multicrispr

DOI: 10.18129/B9.bioc.multicrispr    

Multi-locus multi-purpose Crispr/Cas design

Bioconductor version: Release (3.13)

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], Johannes Graumann [sad, ctb], Mette Bentsen [ctb], Jens Preussner [ctb], Michael Lawrence [ctb], Hervé Pagès [ctb], Mario Looso [sad, rth]

Maintainer: Aditya Bhagwat <aditya.bhagwat at mpi-bn.mpg.de>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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")

 

HTML	R Script	genome_arithmetics
HTML	R Script	grna_design
HTML	R Script	prime_editing
PDF		Reference Manual
Text		NEWS

Details

biocViews	CRISPR, Software
Version	1.2.0
In Bioconductor since	BioC 3.12 (R-4.0) (1 year)
License	GPL-2
Depends	R (>= 4.0)
Imports	assertive, BiocGenerics, Biostrings, BSgenome, CRISPRseek, data.table, GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2, grid, karyoploteR, magrittr, methods, parallel, plyranges, Rbowtie, reticulate, rtracklayer, stats, stringi, tidyr, tidyselect, utils
LinkingTo
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
SystemRequirements
Enhances
URL	https://loosolab.pages.gwdg.de/software/multicrispr/
BugReports	https://gitlab.gwdg.de/loosolab/software/multicrispr/-/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	multicrispr_1.2.0.tar.gz
Windows Binary	multicrispr_1.2.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	multicrispr_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/multicrispr
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/multicrispr
Package Short Url	https://bioconductor.org/packages/multicrispr/
Package Downloads Report	Download Stats