crisprDesign

DOI: 10.18129/B9.bioc.crisprDesign    

This is the development version of crisprDesign; to use it, please install the devel version of Bioconductor.

Comprehensive design of CRISPR gRNAs for nucleases and base editors

Bioconductor version: Development (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>

Citation (from within R, enter citation("crisprDesign")):

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("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 0.99.167
In Bioconductor since BioC 3.16 (R-4.2)
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_0.99.167.tar.gz
Windows Binary crisprDesign_0.99.167.zip
macOS Binary (x86_64) crisprDesign_0.99.167.tgz
macOS Binary (arm64) crisprDesign_0.99.163.tgz
Source Repository git clone https://git.bioconductor.org/packages/crisprDesign
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/crisprDesign
Package Short Url https://bioconductor.org/packages/crisprDesign/
Package Downloads Report Download Stats

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