crisprScore

DOI: 10.18129/B9.bioc.crisprScore  

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

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	crisprScore
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	CRISPR, FunctionalGenomics, FunctionalPrediction, Software
Version	1.2.0
In Bioconductor since	BioC 3.15 (R-4.2) (1 year)
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
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, testthat
SystemRequirements
Enhances
URL	https://github.com/crisprVerse/crisprScore/issues
BugReports	https://github.com/crisprVerse/crisprScore
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_1.2.0.tar.gz
Windows Binary	crisprScore_1.2.0.zip
macOS Binary (x86_64)	crisprScore_1.2.0.tgz
macOS Binary (arm64)	crisprScore_1.2.0.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