caRpools: an R package for exploratory data analysis and documentation of pooled CRISPR/Cas9 screens

被引：40

作者：

Winter, Jan ^{[1
,2
]}

Breinig, Marco ^{[1
,2
]}

Heigwer, Florian ^{[1
,2
]}

Bruegemann, Dirk ^{[1
,2
]}

Leible, Svenja ^{[1
,2
]}

Pelz, Oliver ^{[1
,2
]}

Zhan, Tianzuo ^{[1
,2
,3
]}

Boutros, Michael ^{[1
,2
]}

机构：

[1] German Canc Res Ctr, Div Signaling & Funct Genom, Heidelberg, Germany

[2] Heidelberg Univ, Heidelberg, Germany

[3] Heidelberg Univ, Dept Med 2, Univ Hosp Mannheim, Med Fac Mannheim, Mannheim, Germany

来源：

BIOINFORMATICS | 2016年 / 32卷 / 04期

关键词：

D O I：

10.1093/bioinformatics/btv617

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Motivation: Genetic screens by CRISPR/Cas9-mediated genome engineering have become a powerful tool for functional genomics. However, there is currently a lack of end-to-end software pipelines to analyze CRISPR/Cas9 screens based on next generation sequencing. Results: The CRISPR-AnalyzeR for pooled screens (caRpools) is an R package for exploratory data analysis that provides a complete workflow to analyze CRISPR/Cas9 screens. To further support the analysis of large-scale screens, caRpools integrates screening documentation and generation of standardized analysis reports.

引用

页码：632 / 634

页数：3

共 9 条

[1] Analysis of cell-based RNAi screens [J].

Boutros, Michael ;

Bras, Ligia P. ;

Huber, Wolfgang .

GENOME BIOLOGY, 2006, 7 (07)

[2] HiTSelect: a comprehensive tool for high-complexity-pooled screen analysis [J].

Diaz, Aaron A. ;

Qin, Han ;

Ramalho-Santos, Miguel ;

Song, Jun S. .

NUCLEIC ACIDS RESEARCH, 2015, 43 (03) :e16

[3] Genome-wide recessive genetic screening in mammalian cells with a lentiviral CRISPR-guide RNA library [J].

Koike-Yusa, Hiroko ;

Li, Yilong ;

Tan, E-Pien ;

Velasco-Herrera, Martin Del Castillo ;

Yusa, Kosuke .

NATURE BIOTECHNOLOGY, 2014, 32 (03) :267-273

[4] MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens [J].

Li, Wei ;

Xu, Han ;

Xiao, Tengfei ;

Cong, Le ;

Love, Michael I. ;

Zhang, Feng ;

Irizarry, Rafael A. ;

Liu, Jun S. ;

Brown, Myles ;

Liu, X. Shirley .

GENOME BIOLOGY, 2014, 15 (12) :554

[5] Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 [J].

Love, Michael I. ;

Huber, Wolfgang ;

Anders, Simon .

GENOME BIOLOGY, 2014, 15 (12)

[6] Flexible guide-RNA design for CRISPR applications using Protospacer Workbench [J].

MacPherson, Cameron Ross ;

Scherf, Artur .

NATURE BIOTECHNOLOGY, 2015, 33 (08) :805-806

[7] web cellHTS2: A web-application for the analysis of high-throughput screening data [J].

Pelz, Oliver ;

Gilsdorf, Moritz ;

Boutros, Michael .

BMC BIOINFORMATICS, 2010, 11

[8] Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cells [J].

Shalem, Ophir ;

Sanjana, Neville E. ;

Hartenian, Ella ;

Shi, Xi ;

Scott, David A. ;

Mikkelsen, Tarjei S. ;

Heckl, Dirk ;

Ebert, Benjamin L. ;

Root, David E. ;

Doench, John G. ;

Zhang, Feng .

SCIENCE, 2014, 343 (6166) :84-87

[9] Genetic Screens in Human Cells Using the CRISPR-Cas9 System [J].

Wang, Tim ;

Wei, Jenny J. ;

Sabatini, David M. ;

Lander, Eric S. .

SCIENCE, 2014, 343 (6166) :80-84

← 1 →