Computational Biology Research Centre, Human Technopole, Viale Rita Levi-Montalcini, 1, 20157 Milano, Italy.
Cancer Dependency Map Analytics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
Cell Rep Methods. 2023 Jan 3;3(1):100373. doi: 10.1016/j.crmeth.2022.100373. eCollection 2023 Jan 23.
A limitation of pooled CRISPR-Cas9 screens is the high false-positive rate in detecting essential genes arising from copy-number-amplified genomics regions. To solve this issue, we previously developed CRISPRcleanR: a computational method implemented as R/python package and in a dockerized version. CRISPRcleanR detects and corrects biased responses to CRISPR-Cas9 targeting in an unsupervised fashion, accurately reducing false-positive signals while maintaining sensitivity in identifying relevant genetic dependencies. Here, we present CRISPRcleanR , a web application enabling access to CRISPRcleanR through an intuitive interface. CRISPRcleanR removes the complexity of R/python language user interactions; provides user-friendly access to a complete analytical pipeline, not requiring any data pre-processing and generating gene-level summaries of essentiality with associated statistical scores; and offers a range of interactively explorable plots while supporting a more comprehensive range of CRISPR guide RNAs' libraries than the original package. CRISPRcleanR is available at https://crisprcleanr-webapp.fht.org/.
池化 CRISPR-Cas9 筛选的一个局限性是，在检测由于基因组区域拷贝数扩增而产生的必需基因时，假阳性率很高。为了解决这个问题，我们之前开发了 CRISPRcleanR：一种作为 R/python 包实现的计算方法，以及一个 Docker 化版本。CRISPRcleanR 以非监督的方式检测和纠正对 CRISPR-Cas9 靶向的偏置反应，在准确降低假阳性信号的同时，保持识别相关遗传依赖性的敏感性。在这里，我们介绍了 CRISPRcleanR ，这是一个通过直观界面访问 CRISPRcleanR 的网络应用程序。CRISPRcleanR 消除了 R/python 语言用户交互的复杂性；提供了对完整分析管道的用户友好访问，无需任何数据预处理，并生成具有相关统计评分的必需基因的基因级摘要；并提供了一系列可交互式探索的图，同时支持比原始包更广泛的 CRISPR 向导 RNA 库。CRISPRcleanR 可在 https://crisprcleanr-webapp.fht.org/ 获得。
