清脆的
计算生物学
生物
计算机科学
鉴定(生物学)
基因组编辑
管道(软件)
Cas9
规范化(社会学)
遗传学
基因
操作系统
人类学
植物
社会学
作者
Binbin Wang,Mei Wang,Wubing Zhang,Tengfei Xiao,Chen-Hao Chen,Alexander T.H. Wu,Feizhen Wu,Nicole Traugh,Xiaoqing Wang,Ziyi Li,Shenglin Mei,Yingbo Cui,Sailing Shi,Jesse J. Lipp,Matthias Hinterndorfer,Johannes Zuber,Myles Brown,Wei Li,X. Shirley Liu
出处
期刊:Nature Protocols
[Springer Nature]
日期:2019-02-01
卷期号:14 (3): 756-780
被引量:235
标识
DOI:10.1038/s41596-018-0113-7
摘要
Genome-wide screening using CRISPR coupled with nuclease Cas9 (CRISPR-Cas9) is a powerful technology for the systematic evaluation of gene function. Statistically principled analysis is needed for the accurate identification of gene hits and associated pathways. Here, we describe how to perform computational analysis of CRISPR screens using the MAGeCKFlute pipeline. MAGeCKFlute combines the MAGeCK and MAGeCK-VISPR algorithms and incorporates additional downstream analysis functionalities. MAGeCKFlute is distinguished from other currently available tools by its comprehensive pipeline, which contains a series of functions for analyzing CRISPR screen data. This protocol explains how to use MAGeCKFlute to perform quality control (QC), normalization, batch effect removal, copy-number bias correction, gene hit identification and downstream functional enrichment analysis for CRISPR screens. We also describe gene identification and data analysis in CRISPR screens involving drug treatment. Completing the entire MAGeCKFlute pipeline requires ~3 h on a desktop computer running Linux or Mac OS with R support.
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