scMappR

scMappR assigns cell-type specificity scores to differentially expressed genes (DEGs) from bulk RNA-seq by integrating single-cell RNA-seq (scRNA-seq)-derived cell-type expression profiles to identify the cellular origins of differential expression in heterogeneous samples.

Key Features:

• Integration of scRNA-seq and bulk RNA-seq: Leverages scRNA-seq-derived cell-type expression profiles to re-calibrate and interpret bulk RNA-seq differential expression results.
• Cell-Type Specificity Scores: Computes specificity scores that indicate the likelihood that individual DEGs are expressed in particular cell types.
• Benchmarking and Validation: Validated using RNA-seq from sorted blood cells and applied to a kidney regeneration in mice case study that identified immune-cell expressed DEGs.
• Curated scRNA-seq Expression Matrices: Provides curated scRNA-seq expression matrices for approximately 100 human and mouse tissues to support cell-type assignment.
• R package implementation: Available as an R package for integration into computational analysis workflows.

Scientific Applications:

• Tissue regeneration studies: Assigns DEGs to cell types in models such as kidney regeneration in mice to reveal cellular contributors to regeneration.
• Immune response analysis: Identifies immune-cell-expressed DEGs and clarifies immune contributions to bulk expression changes.
• Disease and heterogeneous tissue analysis: Deconvolves bulk RNA-seq differential expression to determine cellular origins of changes in complex tissues and disease contexts.

Methodology:

Integrates bulk RNA-seq with scRNA-seq-derived cell-type expression profiles and utilizes existing deconvolution methods to assign specificity scores to DEGs; accepts user-supplied scRNA-seq data.