crisprBowtie
Bowtie-based alignment of CRISPR gRNA spacer sequences
Bioconductor version: Release (3.19)
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 "4.4") 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")| Introduction to crisprBowtie | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Alignment, CRISPR, FunctionalGenomics, Software |
| Version | 1.8.0 |
| 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_1.8.0.tar.gz |
| Windows Binary (x86_64) | crisprBowtie_1.8.0.zip |
| macOS Binary (x86_64) | crisprBowtie_1.8.0.tgz |
| macOS Binary (arm64) | crisprBowtie_1.8.0.tgz |
| 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 |