CLEANSER

CLEANSER filters ambient gRNAs in single-cell CRISPR screens using a mixture model, improving accuracy in gRNA-cell assignment and differential gene expression analysis.

Key Features:

• Ambient gRNA Filtering: CLEANSER uses a mixture model to distinguish native gRNA-cell assignments from ambient contaminating gRNAs.
• Normalization Parameters: CLEANSER includes both gRNA-specific and cell-specific normalization parameters to correct for confounding technical factors.
• Probability Output: CLEANSER outputs the probability that a gRNA-cell assignment derives from the native distribution rather than the ambient distribution.
• Cross-Format Performance: CLEANSER increases gRNA-cell assignment accuracy across multiple screen formats.

Scientific Applications:

• Single-Cell CRISPR Screen Analysis: CLEANSER improves gRNA-cell assignment accuracy in perturb-seq experiments.
• Differential Gene Expression Analysis: CLEANSER improves outcomes in differential gene expression analysis by filtering ambient gRNA noise.
• Ambient gRNA Characterization: CLEANSER was developed using CRISPR barnyard assay datasets to characterize ambient gRNA contamination in perturb-seq screens.

Methodology:

CLEANSER employs a mixture model with gRNA and cell-specific normalization parameters. The method was developed using CRISPR barnyard assay datasets to characterize ambient gRNAs in perturb-seq screens.