Tag: CRISPR

CRISPRO v1.0.2 – Analysis and Visualization of Saturating Mutagenesis CRISPR Screens

CRISPRO v1.0.2

:: DESCRIPTION

CRISPRO is a pipeline to process next generation sequnecing data from saturating mutagenesis CRISPR screens, whereby sgRNAs are mapped to amino acids of the protein, allowing for the inference of functional scores for amino acids in a protein.

::DEVELOPER

bauer lab

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux /  Windows
  • Python
  • R

:: DOWNLOAD

CRISPRO

:: MORE INFORMATION

Citation

Schoonenberg VAC, Cole MA, Yao Q, Macias-Treviño C, Sher F, Schupp PG, Canver MC, Maeda T, Pinello L, Bauer DE.
CRISPRO: identification of functional protein coding sequences based on genome editing dense mutagenesis.
Genome Biol. 2018 Oct 19;19(1):169. doi: 10.1186/s13059-018-1563-5. PMID: 30340514; PMCID: PMC6195731.

CRISPRitz – Perform in-silico CRISPR analysis and Assessment

CRISPRitz

:: DESCRIPTION

CRISPRitz is a software package containing 5 different tools dedicated to perform predictive analysis and result assessement on CRISPR/Cas experiments.

::DEVELOPER

Pinello Lab.

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux
  • Conda

:: DOWNLOAD

CRISPRitz

:: MORE INFORMATION

Citation

Cancellieri S, Canver MC, Bombieri N, Giugno R, Pinello L.
CRISPRitz: rapid, high-throughput and variant-aware in silico off-target site identification for CRISPR genome editing.
Bioinformatics. 2020 Apr 1;36(7):2001-2008. doi: 10.1093/bioinformatics/btz867. PMID: 31764961; PMCID: PMC7141852.

sgRNA online 1.2 – Identifies efficient sgRNAs for CRISPR editing of mouse and human Genomes

sgRNA online 1.2

:: DESCRIPTION

sgRNA online is an online tool that identifies efficient sgRNAs for CRISPR editing of mouse and human genomes. It supports both classic Cas9 and xCa9 3.7.

::DEVELOPER

Yongbing Zhao

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 No

:: MORE INFORMATION

 

CRISPR-GA – CRISPR Genome Analyzer

CRISPR-GA

:: DESCRIPTION

CRISPR-GA is a platform to assess the quality of gene editing using next gen sequencing data. It provides an easy, sensitive, and comprehensive analysis of gene editing results.

::DEVELOPER

GClab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Genome Editing Assessment using CRISPR Genome Analyzer (CRISPR-GA).
Güell M, Yang L, Church G.
Bioinformatics. 2014 Jul 1. pii: btu427.

CRISPRdirect – Rational Design of CRISPR/Cas Target

CRISPRdirect

:: DESCRIPTION

CRISPRdirect is a web server for selecting rational CRISPR/Cas targets from an input sequence.

::DEVELOPER

Database Center for Life Science (DBCLS)

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

CRISPRdirect: software for designing CRISPR/Cas guide RNA with reduced off-target sites.
Naito Y, Hino K, Bono H, Ui-Tei K.
Bioinformatics. 2014 Nov 20. pii: btu743.

CINDEL – CRISPR AsCpf1 INDEL Score

CINDEL

:: DESCRIPTION

CINDEL is a regression-based model for CRISPR AsCpf1 Indel score, trained with hundreds of in-vitro datasets that Prof. Hyungbum Kim’s lab generated.

:: DEVELOPER

BIG Lab. (BIOINFORMATICS & GENOMICS)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Kim HK, Song M, Lee J, Menon AV, Jung S, Kang YM, Choi JW, Woo E, Koh HC, Nam JW, Kim H.
In vivo high-throughput profiling of CRISPR-Cpf1 activity.
Nat Methods. 2017 Feb;14(2):153-159. doi: 10.1038/nmeth.4104. Epub 2016 Dec 19. PMID: 27992409.

CCTop 1.0.0 – CRISPR/Cas9 Target Online Predictor

CCTop 1.0.0

:: DESCRIPTION

CCTop is a CRISPR/Cas9 target online predictor

::DEVELOPER

The Centre for Organismal Studies (COS) Heidelberg

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

CCTop

:: MORE INFORMATION

Citation

CCTop: An Intuitive, Flexible and Reliable CRISPR/Cas9 Target Prediction Tool.
Stemmer M, Thumberger T, Del Sol Keyer M, Wittbrodt J, Mateo JL.
PLoS One. 2015 Apr 24;10(4):e0124633. doi: 10.1371/journal.pone.0124633.

CRISPRTarget – A Tool to Explore Targets of CRISPR RNAs

CRISPRTarget

:: DESCRIPTION

CRISPRTarget predicts the most likely targets of CRISPR RNAs

::DEVELOPER

Dr Chris Brown’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

RNA Biol. 2013 May;10(5):817-27. doi: 10.4161/rna.24046. Epub 2013 Mar 14.
CRISPRTarget: bioinformatic prediction and analysis of crRNA targets.
Biswas A1, Gagnon JN, Brouns SJ, Fineran PC, Brown CM.

CRISPRDirection 2.0 – Accurate Computational Prediction of Transcribed Strand of CRISPR non-coding RNAs

CRISPRDirection 2.0

:: DESCRIPTION

CRISPRDirection is an algorithm that accurately predicts the strand of the resulting crRNAs.

::DEVELOPER

Dr Chris Brown’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • Java

:: DOWNLOAD

 CRISPRDirection

:: MORE INFORMATION

Citation:

Accurate computational prediction of the transcribed strand of CRISPR non-coding RNAs.
Biswas A, Fineran PC, Brown CM.
Bioinformatics. 2014 Jul 1;30(13):1805-13. doi: 10.1093/bioinformatics/btu114.

Cas-Designer 2.4 – A Bulge-allowed quick guide-RNA Designer for CRISPR/Cas derived RGENs.

Cas-Designer 2.4

:: DESCRIPTION

Cas-Designer provides all possible RGEN targets in the given input sequence (e.g. exon), with the useful information including potential off-target numbers within 2nt mismatches and optional 3nt bulge via Cas-OFFinder, and out-of-frame scores via Microhomology-predictor.

::DEVELOPER

Genome Engineering Lab. Seoul National University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX

:: DOWNLOAD

 Cas-Designer

:: MORE INFORMATION

Citation:

Cas-Designer: A web-based tool for choice of CRISPR-Cas9 target sites.
Park J, Bae S, Kim JS.
Bioinformatics. 2015 Sep 10. pii: btv537.