNodes deleteNodes,character-method
Deprecated functionsaddEdgeBetweenContainers addLegend.color addLegend.shape addLegend.size att.mape cea deleteSelectedEdges deleteSelectedNodes Deprecated deSelectEdges deSelectGraph deSelectNodes getContainerComponets getEdgeIDs getEdges getNodeIDs getNodes getSourceEdgeIDs getTargetEdgeIDs gtoy.rm mergeNodes nesthc selectAllEdges selectAllNodes selectGraph setArrowDirection updateContainerSize updateCoordXY updateGraph
Exit the RedeR R-to-Java interfaceexitd exitd,RedPort-method
Exit the RedeR R-to-Java interfaceexitRedeR
Get graphs from RedeRgetGraph getGraph,RedPort-method
Get graphs from RedeRgetGraphFromRedeR
mergeOutEdgesmergeOutEdges mergeOutEdges,numeric_Or_missing-method
nestNodesnestNodes nestNodes,character-method
Ping RedeR appping ping,RedPort-method
Ping RedeR apppingRedeR
Pre-processed igraph object for RedeR case studies.hs.inter RedeR-data1
Pre-processed dataset for RedeR case studies.ER.limma RedeR-data2
Constructor of RedPort-class objectsRedPort
RedPort: An S4 class for RedeR graphicsRedPort-class
Relaxrelax relax,RedPort-method
RelaxrelaxRedeR
Reset RedeR appresetd resetd,RedPort-method
Reset RedeR appresetRedeR
selectEdgesselectEdges selectEdges,character-method selectEdges,data.frame-method
selectNodesselectNodes selectNodes,character-method
Start RedeR app from RstartRedeR
Subgraph of a graphsubg
Transforming edge and vertex attributesatt.adde att.addv att.mapv att.sete att.setv transform.attributes
Update graph layoutupdateLayoutFromRedeR
Versionversion version,RedPort-method