Package: crisprScore 1.17.0

Jean-Philippe Fortin

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

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.

Authors:Jean-Philippe Fortin [aut, cre, cph], Aaron Lun [aut], Luke Hoberecht [ctb], Pirunthan Perampalam [ctb]

crisprScore_1.17.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
crisprScore/json (API)

# Install 'crisprScore' in R:

install.packages('crisprScore', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/crisprverse/crisprscore/issues

Datasets:

scoringMethodsInfo - Data.frame detailing available scoring methods

On BioConductor:crisprScore-1.17.0(bioc 3.24)crisprScore-1.16.0(bioc 3.23)

crispr functionalgenomics functionalprediction bioconductor bioconductor-package crispr-cas9 crispr-design crispr-target genomics grna grna-sequence grna-sequences scoring-algorithm sgrna sgrna-design

7.93 score 27 stars 4 packages 22 scripts 490 downloads 10 exports 66 dependencies

Last updated from:8fb666dd51. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	181
linux-devel-x86_64	NOTE	254
source / vignettes	OK	233
linux-release-x86_64	NOTE	223
macos-release-arm64	NOTE	150
macos-oldrel-arm64	NOTE	191
windows-devel	NOTE	538
windows-release	NOTE	415
windows-oldrel	NOTE	549
wasm-release	OK	140

Exports:getCasRxRFScores getCFDScores getCRISPRaterScores getCRISPRscanScores getDeepHFScores getEnPAMGBScores getLindelScores getMITScores getRuleSet1Scores getRuleSet3Scores

Dependencies:AnnotationDbi AnnotationHub askpass Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocManager BiocVersion Biostrings bit bit64 blob cachem cli cpp11 crayon crisprScoreData curl DBI dbplyr dplyr ExperimentHub fastmap filelock generics glue here httr httr2 IRanges jsonlite KEGGREST lattice lifecycle magrittr Matrix memoise mime openssl pillar pkgconfig png purrr R6 randomForest rappdirs Rcpp RcppTOML reticulate rlang rprojroot RSQLite S4Vectors Seqinfo stringi stringr sys tibble tidyr tidyselect utf8 vctrs withr XVector yaml

On-target and off-target scoring for CRISPR gRNAs

Rendered fromcrisprScore.Rmdusingknitr::rmarkdown

Last update: 2025-11-20
Started: 2021-05-27

Help page	Topics
Calculate on-target sgRNA activity scores for CasRx using CasRx-RF	getCasRxRFScores
Calculate CFD off-target specificity scores	getCFDScores
Calculate on-target sgRNA activity scores for Cas9 using CRISPRater	getCRISPRaterScores
Calculate on-target sgRNA activity scores for Cas9 using CRISPRscan	getCRISPRscanScores
Calculate on-target sgRNA activity scores for Cas9 using DeepHF	getDeepHFScores
Calculate on-target sgRNA activity scores for enCas12a using enPAM+GB	getEnPAMGBScores
Predict frameshift ratios from CRISPR/Cas9 indel prediction using Lindel	getLindelScores
Calculate MIT off-target specificity scores for CRISPR/Cas9	getMITScores
Calculate on-target sgRNA activity scores for Cas9 using Rule Set 1	getRuleSet1Scores
Calculate on-target sgRNA activity scores for SpCas9 using Rule Set 3	getRuleSet3Scores
data.frame detailing available scoring methods	scoringMethodsInfo

Package: crisprScore 1.17.0

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

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Usage by other packages (reverse dependencies)