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bioRxiv · 10.1101/2022.03.11.483924

CRISPRcleanR WebApp: an interactive web application for processing genome-wide pooled CRISPR-Cas9 viability screen

Vinceti, A.·De Lucia, R. R.·Cremaschi, P.·Perron, U.·Karakoc, E.·Mauri, L.·Fernandez, C.·Kluczynski, K. H.·Anderson, D. S.·Iorio, F.
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Abstract

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 CRISPRcleanRWebApp, 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: https://crisprcleanr-webapp.fht.org/. HighlightsO_LICRISPR-Cas9 screens are widely used for the identification of cancer dependencies C_LIO_LIIn such screens, false-positives arise from targeting copy number amplified genes C_LIO_LICRISPRcleanR corrects this bias in an unsupervised fashion C_LIO_LICRISPRcleanRWebApp is a web user-friendly front-end for CRISPRcleanR C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/483924v2_ufig1.gif" ALT="Figure 1"> View larger version (56K): org.highwire.dtl.DTLVardef@739480org.highwire.dtl.DTLVardef@1a6c0aorg.highwire.dtl.DTLVardef@ab2b8eorg.highwire.dtl.DTLVardef@1b8a623_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Vinceti, A., De Lucia, R. R., Cremaschi, P., Perron, U., Karakoc, E., Mauri, L., Fernandez, C., Kluczynski, K. H., Anderson, D. S., Iorio, F.. 2022-03-11. CRISPRcleanR WebApp: an interactive web application for processing genome-wide pooled CRISPR-Cas9 viability screen. https://doi.org/10.1101/2022.03.11.483924

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