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 collabor...

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Autores principales: Cui, Yingbo, Wang, Zihang, Köster, Johannes, Liao, Xiangke, Peng, Shaoliang, Tang, Tao, Huang, Chun, Yang, Canqun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2021
Materias:
Software
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8223366/
https://www.ncbi.nlm.nih.gov/pubmed/34167459
http://dx.doi.org/10.1186/s12859-021-04275-5
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author Cui, Yingbo
Wang, Zihang
Köster, Johannes
Liao, Xiangke
Peng, Shaoliang
Tang, Tao
Huang, Chun
Yang, Canqun
author_facet Cui, Yingbo
Wang, Zihang
Köster, Johannes
Liao, Xiangke
Peng, Shaoliang
Tang, Tao
Huang, Chun
Yang, Canqun
author_sort Cui, Yingbo
collection PubMed
description 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12859-021-04275-5.
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spelling pubmed-82233662021-06-24 VISPR-online: a web-based interactive tool to visualize CRISPR screening experiments Cui, Yingbo Wang, Zihang Köster, Johannes Liao, Xiangke Peng, Shaoliang Tang, Tao Huang, Chun Yang, Canqun BMC Bioinformatics Software 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12859-021-04275-5. BioMed Central 2021-06-24 /pmc/articles/PMC8223366/ /pubmed/34167459 http://dx.doi.org/10.1186/s12859-021-04275-5 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Software
Cui, Yingbo
Wang, Zihang
Köster, Johannes
Liao, Xiangke
Peng, Shaoliang
Tang, Tao
Huang, Chun
Yang, Canqun
VISPR-online: a web-based interactive tool to visualize CRISPR screening experiments
title VISPR-online: a web-based interactive tool to visualize CRISPR screening experiments
title_full VISPR-online: a web-based interactive tool to visualize CRISPR screening experiments
title_fullStr VISPR-online: a web-based interactive tool to visualize CRISPR screening experiments
title_full_unstemmed VISPR-online: a web-based interactive tool to visualize CRISPR screening experiments
title_short VISPR-online: a web-based interactive tool to visualize CRISPR screening experiments
title_sort vispr-online: a web-based interactive tool to visualize crispr screening experiments
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8223366/
https://www.ncbi.nlm.nih.gov/pubmed/34167459
http://dx.doi.org/10.1186/s12859-021-04275-5
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