GraphExperiment
This is the development version of GraphExperiment; for the stable release version, see GraphExperiment.
All Bioconductor versions of GraphExperiment
3.24 (devel), 3.23 (release)
S4 Class for Quantitative Data and Associated Networks
Bioconductor version: 3.24 · Package version: 1.1.2
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.
Author: Fabricio Almeida-Silva [aut, cre] 
Maintainer: Fabricio Almeida-Silva <fabricio_almeidasilva at hotmail.com>
Citation
From within R, enter citation("GraphExperiment"):
Fabricio Almeida-Silva. GraphExperiment: S4 Class for Quantitative Data and Associated Networks. doi:10.18129/B9.bioc.GraphExperiment, R package version 1.1.2, https://bioconductor.org/packages/GraphExperiment.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("GraphExperiment")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.1.2 |
| License | GPL-3 |
| URL | https://github.com/almeidasilvaf/GraphExperiment |
| Bug Reports | https://support.bioconductor.org/tag/GraphExperiment |
| Last updated | 2026-06-17 |
| In Bioconductor since | BioC 3.23 (R-4.6) (less than a year) |
| Downloads rank | 2279 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | DataImport, DataRepresentation, GeneExpression, Infrastructure, Network, SingleCell, Software, Transcriptomics |
| Package Short Url | https://bioconductor.org/packages/GraphExperiment/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("GraphExperiment")| Introduction to the GraphExperiment class | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | GraphExperiment_1.1.2.tar.gz |
| Windows binary (x86_64) | GraphExperiment_1.1.2.zip |
| macOS binary (arm64) | GraphExperiment_1.1.2.tgz |
| macOS binary (x86_64) | GraphExperiment_1.1.2.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/GraphExperiment |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/GraphExperiment |
| Package Downloads Report | Download Stats |
Dependencies
Depends: SingleCellExperiment, igraph
Imports: methods, SummarizedExperiment, BiocBaseUtils, S4Vectors
Suggests: knitr, BiocStyle, testthat, rmarkdown, covr, sessioninfo