crisprBwa
This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see crisprBwa.
BWA-based alignment of CRISPR gRNA spacer sequences
Bioconductor version: 3.18
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("crisprBwa")):
Installation
To install this package, start R (version "4.3") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Alignment, CRISPR, FunctionalGenomics, Software |
| Version | 1.6.0 |
| 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_1.6.0.tar.gz |
| Windows Binary | |
| macOS Binary (x86_64) | crisprBwa_1.6.0.tgz |
| macOS Binary (arm64) | crisprBwa_1.6.0.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 |