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multicrispr

Multi-locus multi-purpose Crispr/Cas design


Bioconductor version: Release (3.18)

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 [ctb], 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 "4.3") 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 1.12.3
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License GPL-2
Depends R (>= 4.0)
Imports assertive.base, assertive.files, assertive.numbers, assertive.reflection, assertive.sets, 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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Build Report Build Report

Package Archives

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

Source Package multicrispr_1.12.3.tar.gz
Windows Binary multicrispr_1.12.3.zip
macOS Binary (x86_64) multicrispr_1.12.3.tgz
macOS Binary (arm64) multicrispr_1.12.3.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
Old Source Packages for BioC 3.18 Source Archive