Vinceti, Alessandro;
De Lucia, Riccardo Roberto;
Cremaschi, Paolo;
Perron, Umberto;
Karakoc, Emre;
Mauri, Luca;
Fernandez, Carlos;
... Iorio, Francesco; + view all
(2023)
An interactive web application for processing, correcting, and visualizing genome-wide pooled CRISPR-Cas9 screens.
Cell Reports Methods
, 3
(1)
, Article 100373. 10.1016/j.crmeth.2022.100373.
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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/.
| Type: | Article |
|---|---|
| Title: | An interactive web application for processing, correcting, and visualizing genome-wide pooled CRISPR-Cas9 screens |
| Location: | United States |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.1016/j.crmeth.2022.100373 |
| Publisher version: | http://dx.doi.org/10.1016/j.crmeth.2022.100373 |
| Language: | English |
| Additional information: | © 2022 The Authors. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). |
| Keywords: | Science & Technology, Life Sciences & Biomedicine, Biochemical Research Methods, Cell Biology, Biochemistry & Molecular Biology, CIRCULAR BINARY SEGMENTATION, CANCER, VULNERABILITIES, EXPRESSION, DESIGN, REPAIR, CELLS, SET |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Cancer Institute UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Cancer Institute > Research Department of Oncology |
| URI: | https://discovery.ucl.ac.uk/id/eprint/10196833 |
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