Package: crisprScore 1.11.0

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, 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.

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

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crisprScore.pdf |crisprScore.html✨
crisprScore/json (API)
NEWS

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

Peer review:

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

Datasets:

On BioConductor:crisprScore-1.9.3(bioc 3.20)crisprScore-1.8.0(bioc 3.19)

crisprfunctionalgenomicsfunctionalpredictionbioconductorbioconductor-packagecrispr-cas9crispr-designcrispr-targetgenomicsgrnagrna-sequencegrna-sequencesscoring-algorithmsgrnasgrna-design

7.44 score 13 stars 4 packages 17 scripts 311 downloads 14 exports 72 dependencies

Last updated 23 days agofrom:d409224306. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winNOTEOct 30 2024
R-4.5-linuxNOTEOct 30 2024
R-4.4-winNOTEOct 30 2024
R-4.4-macNOTEOct 31 2024
R-4.3-winNOTEOct 30 2024
R-4.3-macNOTEOct 31 2024

Exports:getAzimuthScoresgetCasRxRFScoresgetCFDScoresgetCrispraiScoresgetCRISPRaterScoresgetCRISPRscanScoresgetDeepCpf1ScoresgetDeepHFScoresgetDeepSpCas9ScoresgetEnPAMGBScoresgetLindelScoresgetMITScoresgetRuleSet1ScoresgetRuleSet3Scores

Dependencies:AnnotationDbiAnnotationHubaskpassbasiliskbasilisk.utilsBiobaseBiocFileCacheBiocGenericsBiocManagerBiocVersionBiostringsbitbit64blobcachemclicpp11crayoncrisprScoreDatacurlDBIdbplyrdir.expirydplyrExperimentHubfansifastmapfilelockgenericsGenomeInfoDbGenomeInfoDbDataglueherehttrIRangesjsonliteKEGGRESTlatticelifecyclemagrittrMatrixmemoisemimeopensslpillarpkgconfigplogrpngpurrrR6randomForestrappdirsRcppRcppTOMLreticulaterlangrprojrootRSQLiteS4VectorsstringistringrsystibbletidyrtidyselectUCSC.utilsutf8vctrswithrXVectoryamlzlibbioc

On-target and off-target scoring for CRISPR gRNAs

Jean-Philippe Fortin, Aaron Lun, Luke Hoberecht

Rendered fromcrisprScore.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2024-10-04
Started: 2021-05-27

Readme and manuals

Help Manual

Help pageTopics
Calculate on-target sgRNA activity scores for Cas9 using AzimuthgetAzimuthScores
Calculate on-target sgRNA activity scores for CasRx using CasRx-RFgetCasRxRFScores
Calculate CFD off-target specificity scoresgetCFDScores
Calculate on-target sgRNA activity scores for CRISPRa and CRISPRigetCrispraiScores
Calculate on-target sgRNA activity scores for Cas9 using CRISPRatergetCRISPRaterScores
Calculate on-target sgRNA activity scores for Cas9 using CRISPRscangetCRISPRscanScores
Calculate on-target sgRNA activity scores for Cas12a using DeepCpf1getDeepCpf1Scores
Calculate on-target sgRNA activity scores for Cas9 using DeepHFgetDeepHFScores
Calculate on-target sgRNA activity scores for SpCas9 using DeepSpCas9getDeepSpCas9Scores
Calculate on-target sgRNA activity scores for enCas12a using enPAM+GBgetEnPAMGBScores
Predict frameshift ratios from CRISPR/Cas9 indel prediction using LindelgetLindelScores
Calculate MIT off-target specificity scores for CRISPR/Cas9getMITScores
Calculate on-target sgRNA activity scores for Cas9 using Rule Set 1getRuleSet1Scores
Calculate on-target sgRNA activity scores for SpCas9 using Rule Set 3getRuleSet3Scores
data.frame detailing available scoring methodsscoringMethodsInfo
Example CRISPRa gRNAs data.frame for the getCrispraiScores functionsgrnaExampleCrispra
Example CRISPRi gRNAs data.frame for the getCrispraiScores functionsgrnaExampleCrispri
Example TSS data.frame for the getCrispraiScores functiontssExampleCrispra
Example TSS data.frame for the getCrispraiScores functiontssExampleCrispri