SingleCellAlleleExperiment

SingleCellAlleleExperiment defines an S4 class based on SingleCellExperiment that stores single-cell data for immune genes such as HLAs, Igs and KIRs at allele and functional level alongside the usual gene layer.

Key Features:

• Allele-aware data structure: Extends SingleCellExperiment to store allele-aware quantification data for immune genes.
• Multi-level immune gene representation: Stores data for HLA, Ig and KIR genes at both allele and functional level in addition to the standard gene layer.
• scIGD workflow integration: Serves as the core data structure for the single-cell ImmunoGenomic Diversity (scIGD) workflow.
• Data handling and analysis functionalities: Provides methods for further data handling and analysis of allele-aware immune gene quantification data.

Scientific Applications:

• Single-cell immuno-genomic diversity analysis: Enables analysis of allele-level variation in immune genes from single-cell sequencing data within the scIGD workflow.
• HLA typing at single-cell resolution: Supports storage and analysis of HLA allele-specific expression data.
• Immunoglobulin repertoire analysis: Facilitates analysis of Ig gene usage and allele-specific expression in single cells.
• KIR gene diversity studies: Enables investigation of killer cell immunoglobulin-like receptor allele diversity at single-cell level.

Methodology:

Implements an S4 class extending SingleCellExperiment with additional layers for allele and functional level data of immune genes.