shRNA 和 Cas 蛋白技术的最新进展使得使用单个或混合 shRNA 和 sgRNA 来靶向基因或非编码区域的功能筛选方法成为可能。基于 CRISPR 的系统也被开发用于调节 DNA 可及性，从而导致 CRISPR 介导的干扰 (CRISPRi) 或目标基因或基因组 DNA 元件的激活 (CRISPRa)。然而，仍然缺乏用于集成各种功能基因组学筛选输出的软件工具，这些工具可以为全面的数据集成提供一个有凝聚力的框架。在这里，我们开发了 PitViper，这是一款灵活的交互式开源软件，旨在填补这一空白，为所筛选的元素类型提供可靠的结果。它是一个端到端自动化且可重复的生物信息学管道，集成了功能筛选分析的金标准方法。我们的敏感性分析表明，PitViper 是一种有用的工具，可通过基于 CRISPRi 的全基因组筛选来识别白血病细胞系中潜在的超级增强子倾向。它提供了一个强大、灵活和交互式的解决方案，用于集成功能筛选方法的数据分析和再分析，使其成为该领域研究人员的宝贵资源。© 作者 2024。由牛津大学出版社代表 NAR Genomics 出版和生物信息学。

Recent advancements in shRNA and Cas protein technologies have enabled functional screening methods targeting genes or non-coding regions using single or pooled shRNA and sgRNA. CRISPR-based systems have also been developed for modulating DNA accessibility, resulting in CRISPR-mediated interference (CRISPRi) or activation (CRISPRa) of targeted genes or genomic DNA elements. However, there is still a lack of software tools for integrating diverse array of functional genomics screening outputs that could offer a cohesive framework for comprehensive data integration. Here, we developed PitViper, a flexible and interactive open-source software designed to fill this gap, providing reliable results for the type of elements being screened. It is an end-to-end automated and reproducible bioinformatics pipeline integrating gold-standard methods for functional screening analysis. Our sensitivity analyses demonstrate that PitViper is a useful tool for identifying potential super-enhancer liabilities in a leukemia cell line through genome-wide CRISPRi-based screening. It offers a robust, flexible, and interactive solution for integrating data analysis and reanalysis from functional screening methods, making it a valuable resource for researchers in the field.© The Author(s) 2024. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics.