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：用于prime编辑和并行靶向数千个靶标的gRNA设计。


通过 CRISPR/Cas9 技术靶​​向编码基因组引入核苷酸删除/插入已成为标准程序。它迅速催生了多种方法，例如prime编辑、APEX邻近标记或同源定向修复，然而，支持这些方法的生物信息学工具却落后了。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 multicrispr，一种 R/bioconductor 工具，旨在设计单独的 gRNA 和复杂的 gRNA 文库。该软件包易于使用；检测、评分和过滤 gRNA 的效率和特异性；可视化并汇总每个目标或 CRISPR/Cas9 序列的结果；最后返回 gRNA 的基因组范围和序列。为了通用，multicrispr 定义并实现了一个基因组算术框架，作为轻松适应最近引入的技术（例如 Prime 编辑或尚未出现）的基础。其性能和设计概念（例如特定于目标集的过滤）使 multicrispr 成为处理类似筛选方法时的首选工具。