An interactive web application for processing, correcting, and visualizing genome-wide pooled CRISPR-Cas9 screens
Alessandro Vinceti, Riccardo Roberto De Lucia, Paolo Cremaschi, Umberto Perron, Emre Karakoç, Luca Mauri, Carlos Fernandez, Krzysztof Henryk Kluczynski, Daniel Stephen Anderson, Francesco Iorio
Abstract
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 CRISPRcleanRWebApp, a web application enabling access to CRISPRcleanR through an intuitive interface. CRISPRcleanRWebApp 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. CRISPRcleanRWebApp is available at https://crisprcleanr-webapp.fht.org/.