multicrispr

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see multicrispr.

Multi-locus multi-purpose Crispr/Cas design

Bioconductor version: 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>

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

Installation

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	CRISPR, Software
Version	1.2.0
In Bioconductor since	BioC 3.12 (R-4.0) (3.5 years)
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
System Requirements
URL	https://loosolab.pages.gwdg.de/software/multicrispr/
Bug Reports	https://gitlab.gwdg.de/loosolab/software/multicrispr/-/issues

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
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	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
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 3.13	Source Archive