Package: crisprScore 1.16.0
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:
crisprScore_1.16.0.tar.gz
crisprScore_1.16.0.zip(r-4.7)crisprScore_1.16.0.zip(r-4.6)crisprScore_1.16.0.zip(r-4.5)
crisprScore_1.16.0.tgz(r-4.6-any)crisprScore_1.16.0.tgz(r-4.5-any)
crisprScore_1.16.0.tar.gz(r-4.7-any)crisprScore_1.16.0.tar.gz(r-4.6-any)
crisprScore_1.16.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
crisprScore/json (API)
NEWS
| # Install 'crisprScore' in R: |
| install.packages('crisprScore', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/crisprverse/crisprscore/issues
- scoringMethodsInfo - Data.frame detailing available scoring methods
On BioConductor:crisprScore-1.17.0(bioc 3.24)crisprScore-1.16.0(bioc 3.23)
crisprfunctionalgenomicsfunctionalpredictionbioconductorbioconductor-packagecrispr-cas9crispr-designcrispr-targetgenomicsgrnagrna-sequencegrna-sequencesscoring-algorithmsgrnasgrna-design
Last updated from:81c327cfae (on RELEASE_3_23). Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 174 | ||
| linux-devel-x86_64 | NOTE | 257 | ||
| source / vignettes | OK | 220 | ||
| linux-release-x86_64 | NOTE | 260 | ||
| macos-release-arm64 | NOTE | 176 | ||
| macos-oldrel-arm64 | NOTE | 136 | ||
| windows-devel | NOTE | 436 | ||
| windows-release | NOTE | 417 | ||
| windows-oldrel | NOTE | 430 | ||
| wasm-release | OK | 144 |
Exports:getCasRxRFScoresgetCFDScoresgetCRISPRaterScoresgetCRISPRscanScoresgetDeepHFScoresgetEnPAMGBScoresgetLindelScoresgetMITScoresgetRuleSet1ScoresgetRuleSet3Scores
Dependencies:AnnotationDbiAnnotationHubaskpassBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocManagerBiocVersionBiostringsbitbit64blobcachemclicpp11crayoncrisprScoreDatacurlDBIdbplyrdplyrExperimentHubfastmapfilelockgenericsglueherehttrhttr2IRangesjsonliteKEGGRESTlatticelifecyclemagrittrMatrixmemoisemimeopensslpillarpkgconfigpngpurrrR6randomForestrappdirsRcppRcppTOMLreticulaterlangrprojrootRSQLiteS4VectorsSeqinfostringistringrsystibbletidyrtidyselectutf8vctrswithrXVectoryaml
Readme and manuals
Help Manual
| 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 |
