DeeDeeExperiment

DeeDeeExperiment extends the SingleCellExperiment class to integrate and manage omics analysis results by introducing dedicated slots for Differential Expression Analysis (DEA) and Functional Enrichment Analysis (FEA) results, enabling structured storage and retrieval of multiple contrasts and associated metadata within a single data object.

Key Features:

• S4 Class Architecture: Extends SingleCellExperiment with specialized slots for DEA and FEA results.
• DEA Result Storage: Stores Differential Expression Analysis results with support for multiple contrasts.
• FEA Result Storage: Stores Functional Enrichment Analysis results alongside omics data.
• Metadata Integration: Organizes and retrieves contrast-specific metadata within a single object.
• Bioconductor Interoperability: Implements standard Bioconductor S4 class conventions for compatibility with existing workflows.

Scientific Applications:

• Multi-Contrast Omics Studies: Manages differential expression results across multiple experimental conditions and complex designs.
• Functional Enrichment Workflows: Integrates pathway and functional analysis results with underlying omics data.
• Reproducible Research: Standardizes storage of analysis outputs to improve reproducibility and data sharing.
• Downstream Analysis Integration: Provides structured data objects for subsequent statistical and visualization pipelines.

Methodology:

DeeDeeExperiment is implemented as an S4 class within the Bioconductor ecosystem, extending SingleCellExperiment with two additional dedicated slots for DEA and FEA results.