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 (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | 1.17.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (4.5 years) |
| License | MIT + file LICENSE |
| Depends | methods |
| Imports | BiocGenerics, Biostrings, BSgenome, crisprBase(>= 0.99.15), Seqinfo, 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_1.17.0.tar.gz |
| Windows Binary (x86_64) | crisprBowtie_1.17.0.zip |
| macOS Binary (big-sur-x86_64) | crisprBowtie_1.17.0.tgz |
| macOS Binary (sonoma-arm64) | crisprBowtie_1.17.0.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 |