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crisprDesign

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

Comprehensive design of CRISPR gRNAs for nucleases and base editors


Bioconductor version: Development (3.19)

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 "4.4") 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")
Introduction to crisprDesign HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews CRISPR, FunctionalGenomics, GeneTarget, Software
Version 1.5.1
In Bioconductor since BioC 3.16 (R-4.2) (1.5 years)
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
System Requirements
URL https://github.com/crisprVerse/crisprDesign
Bug Reports https://github.com/crisprVerse/crisprDesign/issues
See More
Suggests biomaRt, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BiocStyle, crisprBwa(>= 0.99.7), knitr, rmarkdown, Rbowtie, Rbwa, RCurl, testthat
Linking To
Enhances
Depends On Me crisprViz
Imports Me 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 crisprDesign_1.5.1.tar.gz
Windows Binary crisprDesign_1.5.1.zip
macOS Binary (x86_64) crisprDesign_1.5.1.tgz
macOS Binary (arm64) crisprDesign_1.5.0.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