crisprBase

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see crisprBase.

Base functions and classes for CRISPR gRNA design

Bioconductor version: 3.21

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 "4.5") 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 1.12.0

In Bioconductor since BioC 3.15 (R-4.2) (3.5 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_1.12.0.tar.gz

Windows Binary (x86_64) crisprBase_1.12.0.zip

macOS Binary (x86_64) crisprBase_1.12.0.tgz

macOS Binary (arm64) crisprBase_1.12.0.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