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crisprScore

On-Target and Off-Target Scoring Algorithms for CRISPR gRNAs

Bioconductor version: Release (3.17)

Provides R wrappers of several on-target and off-target scoring methods for CRISPR guide RNAs (gRNAs). The following nucleases are supported: SpCas9, AsCas12a, enAsCas12a, and RfxCas13d (CasRx). The available on-target cutting efficiency scoring methods are RuleSet1, Azimuth, DeepHF, DeepCpf1, enPAM+GB, and CRISPRscan. Both the CFD and MIT scoring methods are available for off-target specificity prediction. The package also provides a Lindel-derived score to predict the probability of a gRNA to produce indels inducing a frameshift for the Cas9 nuclease. Note that DeepHF, DeepCpf1 and enPAM+GB are not available on Windows machines.

Author: Jean-Philippe Fortin [aut, cre, cph], Aaron Lun [aut], Luke Hoberecht [ctb], Pirunthan Perampalam [ctb]

Maintainer: Jean-Philippe Fortin <fortin946 at gmail.com>

Citation (from within R, enter citation("crisprScore")):

Installation

To install this package, start R (version "4.3") and enter: 

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("crisprScore")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("crisprScore")
crisprScore HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews CRISPR, FunctionalGenomics, FunctionalPrediction, Software
Version 1.4.0
In Bioconductor since BioC 3.15 (R-4.2) (1.5 years)
License MIT + file LICENSE
Depends R (>= 4.1), crisprScoreData(>= 1.1.3)
Imports basilisk(>= 1.9.2), basilisk.utils(>= 1.9.1), BiocGenerics, Biostrings, IRanges, methods, randomForest, reticulate, stringr, utils, XVector
Linking To
Suggests BiocStyle, knitr, rmarkdown, testthat
System Requirements
Enhances
URL https://github.com/crisprVerse/crisprScore/issues
Bug Reports https://github.com/crisprVerse/crisprScore
See More
Depends On Me
Imports Me crisprDesign, crisprVerse
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package crisprScore_1.4.0.tar.gz
Windows Binary crisprScore_1.4.0.zip
macOS Binary (x86_64) crisprScore_1.4.0.tgz
macOS Binary (arm64) crisprScore_1.4.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/crisprScore
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/crisprScore
Bioc Package Browser https://code.bioconductor.org/browse/crisprScore/
Package Short Url https://bioconductor.org/packages/crisprScore/
Package Downloads Report Download Stats