crisprScore

This is the development version of crisprScore; for the stable release version, see crisprScore.

On-Target and Off-Target Scoring Algorithms for CRISPR gRNAs


Bioconductor version: Development (3.20)

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 (from within R, enter citation("crisprScore")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 PDF
NEWS Text
LICENSE Text

Details

biocViews CRISPR, FunctionalGenomics, FunctionalPrediction, Software
Version 1.9.3
In Bioconductor since BioC 3.15 (R-4.2) (2.5 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
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Depends On Me
Imports Me crisprDesign, crisprShiny, crisprVerse
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package crisprScore_1.9.3.tar.gz
Windows Binary crisprScore_1.9.3.zip
macOS Binary (x86_64) crisprScore_1.9.3.tgz
macOS Binary (arm64) crisprScore_1.9.3.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