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("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 | ||
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 |
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_1.14.0.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 |