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: ) Maintainer: Fabricio Almeida-Silva