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

Summary 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. CRISPRcleanR WebApp 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. CRISPRcleanR WebApp is freely available at: https://crisprcleanr-webapp.fht.org/ . Highlights CRISPR-Cas9 screens are widely used for the identification of cancer dependencies In such screens, false-positives arise from targeting copy number amplified genes CRISPRcleanR corrects this bias in an unsupervised fashion CRISPRcleanR WebApp is a web user-friendly front-end for CRISPRcleanR Abstract Figure