SpliceR v1.2.0 – Prediction of BE-splice sgRNAs for Base Editor mediated Knockout

SpliceR v1.2.0

:: DESCRIPTION

SpliceR predicts base editing sgRNAs to use in the disruption of splice sites for gene modulation, or knockout. This approach is especially amenable to multiplex gene editing relative to Cas9 nuclease based approaches.

::DEVELOPER

Moriarity Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R

:: DOWNLOAD

SpliceR

:: MORE INFORMATION

Citation

Kluesner MG, Lahr WS, Lonetree CL, Smeester BA, Qiu X, Slipek NJ, Claudio Vázquez PN, Pitzen SP, Pomeroy EJ, Vignes MJ, Lee SC, Bingea SP, Andrew AA, Webber BR, Moriarity BS.
CRISPR-Cas9 cytidine and adenosine base editing of splice-sites mediates highly-efficient disruption of proteins in primary and immortalized cells.
Nat Commun. 2021 Apr 23;12(1):2437. doi: 10.1038/s41467-021-22009-2. PMID: 33893286; PMCID: PMC8065034.

WU-CRISPR – WashU gRNA Designer for CRISPR/Cas9 Knockout

WU-CRISPR

:: DESCRIPTION

WU-CRISPR is the Washington University gRNA designer for CRISPR/Cas9 knockouts.

::DEVELOPER

Xiaowei Wang Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 WU-CRISPR

:: MORE INFORMATION

Citation

WU-CRISPR: characteristics of functional guide RNAs for the CRISPR/Cas9 system.
Wong N, Liu W, Wang X.
Genome Biol. 2015 Nov 2;16(1):218. doi: 10.1186/s13059-015-0784-0.

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.

FastPros 1.0.0 – Screening of Reaction Knockout Strategies for Metabolic Engineering

FastPros 1.0.0

:: DESCRIPTION

FastPros (Fast algorithm of knockout screening for target Production based on shadow price analysis), a new iterative screening algorithm, which uses biomass production maximization to identify sets of metabolic reactions whose simultaneous knockouts result in the production of a target metabolite

::DEVELOPER

Shimizu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • MatLab

:: DOWNLOAD

 FastPros

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Apr 1;30(7):981-7. doi: 10.1093/bioinformatics/btt672. Epub 2013 Nov 19.
FastPros: screening of reaction knockout strategies for metabolic engineering.
Ohno S1, Shimizu H, Furusawa C.

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