CRISPRcleanRWebApp: an interactive web application for processing genome-wide pooled CRISPR-Cas9 viability screens

A limitation of pooled CRISPR-Cas9 viability screens is the high false-positive rate in detecting essential genes arising from copy number-amplified (CNA) regions of the genome. To solve this issue, we 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 WebApp , a web-based application enabling access to CRISPRcleanR through an intuitive graphical web-interface. CRISPRcleanRWebApp removes the complexity of low-level R/python-language user interactions; it provides a 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; it offers a range of interactively explorable plots, while supporting a wider range of CRISPR guide RNAs’ libraries with respect to the original package. CRISPRcleanRWebApp is freely available at: . Highlights ![Figure][1] ### Competing Interest Statement FI receives funding from Open Targets, a public-private initiative involving academia and industry and performs consultancy for the joint CRUK-AstraZeneca Functional Genomics Centre. All other authors declare that they have no competing interests. * ### Abbreviations API : application programming interface AUPRC : Area Under Precision-Recall Curve AUROC : Area Under Receiver Operating Characteristic CCLE : Cancer Cell Line Encyclopaedia CN : copy number CRISPR : Clustered Regularly Interspaced Short Palindromic Repeats DSB : double strand breaks EG : essential genes FDR : false discovery rate GDSC : Genomics of Drug Sensitivity in Cancer dataset logFC : log fold-change MSigDB : molecular signature database NEG : nonessential genes QC : quality control sgRNA : single-guide RNA PPV : positive predicted value SPA : Single Page Application [1]: pending:yes