Package: crisprDesign 1.9.0
Jean-Philippe Fortin
crisprDesign: Comprehensive design of CRISPR gRNAs for nucleases and base editors
Provides a comprehensive suite of functions to design and annotate CRISPR guide RNA (gRNAs) sequences. This includes on- and off-target search, on-target efficiency scoring, off-target scoring, full gene and TSS contextual annotations, and SNP annotation (human only). It currently support five types of CRISPR modalities (modes of perturbations): CRISPR knockout, CRISPR activation, CRISPR inhibition, CRISPR base editing, and CRISPR knockdown. All types of CRISPR nucleases are supported, including DNA- and RNA-target nucleases such as Cas9, Cas12a, and Cas13d. All types of base editors are also supported. gRNA design can be performed on reference genomes, transcriptomes, and custom DNA and RNA sequences. Both unpaired and paired gRNA designs are enabled.
Authors:
crisprDesign_1.9.0.tar.gz
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crisprDesign_1.7.2.tgz(r-4.4-any)crisprDesign_1.7.2.tgz(r-4.3-any)
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crisprDesign.pdf |crisprDesign.html✨
crisprDesign/json (API)
NEWS
| # Install 'crisprDesign' in R: |
| install.packages('crisprDesign', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/crisprverse/crisprdesign/issues
- grListExample - Example of a TxDb object converted to a GRangesList
- grRepeatsExample - Example of a GRanges object containing repeat elements
- guideSetExample - Example of a GuideSet object storing gRNA sequences targeting the CDS of IQSEC3
- guideSetExampleFullAnnotation - Example of a fully-annotated GuideSet object storing gRNA sequences targeting the CDS of IQSEC3
- guideSetExampleWithAlignments - Example of a GuideSet object storing gRNA sequences targeting the CDS of IQSEC3 with off-target alignments.
- tssObjectExample - Example of a GRanges object containing TSS coordinates
On BioConductor:crisprDesign-1.9.0(bioc 3.21)crisprDesign-1.8.0(bioc 3.20)
crisprfunctionalgenomicsgenetargetbioconductorbioconductor-packagecrispr-cas9crispr-designcrispr-targetgenomics-analysisgrnagrna-sequencegrna-sequencessgrnasgrna-design
Last updated 2 months agofrom:61a8bea08d. Checks:OK: 1 NOTE: 4 ERROR: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 29 2024 |
| R-4.5-win | NOTE | Nov 29 2024 |
| R-4.5-linux | NOTE | Nov 29 2024 |
| R-4.4-win | NOTE | Nov 29 2024 |
| R-4.4-mac | ERROR | Oct 17 2024 |
| R-4.3-win | NOTE | Nov 29 2024 |
| R-4.3-mac | ERROR | Oct 17 2024 |
Exports:addCompositeScoresaddConservationScoresaddCrispraiScoresaddCutSitesaddDistanceToTssaddEditedAllelesaddEditingSitesaddExonTableaddGeneAnnotationaddIsoformAnnotationaddNtcsaddOffTargetScoresaddOnTargetScoresaddOpsBarcodesaddPamScoresaddPfamDomainsaddReinitiationFlagaddRepeatsaddRestrictionEnzymesaddSequenceFeaturesaddSNPAnnotationaddSpacerAlignmentsaddSpacerAlignmentsIterativeaddTssAnnotationaddTxTablealignmentsalignments<-bsgenomeconvertToMinMaxGRangesconvertToProtospacerGRangescrisprNucleasecustomSequencescutLengthcutSitesdesignCompleteAnnotationdesignOpsLibraryeditedAllelesenzymeAnnotationenzymeAnnotation<-exonTablefindSpacerPairsfindSpacersflattenGuideSetgeneAnnotationgeneAnnotation<-getBarcodeDistanceMatrixgetConsensusIsoformgetMrnaSequencesgetPAMSequencegetPAMSiteFromStartAndEndgetPreMrnaSequencesgetSpacerAlignmentsgetSpacerSequencegetTssObjectFromTxObjectgetTxDbgetTxInfoDataFrameGuideSetGuideSet2DataFramesmcolsoffTargetsonTargetsPairedGuideSetpamDistancepamLengthpamOrientationpamspamSidepamSitespreparePfamTableprotospacersprototypeSequencequeryTssqueryTxObjectrankSpacersremoveRepeatsremoveSpacersWithSecondaryTargetsseqnamessnpssnps<-spacerDistancespacerLengthspacerstargetOrigintssAnnotationtssAnnotation<-TxDb2GRangesListtxTableupdateOpsLibraryvalidateOpsLibrary
Dependencies:abindAnnotationDbiAnnotationHubaskpassbasiliskbasilisk.utilsBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelBiocVersionbiomaRtBiostringsbitbit64bitopsblobBSgenomecachemclicliprcodetoolscpp11crayoncrisprBasecrisprBowtiecrisprScorecrisprScoreDatacurlDBIdbplyrDelayedArraydigestdir.expirydplyrExperimentHubfansifastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesglueherehmshttrhttr2IRangesjsonliteKEGGRESTlambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigplogrpngprettyunitsprogresspurrrR6randomForestrappdirsRbowtieRcppRcppTOMLRCurlreadrrestfulrreticulateRhtslibrjsonrlangrprojrootRsamtoolsRSQLitertracklayerS4ArraysS4VectorssnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttxdbmakertzdbUCSC.utilsutf8VariantAnnotationvctrsvroomwithrXMLxml2XVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Add on-target composite score to a GuideSet object. | addCompositeScores addCompositeScores,GuideSet-method addCompositeScores,NULL-method addCompositeScores,PairedGuideSet-method |
| Add on-target composite score to a GuideSet object. | addConservationScores addConservationScores,GuideSet-method addConservationScores,NULL-method addConservationScores,PairedGuideSet-method |
| Add CRISPRa/CRISPRi on-target scores to a GuideSet object. | addCrispraiScores addCrispraiScores,GuideSet-method addCrispraiScores,NULL-method addCrispraiScores,PairedGuideSet-method |
| Add distance to TSS for a specificed TSS id | addDistanceToTss addDistanceToTss,GuideSet-method addDistanceToTss,PairedGuideSet-method |
| To add edited alleles for a CRISPR base editing GuideSet | addEditedAlleles |
| Add optimal editing site for base editing gRNAs. | addEditingSites addEditingSites,GuideSet-method addEditingSites,NULL-method addEditingSites,PairedGuideSet-method |
| Add a gene-specific exon table to a GuideSet object. | addExonTable |
| Add gene context annotation to a GuideSet object | addGeneAnnotation addGeneAnnotation,GuideSet-method addGeneAnnotation,PairedGuideSet-method |
| Add isoform-specific annotation to a GuideSet object | addDistanceToTss,NULL-method addIsoformAnnotation addIsoformAnnotation,GuideSet-method addIsoformAnnotation,NULL-method addIsoformAnnotation,PairedGuideSet-method |
| Add non-targeting control (NTC) sequences to GuideSet | addNtcs addNtcs,GuideSet-method addNtcs,NULL-method addNtcs,PairedGuideSet-method |
| Add CFD and MIT scores to a GuideSet object. | addOffTargetScores addOffTargetScores,GuideSet-method addOffTargetScores,NULL-method addOffTargetScores,PairedGuideSet-method |
| Add on-target scores to a GuideSet object. | addOnTargetScores addOnTargetScores,GuideSet-method addOnTargetScores,NULL-method addOnTargetScores,PairedGuideSet-method |
| Add optical pooled screening (OPS) barcodes | addOpsBarcodes |
| Add PAM scores to a GuideSet object. | addPamScores addPamScores,GuideSet-method addPamScores,NULL-method addPamScores,PairedGuideSet-method |
| Add Pfam domains annotation to GuideSet object | addPfamDomains addPfamDomains,GuideSet-method addPfamDomains,NULL-method addPfamDomains,PairedGuideSet-method |
| Add a logical flag for gRNAs leading to potential reinitiation | addReinitiationFlag |
| Annotate a GuideSet object with repeat elements | addRepeats addRepeats,GuideSet-method addRepeats,NULL-method addRepeats,PairedGuideSet-method |
| Restriction enzyme recognition sites in spacer sequences | addRestrictionEnzymes addRestrictionEnzymes,GuideSet-method addRestrictionEnzymes,NULL-method addRestrictionEnzymes,PairedGuideSet-method |
| Add spacer sequence feature annotation columns to a GuideSet object | addSequenceFeatures addSequenceFeatures,GuideSet-method addSequenceFeatures,NULL-method addSequenceFeatures,PairedGuideSet-method |
| Add SNP annotation to a GuideSet object | addGeneAnnotation,NULL-method addSNPAnnotation addSNPAnnotation,GuideSet-method addSNPAnnotation,NULL-method addSNPAnnotation,PairedGuideSet-method |
| Functions for finding and characterizing on- and off-targets of spacer sequences. | addSpacerAlignments addSpacerAlignments,GuideSet-method addSpacerAlignments,NULL-method addSpacerAlignments,PairedGuideSet-method addSpacerAlignmentsIterative addSpacerAlignmentsIterative,GuideSet-method addSpacerAlignmentsIterative,NULL-method addSpacerAlignmentsIterative,PairedGuideSet-method getSpacerAlignments |
| Add TSS context annotation to a GuideSet object | addTssAnnotation addTssAnnotation,GuideSet-method addTssAnnotation,NULL-method addTssAnnotation,PairedGuideSet-method |
| Add a gene-specific transcript table to a GuideSet object. | addTxTable |
| Get complete spacer information | completeSpacers getPAMSequence getPAMSiteFromStartAndEnd getSpacerSequence |
