GraphExperiment
S4 Class for Quantitative Data and Associated Networks
Bioconductor version: 3.23 · Package version: 1.0.2
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("GraphExperiment")Details
| Maintainer | Fabricio Almeida-Silva <fabricio_almeidasilva@hotmail.com> |
| Author | Fabricio Almeida-Silva [aut, cre] (ORCID: <https://orcid.org/0000-0002-5314-2964>) |
| License | GPL-3 |
| URL | https://github.com/almeidasilvaf/GraphExperiment |
| Bug Reports | https://support.bioconductor.org/tag/GraphExperiment |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | DataImport, DataRepresentation, GeneExpression, Infrastructure, Network, SingleCell, Software, Transcriptomics |
| Package Short Url | https://bioconductor.org/packages/GraphExperiment/ |
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 1.0.2, https://bioconductor.org/packages/GraphExperiment.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | GraphExperiment_1.0.2.tar.gz |
| Windows binary (x86_64) | GraphExperiment_1.0.2.zip |
| macOS binary (arm64) | GraphExperiment_1.0.2.tgz |
| macOS binary (x86_64) | GraphExperiment_1.0.2.tgz |
Dependencies
Depends: SingleCellExperiment, igraph
Imports: methods, SummarizedExperiment, BiocBaseUtils, S4Vectors
Suggests: knitr, BiocStyle, testthat, rmarkdown, covr, sessioninfo