crisprBase

DOI: 10.18129/B9.bioc.crisprBase  

Base functions and classes for CRISPR gRNA design

Bioconductor version: Release (3.17)

Provides S4 classes for general nucleases, CRISPR nucleases, CRISPR nickases, and base editors.Several CRISPR-specific genome arithmetic functions are implemented to help extract genomic coordinates of spacer and protospacer sequences. Commonly-used CRISPR nuclease objects are provided that can be readily used in other packages. Both DNA- and RNA-targeting nucleases are supported.

Author: Jean-Philippe Fortin [aut, cre]

Maintainer: Jean-Philippe Fortin <fortin946 at gmail.com>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("crisprBase")

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("crisprBase")

 

HTML	R Script	Introduction to crisprBase
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	CRISPR, FunctionalGenomics, Software
Version	1.4.0
In Bioconductor since	BioC 3.15 (R-4.2) (1.5 years)
License	MIT + file LICENSE
Depends	utils, methods, R (>= 4.1)
Imports	BiocGenerics, Biostrings, GenomicRanges, graphics, IRanges, S4Vectors, stringr
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, testthat
SystemRequirements
Enhances
URL	https://github.com/crisprVerse/crisprBase
BugReports	https://github.com/crisprVerse/crisprBase/issues
Depends On Me	crisprDesign, crisprViz
Imports Me	crisprBowtie, crisprBwa, crisprVerse
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	crisprBase_1.4.0.tar.gz
Windows Binary	crisprBase_1.4.0.zip
macOS Binary (x86_64)	crisprBase_1.4.0.tgz
macOS Binary (arm64)	crisprBase_1.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/crisprBase
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/crisprBase
Bioc Package Browser	https://code.bioconductor.org/browse/crisprBase/
Package Short Url	https://bioconductor.org/packages/crisprBase/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive