crisprBowtie

DOI: 10.18129/B9.bioc.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>

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")

 

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

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
LinkingTo
Suggests	BiocStyle, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, testthat
SystemRequirements
Enhances
URL	https://github.com/crisprVerse/crisprBowtie
BugReports	https://github.com/crisprVerse/crisprBowtie/issues
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
Old Source Packages for BioC 3.17	Source Archive