GraphExperiment

GraphExperiment extends SingleCellExperiment with an S4 class infrastructure that stores and retrieves igraph network objects representing associations between assay features and/or observations.

Key Features:

• Network Storage: Stores and retrieves igraph objects representing feature-feature and/or observation-observation associations.
• Feature-Feature Networks: Supports gene coexpression networks (GCNs), gene regulatory networks (GRNs), and co-abundance networks from proteomics and metabolomics data.
• Observation-Observation Networks: Supports cell-cell distances, species-species relationships, and sample-sample similarities.
• S4 Class Extension: Extends SingleCellExperiment to integrate network data with high-dimensional quantitative assay data.

Scientific Applications:

• Gene Coexpression Analysis: Stores and manages gene coexpression networks (GCNs) inferred from transcriptomic data.
• Gene Regulatory Network Analysis: Stores and manages gene regulatory networks (GRNs) representing transcriptional regulation.
• Proteomics and Metabolomics: Stores and manages co-abundance networks from protein and metabolite quantitative data.
• Single-Cell Analysis: Stores cell-cell distance networks alongside single-cell assay data via SingleCellExperiment extension.
• Ecological and Comparative Studies: Stores species-species relationship networks and sample-sample similarity networks.

Methodology:

The S4 class extends SingleCellExperiment and uses igraph objects to represent networks inferred from high-dimensional quantitative data.