aggregateBioVar

aggregateBioVar summarizes single cell gene expression profiles at the level of subject for multi-subject single cell RNA-seq data.

Key Features:

• Input Format: Accepts a SingleCellExperiment object as input for processing multi-subject scRNA-seq data.
• Subject-Level Aggregation: Converts single cell data to aggregate gene-by-subject count matrices organized by assigned cell type.
• Output Structure: Produces a list of SummarizedExperiment objects, where each list element corresponds to an assigned cell type.
• Inter-Subject Metadata: Includes column metadata for individual subjects within the SummarizedExperiment objects.
• Downstream Compatibility: Generates outputs that can be processed using downstream bulk RNA-seq tools.

Scientific Applications:

• Multi-Subject scRNA-seq Analysis: Enables differential gene expression analysis for single cell RNA-seq data collected from multiple subjects, biological samples, or technical replicates.
• Cell Type-Specific Aggregation: Facilitates subject-level summarization of gene expression within individual cell types for comparative analysis.

Methodology:

A SingleCellExperiment object is converted to a list of SummarizedExperiment objects with each element corresponding to an assigned cell type, containing aggregate gene-by-subject count matrices and inter-subject column metadata.