crisprBowtie

DOI: 10.18129/B9.bioc.crisprBowtie    

Bowtie-based alignment of CRISPR gRNA spacer sequences

Bioconductor version: Release (3.15)

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 "4.2") 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 1.0.0
In Bioconductor since BioC 3.15 (R-4.2) (< 6 months)
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/Jfortin1/crisprBowtie
BugReports https://github.com/Jfortin1/crisprBowtie/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package crisprBowtie_1.0.0.tar.gz
Windows Binary crisprBowtie_1.0.0.zip
macOS 10.13 (High Sierra) crisprBowtie_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/crisprBowtie
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/crisprBowtie
Package Short Url https://bioconductor.org/packages/crisprBowtie/
Package Downloads Report Download Stats

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