crisprScore
This is the released version of crisprScore; for the devel version, see crisprScore.
On-Target and Off-Target Scoring Algorithms for CRISPR gRNAs
Bioconductor version: Release (3.23)
Provides R wrappers of several on-target and off-target scoring methods for CRISPR guide RNAs (gRNAs). The following nucleases are supported: SpCas9, AsCas12a, enAsCas12a, and RfxCas13d (CasRx). The available on-target cutting efficiency scoring methods are RuleSet1, RuleSet3, DeepHF, enPAM+GB, and CRISPRscan. Both the CFD and MIT scoring methods are available for off-target specificity prediction. The package also provides a Lindel-derived score to predict the probability of a gRNA to produce indels inducing a frameshift for the Cas9 nuclease. Note that DeepHF and enPAM+GB are not available on Windows machines.
Author: Jean-Philippe Fortin [aut, cre, cph], Aaron Lun [aut], Luke Hoberecht [ctb], Pirunthan Perampalam [ctb]
Maintainer: Jean-Philippe Fortin <fortin946 at gmail.com>
citation("crisprScore")):
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")
BiocManager::install("crisprScore")
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("crisprScore")| crisprScore | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | CRISPR, FunctionalGenomics, FunctionalPrediction, Software |
| Version | 1.16.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (4.5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.1), crisprScoreData(>= 1.1.3) |
| Imports | BiocGenerics, Biostrings, IRanges, methods, randomForest, reticulate, stringr, utils, XVector |
| System Requirements | |
| URL | https://github.com/crisprVerse/crisprScore/issues |
| Bug Reports | https://github.com/crisprVerse/crisprScore |
See More
| Suggests | BiocStyle, knitr, rmarkdown, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | crisprDesign, 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 | crisprScore_1.16.0.tar.gz |
| Windows Binary (x86_64) | crisprScore_1.16.0.zip |
| macOS Binary (big-sur-x86_64) | crisprScore_1.16.0.tgz |
| macOS Binary (sonoma-arm64) | crisprScore_1.16.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/crisprScore |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/crisprScore |
| Bioc Package Browser | https://code.bioconductor.org/browse/crisprScore/ |
| Package Short Url | https://bioconductor.org/packages/crisprScore/ |
| Package Downloads Report | Download Stats |