GraphExperiment

S4 Class for Quantitative Data and Associated Networks

Bioconductor version: 3.23 · Package version: 1.0.2

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.

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("GraphExperiment")