multicrispr

Multi-locus multi-purpose Crispr/Cas design


Bioconductor version: Release (3.19)

This package is for designing Crispr/Cas9 and Prime Editing experiments. It contains functions to (1) define and transform genomic targets, (2) find spacers (4) count offtarget (mis)matches, and (5) compute Doench2016/2014 targeting efficiency. Care has been taken for multicrispr to scale well towards large target sets, enabling the design of large Crispr/Cas9 libraries.

Author: Aditya Bhagwat [aut, cre], Richie ´Cotton [aut], Rene Wiegandt [ctb], Mette Bentsen [ctb], Jens Preussner [ctb], Michael Lawrence [ctb], Hervé Pagès [ctb], Johannes Graumann [sad], Mario Looso [sad, rth]

Maintainer: Aditya Bhagwat <aditya.bhagwat at uni-marburg.de>

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

Installation

To install this package, start R (version "4.4") and enter:


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

BiocManager::install("multicrispr")

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("multicrispr")
genome_arithmetics HTML R Script
grna_design HTML R Script
prime_editing HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews CRISPR, Software
Version 1.14.0
In Bioconductor since BioC 3.12 (R-4.0) (4 years)
License GPL-2
Depends R (>= 4.0)
Imports BiocGenerics, Biostrings, BSgenome, CRISPRseek, data.table, GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2, grid, karyoploteR, magrittr, methods, parallel, plyranges, Rbowtie, reticulate, rtracklayer, stats, stringi, tidyr, tidyselect, utils
System Requirements
URL https://github.com/loosolab/multicrispr
Bug Reports https://github.com/loosolab/multicrispr/issues
See More
Suggests AnnotationHub, BiocStyle, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Scerevisiae.UCSC.sacCer1, ensembldb, IRanges, knitr, magick, rmarkdown, testthat, TxDb.Mmusculus.UCSC.mm10.knownGene
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Package Archives

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

Source Package multicrispr_1.14.0.tar.gz
Windows Binary multicrispr_1.14.0.zip
macOS Binary (x86_64) multicrispr_1.14.0.tgz
macOS Binary (arm64) multicrispr_1.14.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/multicrispr
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/multicrispr
Bioc Package Browser https://code.bioconductor.org/browse/multicrispr/
Package Short Url https://bioconductor.org/packages/multicrispr/
Package Downloads Report Download Stats