GraphExperiment
This is the development version of GraphExperiment; to use it, please install the devel version of Bioconductor.
S4 Class for Quantitative Data and Associated Networks
Bioconductor version: Development (3.23)
GraphExperiment provides users and developers with an S4 class that extends `SingleCellExperiment` by offering infrastructure to store and retrieve networks (`igraph` objects) representing how features are associated with each other. The class was designed to store networks inferred from high-dimensional quantitative data, including gene coexpression networks (GCNs), gene regulatory networks (GRNs), and co-abundance networks (from proteomics and metabolomics), as well as networks inferred from other types of data (e.g., protein-protein interactions).
Author: Fabricio Almeida-Silva [aut, cre]
, Yves Van de Peer [aut]
Maintainer: Fabricio Almeida-Silva <fabricio_almeidasilva at hotmail.com>
citation("GraphExperiment")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("GraphExperiment")
For older versions of R, please refer to the appropriate Bioconductor release.
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 |
Details
| biocViews | DataImport, DataRepresentation, GeneExpression, Infrastructure, Network, SingleCell, Software, Transcriptomics |
| Version | 0.99.1 |
| In Bioconductor since | BioC 3.23 (R-4.6) |
| License | GPL-3 |
| Depends | SingleCellExperiment, igraph |
| Imports | methods, SummarizedExperiment, BiocBaseUtils, S4Vectors |
| System Requirements | |
| URL | https://github.com/almeidasilvaf/GraphExperiment |
| Bug Reports | https://support.bioconductor.org/tag/GraphExperiment |
See More
| Suggests | knitr, BiocStyle, testthat, rmarkdown, covr, sessioninfo |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | GraphExperiment_0.99.1.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (big-sur-arm64) | |
| macOS Binary (sonoma-arm64) | GraphExperiment_0.99.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/GraphExperiment |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/GraphExperiment |
| Bioc Package Browser | https://code.bioconductor.org/browse/GraphExperiment/ |
| Package Short Url | https://bioconductor.org/packages/GraphExperiment/ |
| Package Downloads Report | Download Stats |