multicrispr

DOI: 10.18129/B9.bioc.multicrispr    

This is the development version of multicrispr; to use it, please install the devel version of Bioconductor.

Multi-locus multi-purpose Crispr/Cas design

Bioconductor version: Development (3.12)

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 "4.0") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 0.99.34
In Bioconductor since BioC 3.12 (R-4.0)
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_0.99.34.tar.gz
Windows Binary multicrispr_0.99.34.zip
macOS 10.13 (High Sierra) multicrispr_0.99.34.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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: