scCDC

scCDC detects and corrects gene-specific contamination in droplet-based single-cell and single-nucleus RNA-seq data.

Key Features:

• Gene-specific contamination detection: scCDC identifies contamination-causing genes rather than applying uniform correction across all genes.
• Targeted correction: scCDC corrects expression levels only for detected contaminating genes, including cell-type markers, avoiding over-correction of lowly or non-contaminating genes.
• Improved accuracy over global methods: scCDC excels in decontaminating highly contaminating genes while preventing over-correction that affects other genes.

Scientific Applications:

• Single-cell RNA-seq decontamination: scCDC removes ambient RNA contamination from droplet-based single-cell RNA-seq datasets.
• Single-nucleus RNA-seq decontamination: scCDC removes ambient RNA contamination from droplet-based single-nucleus RNA-seq datasets.
• Cell-type marker preservation: scCDC corrects contaminating cell-type marker genes without erroneously adjusting non-contaminating markers.

Methodology:

scCDC detects contamination-causing genes and corrects expression levels of these genes only, in contrast to global decontamination methods such as DecontX, CellBender, SoupX, and scAR.