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crisprBowtie

Bowtie-based alignment of CRISPR gRNA spacer sequences

Bioconductor version: Release (3.17)

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")):

Installation

To install this package, start R (version "4.3") and enter: 

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("crisprBowtie")

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("crisprBowtie")
Introduction to crisprBowtie HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Alignment, CRISPR, FunctionalGenomics, Software
Version 1.4.0
In Bioconductor since BioC 3.15 (R-4.2) (1.5 years)
License MIT + file LICENSE
Depends methods
Imports BiocGenerics, Biostrings, BSgenome, crisprBase(>= 0.99.15), GenomeInfoDb, GenomicRanges, IRanges, Rbowtie, readr, stats, stringr, utils
Linking To
Suggests BiocStyle, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, testthat
System Requirements
Enhances
URL https://github.com/crisprVerse/crisprBowtie
Bug Reports https://github.com/crisprVerse/crisprBowtie/issues
See More
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 crisprBowtie_1.4.0.tar.gz
Windows Binary crisprBowtie_1.4.0.zip
macOS Binary (x86_64) crisprBowtie_1.4.0.tgz
macOS Binary (arm64) crisprBowtie_1.4.0.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