crisprBase

Base functions and classes for CRISPR gRNA design

Bioconductor version: Release (3.20)

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 "4.4") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	CRISPR, FunctionalGenomics, Software
Version	1.10.0
In Bioconductor since	BioC 3.15 (R-4.2) (2.5 years)
License	MIT + file LICENSE
Depends	utils, methods, R (>= 4.1)
Imports	BiocGenerics, Biostrings, GenomicRanges, graphics, IRanges, S4Vectors, stringr
System Requirements
URL	https://github.com/crisprVerse/crisprBase
Bug Reports	https://github.com/crisprVerse/crisprBase/issues

Suggests	BiocStyle, knitr, rmarkdown, testthat
Linking To
Enhances
Depends On Me	crisprDesign, crisprViz
Imports Me	crisprBowtie, crisprBwa, crisprShiny, 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	crisprBase_1.10.0.tar.gz
Windows Binary (x86_64)	crisprBase_1.10.0.zip
macOS Binary (x86_64)	crisprBase_1.10.0.tgz
macOS Binary (arm64)	crisprBase_1.10.0.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