crisprScore
This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see crisprScore.
On-Target and Off-Target Scoring Algorithms for CRISPR gRNAs
Bioconductor version: 3.17
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, Azimuth, DeepHF, DeepCpf1, 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, DeepCpf1 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")):
Installation
To install this package, start R (version "4.3") 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 | 1.4.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (2 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.1), crisprScoreData(>= 1.1.3) |
| Imports | basilisk(>= 1.9.2), basilisk.utils(>= 1.9.1), 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, 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_1.4.0.tar.gz |
| Windows Binary | crisprScore_1.4.0.zip |
| macOS Binary (x86_64) | crisprScore_1.4.0.tgz |
| macOS Binary (arm64) | crisprScore_1.4.0.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 |
| Old Source Packages for BioC 3.17 | Source Archive |