DOI: 10.18129/B9.bioc.crisprScore    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see crisprScore.

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

Bioconductor version: 3.15

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>

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biocViews CRISPR, FunctionalGenomics, FunctionalPrediction, Software
Version 1.0.0
In Bioconductor since BioC 3.15 (R-4.2) (0.5 years)
License MIT + file LICENSE
Depends R (>= 4.1), crisprScoreData
Imports basilisk(>= 1.3.5), BiocGenerics, Biostrings, IRanges, methods, randomForest, reticulate, stringr, utils, XVector
Suggests BiocStyle, knitr, rmarkdown, testthat
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