Package: crisprBase 1.11.0
Jean-Philippe Fortin
crisprBase: Base functions and classes for CRISPR gRNA design
Provides S4 classes for general nucleases, CRISPR nucleases, CRISPR nickases, and base editors.Several CRISPR-specific genome arithmetic functions are implemented to help extract genomic coordinates of spacer and protospacer sequences. Commonly-used CRISPR nuclease objects are provided that can be readily used in other packages. Both DNA- and RNA-targeting nucleases are supported.
Authors:
crisprBase_1.11.0.tar.gz
crisprBase_1.11.0.zip(r-4.5)crisprBase_1.11.0.zip(r-4.4)crisprBase_1.11.0.zip(r-4.3)
crisprBase_1.11.0.tgz(r-4.4-any)crisprBase_1.9.1.tgz(r-4.3-any)
crisprBase_1.11.0.tar.gz(r-4.5-noble)crisprBase_1.11.0.tar.gz(r-4.4-noble)
crisprBase_1.11.0.tgz(r-4.4-emscripten)crisprBase_1.11.0.tgz(r-4.3-emscripten)
crisprBase.pdf |crisprBase.html✨
crisprBase/json (API)
NEWS
| # Install 'crisprBase' in R: |
| install.packages('crisprBase', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/crisprverse/crisprbase/issues
- AsCas12a - AsCas12a CrisprNuclease object
- BE4max - BE4max BaseEditor object
- CasRx - CasRx CrisprNuclease object
- Csm - Csm CrisprNuclease object
- MAD7 - MAD7 CrisprNuclease object
- SaCas9 - SaCas9 CrisprNuclease object
- SpCas9 - SpCas9 CrisprNuclease object
- SpGCas9 - SpGCas9 CrisprNuclease object
- enAsCas12a - EnAsCas12a CrisprNuclease object
- restrictionEnzymes - List of Nuclease objects representing common restriction enzymes
On BioConductor:crisprBase-1.9.1(bioc 3.20)crisprBase-1.8.0(bioc 3.19)
crisprfunctionalgenomicsbioconductorbioconductor-packagecrispr-cas9crispr-designcrispr-targetgrnagrna-sequencegrna-sequences
Last updated 23 days agofrom:d22a71546e. Checks:OK: 3 NOTE: 4. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 30 2024 |
| R-4.5-win | NOTE | Oct 30 2024 |
| R-4.5-linux | NOTE | Oct 30 2024 |
| R-4.4-win | NOTE | Oct 30 2024 |
| R-4.4-mac | NOTE | Oct 30 2024 |
| R-4.3-win | OK | Oct 30 2024 |
| R-4.3-mac | OK | Oct 22 2024 |
Exports:annotateMismatchesBaseEditorbaseEditorNamebaseEditorName<-CrisprNickaseCrisprNucleasecutSiteseditingStrandeditingStrand<-editingWeightseditingWeights<-extractPamFromTargetextractProtospacerFromTargetgetAvailableCrisprNucleasesgetCutSiteFromPamSitegetCutSiteRangesgetEditingSiteFromPamSitegetPamRangesgetProtospacerRangesgetTargetRangeshasSpacerGapisCuttingisDnaseisRnasemetadatametadata<-motifLengthmotifsNickasenickaseNamenickaseName<-nickingStrandnickingStrand<-NucleasenucleaseNamenucleaseName<-pamIndicespamLengthpamspamSidepamSide<-plotEditingWeightsprototypeSequenceshowspacerGapspacerGap<-spacerIndicesspacerLengthspacerLength<-targetLengthtargetTypetargetType<-weightsweights<-
Dependencies:askpassBiocGenericsBiostringsclicrayoncurlGenomeInfoDbGenomeInfoDbDataGenomicRangesgluehttrIRangesjsonlitelifecyclemagrittrmimeopensslR6rlangS4VectorsstringistringrsysUCSC.utilsvctrsXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Annotate mismatches between spacer and protospacer sequences | annotateMismatches |
| AsCas12a CrisprNuclease object | AsCas12a |
| An S4 class to represent a base editor | BaseEditor BaseEditor-class baseEditorName baseEditorName,BaseEditor-method baseEditorName<- baseEditorName<-,BaseEditor-method editingStrand editingStrand,BaseEditor-method editingStrand<- editingStrand<-,BaseEditor-method editingWeights editingWeights,BaseEditor-method editingWeights<- editingWeights<-,BaseEditor-method show,BaseEditor-method |
