crisprBwa

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see crisprBwa.

BWA-based alignment of CRISPR gRNA spacer sequences

Bioconductor version: 3.21

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 "4.5") and enter:


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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Alignment, CRISPR, FunctionalGenomics, Software

Version 1.12.0

In Bioconductor since BioC 3.15 (R-4.2) (3.5 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

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_1.12.0.tar.gz

Windows Binary (x86_64)

macOS Binary (x86_64) crisprBwa_1.12.0.tgz

macOS Binary (arm64) crisprBwa_1.12.0.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/

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