crisprDesign

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see crisprDesign.

Comprehensive design of CRISPR gRNAs for nucleases and base editors

Bioconductor version: 3.21

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 "4.5") 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")

Introduction to crisprDesign HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews CRISPR, FunctionalGenomics, GeneTarget, Software

Version 1.10.0

In Bioconductor since BioC 3.16 (R-4.2) (3 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, txdbmaker, utils, VariantAnnotation

System Requirements

URL https://github.com/crisprVerse/crisprDesign

Bug Reports https://github.com/crisprVerse/crisprDesign/issues

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 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 crisprDesign_1.10.0.tar.gz

Windows Binary (x86_64) crisprDesign_1.10.0.zip

macOS Binary (x86_64) crisprDesign_1.10.0.tgz

macOS Binary (arm64) crisprDesign_1.10.0.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/

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