DropletQC

DropletQC computes a nuclear fraction metric from droplet-based single-cell RNA-seq data to distinguish droplets containing intact cells, damaged cells, and ambient RNA for quality control.

Key Features:

• Novel QC Metric - Nuclear Fraction: Quantifies the proportion of RNA in each droplet that originates from unspliced, nuclear pre-mRNA.
• Detection of Empty Droplets: Uses the nuclear fraction metric to improve identification of droplets lacking cellular content.
• Identification of Damaged Cells: Detects droplets containing damaged (partially lysed) cells that contribute ambient RNA.
• Integration with Existing Workflows: Implemented as an R package and designed to complement computational methods such as EmptyDrops.

Scientific Applications:

• High-throughput scRNA-seq quality control: Improves discrimination of intact cells, damaged cells, and ambient RNA in droplet-based single-cell RNA-seq experiments to reduce noise and artifacts.

Methodology:

Computes a nuclear fraction metric from reads assigned to unspliced (nuclear pre-mRNA) transcripts per droplet and applies that metric to distinguish empty droplets, intact cells, and damaged cells; implemented in R and used alongside EmptyDrops.