crisprBowtie
Bowtie-based alignment of CRISPR gRNA spacer sequences
Bioconductor version: 3.23 · Package version: 1.16.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("crisprBowtie")Details
| Maintainer | Jean-Philippe Fortin <fortin946@gmail.com> |
| Author | Jean-Philippe Fortin [aut, cre] |
| License | MIT + file LICENSE |
| URL | https://github.com/crisprVerse/crisprBowtie |
| Bug Reports | https://github.com/crisprVerse/crisprBowtie/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Alignment, CRISPR, FunctionalGenomics, Software |
| Package Short Url | https://bioconductor.org/packages/crisprBowtie/ |
Citation
From within R, enter citation("crisprBowtie"):
Jean-Philippe Fortin. crisprBowtie: Bowtie-based alignment of CRISPR gRNA spacer sequences. doi:10.18129/B9.bioc.crisprBowtie, R package version 1.16.0, https://bioconductor.org/packages/crisprBowtie.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | crisprBowtie_1.16.0.tar.gz |
| Windows binary (x86_64) | crisprBowtie_1.16.0.zip |
| macOS binary (arm64) | crisprBowtie_1.16.0.tgz |
| macOS binary (x86_64) | crisprBowtie_1.16.0.tgz |
Dependencies
Depends: methods
Imports: BiocGenerics, Biostrings, BSgenome, crisprBase (>= 0.99.15), Seqinfo, GenomicRanges, IRanges, Rbowtie, readr, stats, stringr, utils
Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, testthat
Reverse dependencies
Imports Me (2): crisprDesign, crisprVerse