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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>

Citation (from within R, enter citation("crisprBase")):

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

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
Linking To
Suggests BiocStyle, knitr, rmarkdown, testthat
System Requirements
Enhances
URL https://github.com/crisprVerse/crisprBase
Bug Reports https://github.com/crisprVerse/crisprBase/issues
See More
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