Registration and Call for Abstracts Open for Bioc2024

crisprBase

This is the development version of crisprBase; for the stable release version, see crisprBase.

Base functions and classes for CRISPR gRNA design


Bioconductor version: Development (3.19)

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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.7.1
In Bioconductor since BioC 3.15 (R-4.2) (2 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
See More
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_1.7.1.tar.gz
Windows Binary
macOS Binary (x86_64) crisprBase_1.7.1.tgz
macOS Binary (arm64)
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