Tag: CRISPR-Cas9

CoRe v1.0.2 – Identifying Core-fitness Genes in Genome-wide Pooled CRISPR-Cas9 Screens

CoRe v1.0.2

:: DESCRIPTION

CoRe is an R package implementing existing and novel methods for the identification of core-fitness genes (at two different level of stringency) from joint analyses of multiple CRISPR-Cas9 screens.

::DEVELOPER

CoRe team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

CoRe

:: MORE INFORMATION

Citation

Vinceti A, Karakoc E, Pacini C, Perron U, De Lucia RR, Garnett MJ, Iorio F.
CoRe: a robustly benchmarked R package for identifying core-fitness genes in genome-wide pooled CRISPR-Cas9 screens.
BMC Genomics. 2021 Nov 17;22(1):828. doi: 10.1186/s12864-021-08129-5. PMID: 34789150.

MAGeCK 0.5.9.4 / MAGeCK-VISPR 0.5.6 – Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout + Visualization of CRISPR Screens

MAGeCK 0.5.9.4 / MAGeCK-VISPR 0.5.6

:: DESCRIPTION

MAGeCK is a computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology.

MAGeCK-VISPR is a comprehensive quality control, analysis and visualization workflow for CRISPR/Cas9 screens.

::DEVELOPER

X. Shirley Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Python

:: DOWNLOAD

 MAGeCK ,MAGeCK-VISPR

:: MORE INFORMATION

Citation

Quality control, modeling, and visualization of CRISPR screens with MAGeCK-VISPR.
Li W, Köster J, Xu H, Chen CH, Xiao T, Liu JS, Brown M, Liu XS.
Genome Biol. 2015 Dec 16;16:281. doi: 10.1186/s13059-015-0843-6.

Genome Biol. 2014;15(12):554.
MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens.
Li W, Xu H, Xiao T, Cong L, Love MI, Zhang F, Irizarry RA, Liu JS, Brown M, Liu XS.

CRISPRseek 1.30.1 – Design of Target-specific Guide RNAs in CRISPR-Cas9, Genome-editing Systems

CRISPRseek 1.30.1

:: DESCRIPTION

CRISPRseek is a highly flexible, open source software package to identify gRNAs that target a given input sequence while minimizing off-target cleavage at other sites within any selected genome.

:: DEVELOPER

Program in Gene Function and Expression@umassmed

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux /MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 CRISPRseek

:: MORE INFORMATION

Citation:

CRISPRseek: a bioconductor package to identify target-specific guide RNAs for CRISPR-Cas9 genome-editing systems.
Zhu LJ, Holmes BR, Aronin N, Brodsky MH.
PLoS One. 2014 Sep 23;9(9):e108424. doi: 10.1371/journal.pone.0108424