Package: GraphExperiment
Title: S4 Class for Quantitative Data and Associated Networks
Version: 1.1.2
Date: 2026-03-01
Authors@R: 
    c(
    person(given = "Fabricio",
           family = "Almeida-Silva",
           role = c("aut", "cre"),
           email = "fabricio_almeidasilva@hotmail.com",
           comment = c(ORCID = "0000-0002-5314-2964"))
    )
Description: 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.
License: GPL-3
URL: https://github.com/almeidasilvaf/GraphExperiment
BugReports: https://support.bioconductor.org/tag/GraphExperiment
Encoding: UTF-8
biocViews: DataRepresentation, DataImport, Infrastructure,
        GeneExpression, Transcriptomics, Network, SingleCell
Depends: SingleCellExperiment, igraph
Imports: methods, SummarizedExperiment, BiocBaseUtils, S4Vectors
Suggests: knitr, BiocStyle, testthat, rmarkdown, covr, sessioninfo
Config/testthat/edition: 3
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
VignetteBuilder: knitr
Config/pak/sysreqs: libglpk-dev libxml2-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-06-17 07:50:08 UTC
RemoteUrl: https://github.com/bioc/GraphExperiment
RemoteRef: HEAD
RemoteSha: a7e32171d97d7c99cf0968c577884a333d11f9ef
NeedsCompilation: no
Packaged: 2026-06-17 11:50:59 UTC; root
Author: Fabricio Almeida-Silva [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-5314-2964>)
Maintainer: Fabricio Almeida-Silva <fabricio_almeidasilva@hotmail.com>
Built: R 4.6.0; ; 2026-06-17 11:53:32 UTC; windows
