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Bowtie-based alignment of CRISPR gRNA spacer sequences

Bioconductor version: Release (3.18)

Provides a user-friendly interface to map on-targets and off-targets of CRISPR gRNA spacer sequences using bowtie. The alignment is fast, and can be performed using either commonly-used or custom CRISPR nucleases. The alignment can work with any reference or custom genomes. Both DNA- and RNA-targeting nucleases are supported.

Author: Jean-Philippe Fortin [aut, cre]

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

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


To install this package, start R (version "4.3") 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 crisprBowtie HTML R Script
Reference Manual PDF


biocViews Alignment, CRISPR, FunctionalGenomics, Software
Version 1.6.0
In Bioconductor since BioC 3.15 (R-4.2) (2 years)
License MIT + file LICENSE
Depends methods
Imports BiocGenerics, Biostrings, BSgenome, crisprBase(>= 0.99.15), GenomeInfoDb, GenomicRanges, IRanges, Rbowtie, readr, stats, stringr, utils
System Requirements
URL https://github.com/crisprVerse/crisprBowtie
Bug Reports https://github.com/crisprVerse/crisprBowtie/issues
See More
Suggests BiocStyle, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, testthat
Linking To
Depends On Me
Imports Me crisprDesign, crisprVerse
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package crisprBowtie_1.6.0.tar.gz
Windows Binary crisprBowtie_1.6.0.zip
macOS Binary (x86_64) crisprBowtie_1.6.0.tgz
macOS Binary (arm64) crisprBowtie_1.6.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/crisprBowtie
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/crisprBowtie
Bioc Package Browser https://code.bioconductor.org/browse/crisprBowtie/
Package Short Url https://bioconductor.org/packages/crisprBowtie/
Package Downloads Report Download Stats