Guide assignment in single-cell CRISPR screens using crispat.

ABSTRACT:

Motivation

Pooled single-cell CRISPR screens have emerged as a powerful tool in functional genomics to probe the effect of genetic interventions at scale. A crucial step in the analysis of the resulting data is the assignment of cells to gRNAs corresponding to a specific genetic intervention. However, this step is challenging due to a lack of systematic benchmarks and accessible software to apply and compare different guide assignment strategies. To address this, we here propose crispat (CRISPR guide assignment tool), a Python package to facilitate the choice of a suitable guide assignment strategy for single-cell CRISPR screens.

Results

We demonstrate the package on four single-cell CRISPR interference screens at low multiplicity of infection from two studies, where crispat

SUBMITTER: Braunger JM 

PROVIDER: S-EPMC11399228 | biostudies-literature | 2024 Sep

REPOSITORIES: biostudies-literature