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✨
DESCRIPTION |NEWS
card.svg |card.png
RedeR/json (API)

# 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)

gui graphandnetwork network networkenrichment networkinference software systemsbiology

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

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

Target	Result	Time
bioc-checks	WARNING	171
linux-devel-x86_64	OK	171
source / vignettes	OK	192
linux-release-x86_64	OK	167
macos-release-arm64	OK	113
macos-oldrel-arm64	OK	105
windows-devel	OK	3140
windows-release	OK	88
windows-oldrel	OK	92
wasm-release	OK	123

Exports:addEdges addGraph addGraphToRedeR addLegendToRedeR addNodes att.adde att.addv att.mapv att.sete att.setv calld deleteEdges deleteNodes exitd exitRedeR getGraph getGraphFromRedeR mergeOutEdges nestNodes ping pingRedeR rederInfo RedPort relax relaxRedeR resetd resetRedeR selectEdges selectNodes startRedeR subg updateLayoutFromRedeR version

Dependencies:cli cpp11 farver glue igraph labeling lattice lifecycle magrittr Matrix pkgconfig R6 RColorBrewer rlang scales vctrs viridisLite

RedeR: bridging network analysis and visualization

Rendered fromRedeR.Rmdusingknitr::rmarkdown

Last update: 2026-02-18
Started: 2017-10-12

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
addEdges	addEdges addEdges,character-method addEdges,data.frame-method
Adding 'igraph' objects to RedeR	addGraph addGraph,RedPort-method
Adding 'igraph' objects to RedeR	addGraphToRedeR
Adding graph legends to the RedeR app	addLegendToRedeR
addNodes	addNodes addNodes,character-method
Call RedeR app from R	calld calld,RedPort-method
deleteEdges	deleteEdges deleteEdges,character-method deleteEdges,data.frame-method
deleteNodes	deleteNodes deleteNodes,character-method
Exit the RedeR R-to-Java interface	exitd exitd,RedPort-method
Exit the RedeR R-to-Java interface	exitRedeR
Get graphs from RedeR	getGraph getGraph,RedPort-method
Get graphs from RedeR	getGraphFromRedeR
mergeOutEdges	mergeOutEdges mergeOutEdges,numeric_Or_missing-method
nestNodes	nestNodes nestNodes,character-method
Ping RedeR app	ping ping,RedPort-method
Ping RedeR app	pingRedeR
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 Information	rederInfo
Constructor of RedPort-class objects	RedPort
RedPort: An S4 class for RedeR graphics	RedPort-class
Relax	relax relax,RedPort-method
Relax	relaxRedeR
Reset RedeR app	resetd resetd,RedPort-method
Reset RedeR app	resetRedeR
selectEdges	selectEdges selectEdges,character-method selectEdges,data.frame-method
selectNodes	selectNodes selectNodes,character-method
Start RedeR app from R	startRedeR
Subgraph of a graph	subg
Transforming edge and vertex attributes	att.adde att.addv att.mapv att.sete att.setv transform.attributes
Update graph layout	updateLayoutFromRedeR
Version	version version,RedPort-method