VISPR-online：一个基于网络的交互式工具，用于可视化 CRISPR 筛选实验。

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

机构信息

School of Computer, National University of Defense Technology, Changsha, 410073, China.

College of Information Science and Engineering, Hunan University, Changsha, 410006, China.

出版信息

BMC Bioinformatics. 2021 Jun 24;22(1):344. doi: 10.1186/s12859-021-04275-5.

DOI:10.1186/s12859-021-04275-5

PMID:34167459

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC8223366/

Abstract

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 .

摘要

背景

VISPR 是一个用于 CRISPR 筛选实验的交互式可视化和分析框架。然而，它仅支持 MAGeCK 的输出，并且需要安装和手动配置。此外，VISPR 旨在在单台计算机上运行，因此协作者之间的数据共享具有挑战性。

结果

为了使该工具更容易为社区所接受，我们提出了 VISPR-online，这是一个基于网络的通用应用程序，用户只需几个简单的步骤即可在线可视化、探索和共享 CRISPR 筛选数据。VISPR-online 提供了对筛选结果的探索和读取计数变化的可视化。除了 MAGeCK，VISPR-online 还支持另外两个更流行的 CRISPR 筛选分析工具：BAGEL 和 JACKS。它提供了一个交互式环境，用于探索基因的必需性、查看向导 RNA(gRNA)的位置，并允许用户恢复和共享筛选结果。