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crisprBwa

This is the development version of crisprBwa; for the stable release version, see crisprBwa.

BWA-based alignment of CRISPR gRNA spacer sequences


Bioconductor version: Development (3.19)

Provides a user-friendly interface to map on-targets and off-targets of CRISPR gRNA spacer sequences using bwa. 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. Currently not supported on Windows machines.

Author: Jean-Philippe Fortin [aut, cre]

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

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

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("crisprBwa")

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

Details

biocViews Alignment, CRISPR, FunctionalGenomics, Software
Version 1.7.0
In Bioconductor since BioC 3.15 (R-4.2) (2 years)
License MIT + file LICENSE
Depends methods
Imports BiocGenerics, BSgenome, crisprBase(>= 0.99.15), GenomeInfoDb, Rbwa, readr, stats, stringr, utils
System Requirements
URL https://github.com/crisprVerse/crisprBwa
Bug Reports https://github.com/crisprVerse/crisprBwa/issues
See More
Suggests BiocStyle, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, testthat
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me crisprDesign
Links To Me
Build Report Build Report

Package Archives

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

Source Package crisprBwa_1.7.0.tar.gz
Windows Binary
macOS Binary (x86_64) crisprBwa_1.7.0.tgz
macOS Binary (arm64) crisprBwa_1.7.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/crisprBwa
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/crisprBwa
Bioc Package Browser https://code.bioconductor.org/browse/crisprBwa/
Package Short Url https://bioconductor.org/packages/crisprBwa/
Package Downloads Report Download Stats