Targeting the coding genome to introduce nucleotide deletions/insertions via the CRISPR/Cas9 technology has become a standard procedure. It has quickly spawned a multitude of methods such as prime editing, APEX proximity labeling, or homology directed repair, for which supporting bioinformatics tools are, however, lagging behind. New CRISPR/Cas9 applications often require specific gRNA design functionality, and a generic tool is critically missing. Here, we introduce multicrispr, an R/bioconductor tool, intended to design individual gRNAs and complex gRNA libraries. The package is easy to use; detects, scores, and filters gRNAs on both efficiency and specificity; visualizes and aggregates results per target or CRISPR/Cas9 sequence; and finally returns both genomic ranges and sequences of gRNAs. To be generic, multicrispr defines and implements a genomic arithmetic framework as a basis for facile adaptation to techniques recently introduced such as prime editing or yet to arise. Its performance and design concepts such as target set-specific filtering render multicrispr a tool of choice when dealing with screening-like approaches.

中文翻译：

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multicrispr：gRNA设计，可用于数千个靶标的初步编辑和并行靶向。

通过CRISPR / Cas9技术靶向编码基因组以引入核苷酸缺失/插入已成为标准程序。它迅速产生了许多方法，例如主要编辑，APEX邻近标记或同源性修复，但是对于这些方法，支持的生物信息学工具滞后了。新的CRISPR / Cas9应用通常需要特定的gRNA设计功能，而通用工具却严重缺失。在这里，我们介绍了multicrispr，一种R /生物导体工具，旨在设计单个gRNA和复杂的gRNA文库。该包装易于使用；在效率和特异性上检测，评分和过滤gRNA；可视化并汇总每个靶标或CRISPR / Cas9序列的结果; 最后返回gRNA的基因组范围和序列。一般而言，multicrispr定义并实现了基因组算术框架，以作为对最近引入的技术（如主要编辑或尚未出现的技术）的轻松适应的基础。当处理类似筛选的方法时，它的性能和设计概念（例如特定于目标集的过滤）使multicrispr成为一种选择的工具。