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

Bioconductor version: Release (3.19)

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>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


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


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

crisprScore HTML R Script
Reference Manual PDF


biocViews CRISPR, FunctionalGenomics, FunctionalPrediction, Software
Version 1.8.0
In Bioconductor since BioC 3.15 (R-4.2) (2 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
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Follow Installation instructions to use this package in your R session.

Source Package crisprScore_1.8.0.tar.gz
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macOS Binary (x86_64) crisprScore_1.8.0.tgz
macOS Binary (arm64) crisprScore_1.8.0.tgz
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