VISPR-online: a web-based interactive tool to visualize CRISPR screening experiments

Background VISPR is an interactive visualization and analysis framework for CRISPR screening experiments. However, it only supports the output of MAGeCK, and requires installation and manual configuration. Furthermore, VISPR is designed to run on a single computer, and data sharing between collabora...

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Vydáno v:BMC bioinformatics Ročník 22; číslo 1; s. 344 - 7
Hlavní autoři: Cui, Yingbo, Wang, Zihang, Köster, Johannes, Liao, Xiangke, Peng, Shaoliang, Tang, Tao, Huang, Chun, Yang, Canqun
Médium: Journal Article
Jazyk:angličtina
Vydáno: London BioMed Central 24.06.2021
BioMed Central Ltd
Springer Nature B.V
BMC
Témata:
Algorithms
Bioinformatics
Biomedical and Life Sciences
Clustered Regularly Interspaced Short Palindromic Repeats
Computational Biology/Bioinformatics
Computer Appl. in Life Sciences
CRISPR
CRISPR screening
Data analysis
Data retrieval
Data visualization
Genes
Genomes
gRNA
Internet
Life Sciences
Methods
Microarrays
RNA, Guide, CRISPR-Cas Systems
Screening
Software
Source code
VISPR
Visualization
Visualization (Computers)
Web applications
Web browsers
China
CRISPR
Visualization
VISPR
CRISPR screening
ISSN:1471-2105, 1471-2105
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Shrnutí:Background VISPR is an interactive visualization and analysis framework for CRISPR screening experiments. However, it only supports the output of MAGeCK, and requires installation and manual configuration. Furthermore, VISPR is designed to run on a single computer, and data sharing between collaborators is challenging. Results To make the tool easily accessible to the community, we present VISPR-online, a web-based general application allowing users to visualize, explore, and share CRISPR screening data online with a few simple steps. VISPR-online provides an exploration of screening results and visualization of read count changes. Apart from MAGeCK, VISPR-online supports two more popular CRISPR screening analysis tools: BAGEL and JACKS. It provides an interactive environment for exploring gene essentiality, viewing guide RNA (gRNA) locations, and allowing users to resume and share screening results. Conclusions VISPR-online allows users to visualize, explore and share CRISPR screening data online. It is freely available at http://vispr-online.weililab.org , while the source code is available at https://github.com/lemoncyb/VISPR-online .
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ISSN:1471-2105
1471-2105
DOI:10.1186/s12859-021-04275-5