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Comprehensive design of CRISPR gRNAs for nucleases and base editors

Bioconductor version: Release (3.19)

Provides a comprehensive suite of functions to design and annotate CRISPR guide RNA (gRNAs) sequences. This includes on- and off-target search, on-target efficiency scoring, off-target scoring, full gene and TSS contextual annotations, and SNP annotation (human only). It currently support five types of CRISPR modalities (modes of perturbations): CRISPR knockout, CRISPR activation, CRISPR inhibition, CRISPR base editing, and CRISPR knockdown. All types of CRISPR nucleases are supported, including DNA- and RNA-target nucleases such as Cas9, Cas12a, and Cas13d. All types of base editors are also supported. gRNA design can be performed on reference genomes, transcriptomes, and custom DNA and RNA sequences. Both unpaired and paired gRNA designs are enabled.

Author: Jean-Philippe Fortin [aut, cre], Luke Hoberecht [aut]

Maintainer: Jean-Philippe Fortin <fortin946 at>

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


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:

Introduction to crisprDesign HTML R Script
Reference Manual PDF


biocViews CRISPR, FunctionalGenomics, GeneTarget, Software
Version 1.6.0
In Bioconductor since BioC 3.16 (R-4.2) (1.5 years)
License MIT + file LICENSE
Depends R (>= 4.2.0), crisprBase(>= 1.1.3)
Imports AnnotationDbi, BiocGenerics, Biostrings, BSgenome, crisprBowtie(>= 0.99.8), crisprScore(>= 1.1.6), GenomeInfoDb, GenomicFeatures, GenomicRanges(>= 1.38.0), IRanges, Matrix, MatrixGenerics, methods, rtracklayer, S4Vectors, stats, txdbmaker, utils, VariantAnnotation
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Suggests biomaRt, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BiocStyle, crisprBwa(>= 0.99.7), knitr, rmarkdown, Rbowtie, Rbwa, RCurl, testthat
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Depends On Me crisprViz
Imports Me crisprShiny, crisprVerse
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Source Package crisprDesign_1.6.0.tar.gz
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macOS Binary (x86_64) crisprDesign_1.6.0.tgz
macOS Binary (arm64) crisprDesign_1.6.0.tgz
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