Package: RedeR 3.9.0

Mauro Castro

RedeR: Interactive visualization and manipulation of nested networks

RedeR combines an R package 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_3.9.0.tar.gz
RedeR_3.9.0.zip(r-4.7)RedeR_3.9.0.zip(r-4.6)RedeR_3.9.0.zip(r-4.5)
RedeR_3.9.0.tgz(r-4.6-any)RedeR_3.9.0.tgz(r-4.5-any)
RedeR_3.9.0.tar.gz(r-4.7-any)RedeR_3.9.0.tar.gz(r-4.6-any)
RedeR_3.9.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
RedeR/json (API)
NEWS

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

Bug tracker:https://github.com/sysbiolab/reder/issues

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

On BioConductor:RedeR-3.9.0(bioc 3.24)RedeR-3.8.0(bioc 3.23)

guigraphandnetworknetworknetworkenrichmentnetworkinferencesoftwaresystemsbiology

6.88 score 7 packages 121 scripts 719 downloads 21 mentions 33 exports 17 dependencies

Last updated from:50490c5fc2. Checks:1 WARNING, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING170
linux-devel-x86_64OK204
source / vignettesOK194
linux-release-x86_64OK165
macos-release-arm64OK88
macos-oldrel-arm64OK108
windows-develOK397
windows-releaseOK87
windows-oldrelOK449
wasm-releaseOK125

Exports:addEdgesaddGraphaddGraphToRedeRaddLegendToRedeRaddNodesatt.addeatt.addvatt.mapvatt.seteatt.setvcallddeleteEdgesdeleteNodesexitdexitRedeRgetGraphgetGraphFromRedeRmergeOutEdgesnestNodespingpingRedeRrederInfoRedPortrelaxrelaxRedeRresetdresetRedeRselectEdgesselectNodesstartRedeRsubgupdateLayoutFromRedeRversion

Dependencies:clicpp11farverglueigraphlabelinglatticelifecyclemagrittrMatrixpkgconfigR6RColorBrewerrlangscalesvctrsviridisLite

RedeR: bridging network analysis and visualization

Sysbiolab - Bioinformatics and Systems Biology Laboratory.

Rendered fromRedeR.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2026-02-18
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
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
RedeR Attribute InformationrederInfo
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