Package: GraphExperiment 1.0.1

Fabricio Almeida-Silva

GraphExperiment: S4 Class for Quantitative Data and Associated Networks

GraphExperiment provides users and developers with an S4 class that extends `SingleCellExperiment` by offering infrastructure to store and retrieve networks (`igraph` objects) representing how assay features and/or observations are associated with each other. The class was designed to store networks inferred from high-dimensional quantitative data, with feature-feature networks including gene coexpression networks (GCNs), gene regulatory networks (GRNs), and co-abundance networks (from proteomics and metabolomics), and observation-observation network including cell-cell distances, species-species relationships, and sample-sample similarities.

Authors:Fabricio Almeida-Silva [aut, cre], Yves Van de Peer [aut]

GraphExperiment_1.0.1.tar.gz
GraphExperiment_1.0.1.zip(r-4.7)GraphExperiment_1.0.1.zip(r-4.6)GraphExperiment_1.0.1.zip(r-4.5)
GraphExperiment_1.0.1.tgz(r-4.6-any)GraphExperiment_1.0.1.tgz(r-4.5-any)
GraphExperiment_1.0.1.tar.gz(r-4.7-any)GraphExperiment_1.0.1.tar.gz(r-4.6-any)
GraphExperiment_1.0.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
GraphExperiment/json (API)
NEWS

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

Bug tracker:https://github.com/almeidasilvaf/graphexperiment/issues

On BioConductor:GraphExperiment-1.1.1(bioc 3.24)GraphExperiment-1.0.1(bioc 3.23)

datarepresentationdataimportinfrastructuregeneexpressiontranscriptomicsnetworksinglecellbioconductorbioinformaticsoop

4.48 score 1 stars 190 downloads 15 exports 28 dependencies

Last updated from:4494c104f4 (on RELEASE_3_23). Checks:1 NOTE, 9 OK. Indexed: no.

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bioc-checksNOTE166
linux-devel-x86_64OK309
source / vignettesOK250
linux-release-x86_64OK297
macos-release-arm64OK209
macos-oldrel-arm64OK296
windows-develOK570
windows-releaseOK558
windows-oldrelOK538
wasm-releaseOK128

Exports:colDatacolGraphcolGraph<-colGraphNamescolGraphNames<-colGraphscolGraphs<-GraphExperimentrowDatarowGraphrowGraph<-rowGraphNamesrowGraphNames<-rowGraphsrowGraphs<-

Dependencies:abindBiobaseBiocBaseUtilsBiocGenericsclicpp11DelayedArraygenericsGenomicRangesglueigraphIRangeslatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatspkgconfigrlangS4ArraysS4VectorsSeqinfoSingleCellExperimentSparseArraySummarizedExperimentvctrsXVector

Introduction to the GraphExperiment class

Fabricio Almeida-Silva, Yves Van de Peer

Rendered fromGraphExperiment.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2026-05-22
Started: 2026-03-16

Readme and manuals

Help Manual

Help pageTopics
'GraphExperiment' S4 classGraphExperiment GraphExperiment-class
Coercion methods for 'GraphExperiment' objectscoerce,RangedSummarizedExperiment,GraphExperiment-method coerce,SingleCellExperiment,GraphExperiment-method coerce,SummarizedExperiment,GraphExperiment-method GraphExperiment-coerce
Methods for 'GraphExperiment' objectscolData colData,GraphExperiment-method colGraph colGraph,GraphExperiment,ANY-method colGraph,GraphExperiment,missing-method colGraph<- colGraph<-,GraphExperiment-method colGraphNames colGraphNames,GraphExperiment-method colGraphNames<- colGraphNames<-,GraphExperiment,character-method colGraphs colGraphs,GraphExperiment-method colGraphs<- colGraphs<-,GraphExperiment-method GraphExperiment-methods rowData rowData,GraphExperiment-method rowGraph rowGraph,GraphExperiment,ANY-method rowGraph,GraphExperiment,missing-method rowGraph<- rowGraph<-,GraphExperiment-method rowGraphNames rowGraphNames,GraphExperiment-method rowGraphNames<- rowGraphNames<-,GraphExperiment,character-method rowGraphs rowGraphs,GraphExperiment-method rowGraphs<- rowGraphs<-,GraphExperiment-method
Subsetting 'GraphExperiment' objectsGraphExperiment-subset [,GraphExperiment,ANY,ANY,ANY-method