| BE4max BaseEditor object | BE4max |
| CasRx CrisprNuclease object | CasRx |
| An S4 class to represent a CRISPR nickase. | CrisprNickase CrisprNickase-class hasSpacerGap,CrisprNickase-method pamIndices,CrisprNickase-method pamLength,CrisprNickase-method pams,CrisprNickase-method pamSide,CrisprNickase-method pamSide<-,CrisprNickase-method prototypeSequence,CrisprNickase-method show,CrisprNickase-method spacerGap,CrisprNickase-method spacerGap<-,CrisprNickase-method spacerIndices,CrisprNickase-method spacerLength,CrisprNickase-method spacerLength<-,CrisprNickase-method targetLength,CrisprNickase-method |
| Csm CrisprNuclease object | Csm |
| enAsCas12a CrisprNuclease object | enAsCas12a |
| Extract PAM sequences from target sequences | extractPamFromTarget |
| Extract protospacer sequences from target sequences | extractProtospacerFromTarget |
| Return list of available CrisprNuclease objects in crisprBase | getAvailableCrisprNucleases |
| Return cut site coordinates from PAM site coordinates | getCutSiteFromPamSite |
| Construct a cut site GRanges from a list of PAM sites | getCutSiteRanges |
| Return optimal editing site coordinates from PAM site coordinates | getEditingSiteFromPamSite |
| Construct a PAM GRanges from a list of PAM sites | getPamRanges |
| Construct a protospacer GRanges from a list of PAM sites | getProtospacerRanges |
| Construct a target GRanges from a list of PAM sites | getTargetRanges |
| MAD7 CrisprNuclease object | MAD7 |
| An S4 class to represent a nuclease. | cutSites cutSites,Nuclease-method isCutting isCutting,Nuclease-method isDnase isDnase,Nuclease-method isRnase isRnase,Nuclease-method motifLength motifLength,Nuclease-method motifs motifs,Nuclease-method Nuclease Nuclease-class nucleaseName nucleaseName,Nuclease-method nucleaseName<- nucleaseName<-,Nuclease-method show,Nuclease-method targetType targetType,Nuclease-method targetType<- targetType<-,Nuclease-method weights weights,Nuclease-method weights<- weights<-,Nuclease-method |
| An S4 class to represent a nickase | cutSites,Nickase-method isCutting,Nickase-method motifLength,Nickase-method motifs,Nickase-method Nickase Nickase-class nickaseName nickaseName,Nickase-method nickaseName<- nickaseName<-,Nickase-method nickingStrand nickingStrand,Nickase-method nickingStrand<- nickingStrand<-,Nickase-method show,Nickase-method weights,Nickase-method weights<-,Nickase-method |
| Quick plot to visualize editing weights | plotEditingWeights |
| List of Nuclease objects representing common restriction enzymes | restrictionEnzymes |
| SaCas9 CrisprNuclease object | SaCas9 |
| An S4 class to represent a CRISPR nuclease. | CrisprNuclease CrisprNuclease-class hasSpacerGap hasSpacerGap,CrisprNuclease-method pamIndices pamIndices,CrisprNuclease-method pamLength pamLength,CrisprNuclease-method pams pams,CrisprNuclease-method pamSide pamSide,CrisprNuclease-method pamSide<- pamSide<-,CrisprNuclease-method prototypeSequence prototypeSequence,CrisprNuclease-method show,CrisprNuclease-method spacerGap spacerGap,CrisprNuclease-method spacerGap<- spacerGap<-,CrisprNuclease-method spacerIndices spacerIndices,CrisprNuclease-method spacerLength spacerLength,CrisprNuclease-method spacerLength<- spacerLength<-,CrisprNuclease-method targetLength targetLength,CrisprNuclease-method |
| SpCas9 CrisprNuclease object | SpCas9 |
| SpGCas9 CrisprNuclease object | SpGCas9 |
