An interactive web application for processing, correcting, and visualizing genome-wide pooled CRISPR-Cas9 screens

被引：4

作者：

Vinceti, Alessandro ^{[1
]}

De Lucia, Riccardo Roberto ^{[1
]}

Cremaschi, Paolo ^{[1
]}

Perron, Umberto ^{[1
]}

Karakoc, Emre ^{[2
]}

Mauri, Luca ^{[3
]}

Fernandez, Carlos ^{[3
]}

Kluczynski, Krzysztof Henryk ^{[3
]}

Anderson, Daniel Stephen ^{[3
]}

Iorio, Francesco ^{[1
,2
]}

机构：

[1] Human Technopole, Computat Biol Res Ctr, Viale Rita Levi Montalcini 1, I-20157 Milan, Italy

[2] Wellcome Sanger Inst, Canc Dependency Map Analyt, Wellcome Genome Campus, Cambridge CB10 1SA, England

[3] Human Technopole, ICT & Digitalisat, Viale Rita Levi Montalcini 1, I-20157 Milan, Italy

来源：

CELL REPORTS METHODS | 2023年 / 3卷 / 01期

关键词：

CIRCULAR BINARY SEGMENTATION; CANCER; VULNERABILITIES; EXPRESSION; DESIGN; REPAIR; CELLS; SET;

D O I：

10.1016/j.crmeth.2022.100373

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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 sum-maries 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/.

引用

页数：17

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