crisprBase

DOI: 10.18129/B9.bioc.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 (3.16)

Provides S4 classes for general nucleases, CRISPR nucleases 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 "4.2") 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")

 

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

Details

biocViews CRISPR, FunctionalGenomics, Software
Version 1.1.1
In Bioconductor since BioC 3.15 (R-4.2) (< 6 months)
License MIT + file LICENSE
Depends utils, methods, R (>= 4.1)
Imports BiocGenerics, Biostrings, GenomicRanges, IRanges, S4Vectors, stringr
LinkingTo
Suggests knitr, rmarkdown, testthat
SystemRequirements
Enhances
URL https://github.com/Jfortin1/crisprBase
BugReports https://github.com/Jfortin1/crisprBase/issues
Depends On Me
Imports Me crisprBowtie, crisprBwa
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package crisprBase_1.1.1.tar.gz
Windows Binary crisprBase_1.1.1.zip
macOS 10.13 (High Sierra) crisprBase_1.1.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/crisprBase
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/crisprBase
Package Short Url https://bioconductor.org/packages/crisprBase/
Package Downloads Report Download Stats

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