multicrispr
This is the development version of multicrispr; for the stable release version, see multicrispr.
Multi-locus multi-purpose Crispr/Cas design
Bioconductor version: Development (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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")| genome_arithmetics | HTML | R Script |
| grna_design | HTML | R Script |
| prime_editing | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | CRISPR, Software |
| Version | 1.23.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (6 years) |
| License | GPL-2 |
| Depends | R (>= 4.0) |
| Imports | BiocGenerics, Biostrings, BSgenome, CRISPRseek, data.table, Seqinfo, GenomicFeatures, GenomicRanges, ggplot2, grid, karyoploteR, magrittr, methods, parallel, plyranges, Rbowtie, reticulate, rtracklayer, stats, stringi, tidyr, tidyselect, utils |
| System Requirements | |
| URL | https://github.com/bhagwataditya/multicrispr |
| Bug Reports | https://github.com/bhagwataditya/multicrispr/issues |
See More
| Suggests | AnnotationHub, BiocStyle, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Scerevisiae.UCSC.sacCer1, ensembldb, IRanges, GenomeInfoDb, 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_1.23.0.tar.gz |
| Windows Binary (x86_64) | multicrispr_1.23.0.zip |
| macOS Binary (big-sur-x86_64) | multicrispr_1.23.0.tgz |
| macOS Binary (sonoma-arm64) | multicrispr_1.23.0.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 |