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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 (3.19)

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 1.7.3
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, 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_1.7.3.tar.gz
Windows Binary crisprScore_1.7.3.zip
macOS Binary (x86_64) crisprScore_1.7.3.tgz
macOS Binary (arm64) crisprScore_1.7.3.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