Souporcell

Souporcell clusters cells by genotype and detects cross-genotype doublets and ambient RNA contamination in mixed-genotype single-cell RNA sequencing (scRNA-seq) datasets.

Key Features:

• Genetic variant-based clustering: Leverages genetic variants detected in scRNA-seq reads to assign cells to donor genotypes and cluster cells accordingly.
• Doublet detection: Identifies cross-genotype doublets by analyzing genetic variant profiles rather than relying solely on transcriptional expression.
• Ambient RNA estimation: Estimates ambient RNA contamination by analyzing cross-genotype variant contamination signals in scRNA-seq data.

Scientific Applications:

• Multiplexed donor deconvolution: Deconvolves multiplexed scRNA-seq experiments to assign individual cells to their donors of origin.
• Batch effect mitigation: Supports multiplexing across multiple donors to mitigate batch effects and reduce technical variability.
• Improved doublet handling: Enhances detection and removal of cross-genotype doublets in mixed-genotype single-cell studies.

Methodology:

Detects genetic variants in scRNA-seq reads, clusters cells by genotype, detects cross-genotype doublets using variant profiles, and estimates ambient RNA by analyzing cross-genotype variant contamination.