crisprScore
On-Target and Off-Target Scoring Algorithms for CRISPR gRNAs
Bioconductor version: 3.24 · Package version: 1.17.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("crisprScore")Details
| Maintainer | Jean-Philippe Fortin <fortin946@gmail.com> |
| Author | Jean-Philippe Fortin [aut, cre, cph], Aaron Lun [aut], Luke Hoberecht [ctb], Pirunthan Perampalam [ctb] |
| License | MIT + file LICENSE |
| URL | https://github.com/crisprVerse/crisprScore/issues |
| Bug Reports | https://github.com/crisprVerse/crisprScore |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | CRISPR, FunctionalGenomics, FunctionalPrediction, Software |
| Package Short Url | https://bioconductor.org/packages/crisprScore/ |
Citation
From within R, enter citation("crisprScore"):
Jean-Philippe Fortin, Aaron Lun. crisprScore: On-Target and Off-Target Scoring Algorithms for CRISPR gRNAs. doi:10.18129/B9.bioc.crisprScore, R package version 1.17.0, https://bioconductor.org/packages/crisprScore.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | crisprScore_1.17.0.tar.gz |
| Windows binary (x86_64) | crisprScore_1.17.0.zip |
| macOS binary (arm64) | crisprScore_1.17.0.tgz |
| macOS binary (x86_64) | crisprScore_1.17.0.tgz |
Dependencies
Depends: R (>= 4.1), crisprScoreData (>= 1.1.3)
Imports: BiocGenerics, Biostrings, IRanges, methods, randomForest, reticulate, stringr, utils, XVector
Reverse dependencies
Imports Me (3): crisprDesign, crisprShiny, crisprVerse