crisprDesign

DOI: 10.18129/B9.bioc.crisprDesign  

Comprehensive design of CRISPR gRNAs for nucleases and base editors

Bioconductor version: Release (3.16)

Provides a comprehensive suite of functions to design and annotate CRISPR guide RNA (gRNAs) sequences. This includes on- and off-target search, on-target efficiency scoring, off-target scoring, full gene and TSS contextual annotations, and SNP annotation (human only). It currently support five types of CRISPR modalities (modes of perturbations): CRISPR knockout, CRISPR activation, CRISPR inhibition, CRISPR base editing, and CRISPR knockdown. All types of CRISPR nucleases are supported, including DNA- and RNA-target nucleases such as Cas9, Cas12a, and Cas13d. All types of base editors are also supported. gRNA design can be performed on reference genomes, transcriptomes, and custom DNA and RNA sequences. Both unpaired and paired gRNA designs are enabled.

Author: Jean-Philippe Fortin [aut, cre], Luke Hoberecht [aut]

Maintainer: Jean-Philippe Fortin <fortin946 at gmail.com>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("crisprDesign")

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("crisprDesign")

 

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

Details

biocViews	CRISPR, FunctionalGenomics, GeneTarget, Software
Version	1.0.0
In Bioconductor since	BioC 3.16 (R-4.2) (< 6 months)
License	MIT + file LICENSE
Depends	R (>= 4.2.0), crisprBase(>= 1.1.3)
Imports	AnnotationDbi, BiocGenerics, Biostrings, BSgenome, crisprBowtie(>= 0.99.8), crisprScore(>= 1.1.6), GenomeInfoDb, GenomicFeatures, GenomicRanges(>= 1.38.0), IRanges, Matrix, MatrixGenerics, methods, rtracklayer, S4Vectors, stats, utils, VariantAnnotation
LinkingTo
Suggests	biomaRt, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BiocStyle, crisprBwa(>= 0.99.7), knitr, rmarkdown, Rbowtie, Rbwa, RCurl, testthat
SystemRequirements
Enhances
URL	https://github.com/crisprVerse/crisprDesign
BugReports	https://github.com/crisprVerse/crisprDesign/issues
Depends On Me	crisprViz
Imports Me	crisprVerse
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	crisprDesign_1.0.0.tar.gz
Windows Binary	crisprDesign_1.0.0.zip
macOS Binary (x86_64)	crisprDesign_1.0.0.tgz
macOS Binary (arm64)	crisprDesign_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/crisprDesign
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/crisprDesign
Bioc Package Browser	https://code.bioconductor.org/browse/crisprDesign/
Package Short Url	https://bioconductor.org/packages/crisprDesign/
Package Downloads Report	Download Stats