crisprBowtie
This is the development version of crisprBowtie; for the stable release version, see crisprBowtie.
Bowtie-based alignment of CRISPR gRNA spacer sequences
Bioconductor version: Development (3.21)
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("crisprBowtie")
):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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")
Introduction to crisprBowtie | HTML | R Script |
Reference Manual | ||
NEWS | Text | |
LICENSE | Text |
Details
biocViews | Alignment, CRISPR, FunctionalGenomics, Software |
Version | 1.11.0 |
In Bioconductor since | BioC 3.15 (R-4.2) (2.5 years) |
License | MIT + file LICENSE |
Depends | methods |
Imports | BiocGenerics, Biostrings, BSgenome, crisprBase(>= 0.99.15), GenomeInfoDb, GenomicRanges, IRanges, Rbowtie, readr, stats, stringr, utils |
System Requirements | |
URL | https://github.com/crisprVerse/crisprBowtie |
Bug Reports | https://github.com/crisprVerse/crisprBowtie/issues |
See More
Suggests | BiocStyle, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, testthat |
Linking To | |
Enhances | |
Depends On Me | |
Imports Me | crisprDesign, crisprVerse |
Suggests Me | |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | crisprBowtie_1.11.0.tar.gz |
Windows Binary (x86_64) | |
macOS Binary (x86_64) | |
macOS Binary (arm64) | |
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 |