| Convert a GuideSet object into a GRanges containing the range of all targeting gRNAs. | convertToMinMaxGRanges |
| Convert PAM site coordinates to protospacer start and end coordinates | convertToProtospacerGRanges |
| An S4 class to store CRISPR gRNA sequences with modular annotations. | addCutSites addCutSites,GuideSet-method alignments alignments,GuideSet-method alignments<- alignments<-,GuideSet-method bsgenome bsgenome,GuideSet-method crisprNuclease crisprNuclease,GuideSet-method customSequences customSequences,GuideSet-method cutSites,GuideSet-method editedAlleles editedAlleles,GuideSet-method enzymeAnnotation enzymeAnnotation,GuideSet-method enzymeAnnotation<- enzymeAnnotation<-,GuideSet-method exonTable exonTable,GuideSet-method geneAnnotation geneAnnotation,GuideSet-method geneAnnotation<- geneAnnotation<-,GuideSet-method GuideSet GuideSet-class offTargets offTargets,GuideSet-method onTargets onTargets,GuideSet-method pamLength,GuideSet-method pams,GuideSet-method pamSide,GuideSet-method pamSites pamSites,GuideSet-method protospacers protospacers,GuideSet-method prototypeSequence,GuideSet-method snps snps,GuideSet-method snps<- snps<-,GuideSet-method spacerLength,GuideSet-method spacers spacers,GuideSet-method targetOrigin targetOrigin,GuideSet-method tssAnnotation tssAnnotation,GuideSet-method tssAnnotation<- tssAnnotation<-,GuideSet-method txTable txTable,GuideSet-method |
| One-step gRNA design and annotation function | designCompleteAnnotation |
| Design gRNA library for optical pooled screening | designOpsLibrary |
| Find pairs of CRISPR gRNA spacers from a pair of genomic regions. | findSpacerPairs |
| Find CRISPR gRNA spacer sequences from a set of DNA sequences. | findSpacers |
| Create a list of annotation tables from a GuideSet object | flattenGuideSet |
| Get distance between query and target sets of barcodes | getBarcodeDistanceMatrix |
| Get the genomic ranges of a consensus isoform | getConsensusIsoform |
| Retrieve mRNA sequences | getMrnaSequences |
| Retrieve pre-mRNA sequences | getPreMrnaSequences |
| Extract TSS coordinates from a gene model object | getTssObjectFromTxObject |
| getTxDb | getTxDb |
| To obtain a DataFrame of transcript-specific CDS and mRNA coordinates | getTxInfoDataFrame |
| Example of a TxDb object converted to a GRangesList | grListExample |
| Example of a GRanges object containing repeat elements | grRepeatsExample |
| Create a list of annotation tables from a GuideSet object | GuideSet2DataFrames |
| Example of a GuideSet object storing gRNA sequences targeting the CDS of IQSEC3 | guideSetExample |
| Example of a fully-annotated GuideSet object storing gRNA sequences targeting the CDS of IQSEC3 | guideSetExampleFullAnnotation |
| Example of a GuideSet object storing gRNA sequences targeting the CDS of IQSEC3 with off-target alignments. | guideSetExampleWithAlignments |
| An S4 class to store pairs of CRISPR gRNA sequences. | crisprNuclease,PairedGuideSet-method cutLength cutLength,PairedGuideSet-method cutSites,PairedGuideSet-method PairedGuideSet PairedGuideSet-class pamDistance pamDistance,PairedGuideSet-method pamLength,PairedGuideSet-method pamOrientation pamOrientation,PairedGuideSet-method pams,PairedGuideSet-method pamSide,PairedGuideSet-method pamSites,PairedGuideSet-method protospacers,PairedGuideSet-method spacerDistance spacerDistance,PairedGuideSet-method spacerLength,PairedGuideSet-method spacers,PairedGuideSet-method |
| Obtain Pfam domains from biomaRt | preparePfamTable |
| Convenience function to search for TSS coordinates. | queryTss |
| Convenience function to search for gene coordinates. | queryTxObject |
| Recommended gRNA ranking | rankSpacers |
| Remove GuideSet gRNAs that overlap repeat elements | removeRepeats removeRepeats,GuideSet-method removeRepeats,NULL-method removeRepeats,PairedGuideSet-method |
| Remove gRNAs targeting secondary targets | removeSpacersWithSecondaryTargets |
| Example of a GRanges object containing TSS coordinates | tssObjectExample |
| Convert a TxDb object into a GRangesList | TxDb2GRangesList |
| Update OPS library with additional gRNAs | updateOpsLibrary |
| Validate gRNA library for optical pooled screening | validateOpsLibrary |
