crisprDesign
This is the development version of crisprDesign; for the stable release version, see crisprDesign.
Comprehensive design of CRISPR gRNAs for nucleases and base editors
Bioconductor version: Development (3.24)
Provides a comprehensive suite of functions to design and annotate CRISPR guide RNA (gRNAs) sequences. This includes on- and off-target search, on-target efficiency scoring, off-target scoring, full gene and TSS contextual annotations, and SNP annotation (human only). It currently support five types of CRISPR modalities (modes of perturbations): CRISPR knockout, CRISPR activation, CRISPR inhibition, CRISPR base editing, and CRISPR knockdown. All types of CRISPR nucleases are supported, including DNA- and RNA-target nucleases such as Cas9, Cas12a, and Cas13d. All types of base editors are also supported. gRNA design can be performed on reference genomes, transcriptomes, and custom DNA and RNA sequences. Both unpaired and paired gRNA designs are enabled.
Author: Jean-Philippe Fortin [aut, cre], Luke Hoberecht [aut]
Maintainer: Jean-Philippe Fortin <fortin946 at gmail.com>
citation("crisprDesign")):
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("crisprDesign")
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("crisprDesign")| Base editing design with crisprDesign | HTML | R Script |
| Introduction to crisprDesign | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | CRISPR, FunctionalGenomics, GeneTarget, Software |
| Version | 1.15.7 |
| In Bioconductor since | BioC 3.16 (R-4.2) (4 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.2.0), crisprBase(>= 1.1.3) |
| Imports | AnnotationDbi, BiocGenerics, Biostrings(>= 2.77.2), BiocParallel, BSgenome(>= 1.77.1), crisprBowtie(>= 0.99.8), crisprScore(>= 1.15.2), GenomeInfoDb(>= 1.45.7), GenomicFeatures(>= 1.61.4), GenomicRanges(>= 1.61.1), IRanges, Matrix, MatrixGenerics, methods, reticulate, rtracklayer(>= 1.69.1), S4Vectors, Seqinfo, stats, stringr, txdbmaker(>= 1.5.6), utils, VariantAnnotation(>= 1.55.1) |
| System Requirements | |
| URL | https://github.com/crisprVerse/crisprDesign |
| Bug Reports | https://github.com/crisprVerse/crisprDesign/issues |
See More
| Suggests | biomaRt, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BiocStyle, crisprBwa(>= 0.99.7), knitr, rmarkdown, Rbowtie, Rbwa, RCurl, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | crisprViz |
| Imports Me | crisprShiny, crisprVerse |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | crisprDesign_1.15.7.tar.gz |
| Windows Binary (x86_64) | crisprDesign_1.15.7.zip |
| macOS Binary (big-sur-x86_64) | crisprDesign_1.15.7.tgz |
| macOS Binary (sonoma-arm64) | crisprDesign_1.15.7.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/crisprDesign |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/crisprDesign |
| Bioc Package Browser | https://code.bioconductor.org/browse/crisprDesign/ |
| Package Short Url | https://bioconductor.org/packages/crisprDesign/ |
| Package Downloads Report | Download Stats |