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("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 | ||
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 | |
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_1.9.3.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 |