Centre for Organismal Studies, Heidelberg University, Heidelberg, 69120, Germany.
Interdisciplinary Center for Scientific Computing, Heidelberg University, Heidelberg, 69120, Germany.
Bioinformatics. 2024 Sep 2;40(9). doi: 10.1093/bioinformatics/btae535.
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.
We demonstrate the package on four single-cell CRISPR interference screens at low multiplicity of infection from two studies, where crispat identifies strong differences in the number of assigned cells, downregulation of the target genes and number of discoveries across different guide assignment strategies, highlighting the need for a suitable guide assignment strategy to obtain optimal power in single-cell CRISPR screens.
crispat is implemented in python, the source code, installation instructions and tutorials can be found at https://github.com/velten-group/crispat and it can be installed from PyPI (https://pypi.org/project/crispat/). Code to reproduce all findings in this paper is available at https://github.com/velten-group/crispat_analysis, as well as at https://zenodo.org/records/13373265.
池化单细胞 CRISPR 筛选已成为功能基因组学中一种强大的工具，可大规模探究遗传干预的效果。在分析由此产生的数据时，关键步骤是将细胞分配给与特定遗传干预相对应的 gRNA。然而，由于缺乏系统的基准和可访问的软件来应用和比较不同的引导分配策略，因此这一步具有挑战性。为了解决这个问题，我们在这里提出了 crispat（CRISPR 引导分配工具），这是一个 Python 包，用于促进单细胞 CRISPR 筛选中合适的引导分配策略的选择。
我们在来自两项研究的低感染复数的四个单细胞 CRISPR 干扰筛选中展示了该软件包，crispat 确定了不同引导分配策略之间分配的细胞数量、靶基因下调和发现数量的强烈差异，突出了需要合适的引导分配策略来获得单细胞 CRISPR 筛选中的最佳功效。
crispat 是用 python 实现的，源代码、安装说明和教程可以在 https://github.com/velten-group/crispat 上找到，也可以从 PyPI（https://pypi.org/project/crispat/）安装。重现本文所有发现的代码可在 https://github.com/velten-group/crispat_analysis 以及 https://zenodo.org/records/13373265 上找到。
