annotateMismatches | Annotate mismatches between spacer and protospacer sequences |
AsCas12a | AsCas12a CrisprNuclease object |
BaseEditor | An S4 class to represent a base editor |
BaseEditor-class | An S4 class to represent a base editor |
baseEditorName | An S4 class to represent a base editor |
baseEditorName-method | An S4 class to represent a base editor |
baseEditorName<- | An S4 class to represent a base editor |
baseEditorName<--method | An S4 class to represent a base editor |
BE4max | BE4max BaseEditor object |
CasRx | CasRx CrisprNuclease object |
CrisprNickase | An S4 class to represent a CRISPR nickase. |
CrisprNickase-class | An S4 class to represent a CRISPR nickase. |
CrisprNuclease | An S4 class to represent a CRISPR nuclease. |
CrisprNuclease-class | An S4 class to represent a CRISPR nuclease. |
cutSites | An S4 class to represent a nuclease. |
cutSites-method | An S4 class to represent a nickase |
cutSites-method | An S4 class to represent a nuclease. |
editingStrand | An S4 class to represent a base editor |
editingStrand-method | An S4 class to represent a base editor |
editingStrand<- | An S4 class to represent a base editor |
editingStrand<--method | An S4 class to represent a base editor |
editingWeights | An S4 class to represent a base editor |
editingWeights-method | An S4 class to represent a base editor |
editingWeights<- | An S4 class to represent a base editor |
editingWeights<--method | An S4 class to represent a base editor |
enAsCas12a | enAsCas12a CrisprNuclease object |
extractPamFromTarget | Extract PAM sequences from target sequences |
extractProtospacerFromTarget | Extract protospacer sequences from target sequences |
getAvailableCrisprNucleases | Return list of available CrisprNuclease objects in crisprBase |
getCutSiteFromPamSite | Return cut site coordinates from PAM site coordinates |
getCutSiteRanges | Construct a cut site GRanges from a list of PAM sites |
getEditingSiteFromPamSite | Return optimal editing site coordinates from PAM site coordinates |
getPamRanges | Construct a PAM GRanges from a list of PAM sites |
getProtospacerRanges | Construct a protospacer GRanges from a list of PAM sites |
getTargetRanges | Construct a target GRanges from a list of PAM sites |
hasSpacerGap | An S4 class to represent a CRISPR nuclease. |
hasSpacerGap-method | An S4 class to represent a CRISPR nickase. |
hasSpacerGap-method | An S4 class to represent a CRISPR nuclease. |
isCutting | An S4 class to represent a nuclease. |
isCutting-method | An S4 class to represent a nickase |
isCutting-method | An S4 class to represent a nuclease. |
isDnase | An S4 class to represent a nuclease. |
isDnase-method | An S4 class to represent a nuclease. |
isRnase | An S4 class to represent a nuclease. |
isRnase-method | An S4 class to represent a nuclease. |
motifLength | An S4 class to represent a nuclease. |
motifLength-method | An S4 class to represent a nickase |
motifLength-method | An S4 class to represent a nuclease. |
motifs | An S4 class to represent a nuclease. |
motifs-method | An S4 class to represent a nickase |
motifs-method | An S4 class to represent a nuclease. |
Nickase | An S4 class to represent a nickase |
Nickase-class | An S4 class to represent a nickase |
nickaseName | An S4 class to represent a nickase |
nickaseName-method | An S4 class to represent a nickase |
nickaseName<- | An S4 class to represent a nickase |
nickaseName<--method | An S4 class to represent a nickase |
nickingStrand | An S4 class to represent a nickase |
nickingStrand-method | An S4 class to represent a nickase |
nickingStrand<- | An S4 class to represent a nickase |
nickingStrand<--method | An S4 class to represent a nickase |
Nuclease | An S4 class to represent a nuclease. |
Nuclease-class | An S4 class to represent a nuclease. |
nucleaseName | An S4 class to represent a nuclease. |
nucleaseName-method | An S4 class to represent a nuclease. |
nucleaseName<- | An S4 class to represent a nuclease. |
nucleaseName<--method | An S4 class to represent a nuclease. |
pamIndices | An S4 class to represent a CRISPR nuclease. |
pamIndices-method | An S4 class to represent a CRISPR nickase. |
pamIndices-method | An S4 class to represent a CRISPR nuclease. |
pamLength | An S4 class to represent a CRISPR nuclease. |
pamLength-method | An S4 class to represent a CRISPR nickase. |
pamLength-method | An S4 class to represent a CRISPR nuclease. |
pams | An S4 class to represent a CRISPR nuclease. |
pams-method | An S4 class to represent a CRISPR nickase. |
pams-method | An S4 class to represent a CRISPR nuclease. |
pamSide | An S4 class to represent a CRISPR nuclease. |
pamSide-method | An S4 class to represent a CRISPR nickase. |
pamSide-method | An S4 class to represent a CRISPR nuclease. |
pamSide<- | An S4 class to represent a CRISPR nuclease. |
pamSide<--method | An S4 class to represent a CRISPR nickase. |
pamSide<--method | An S4 class to represent a CRISPR nuclease. |
plotEditingWeights | Quick plot to visualize editing weights |
prototypeSequence | An S4 class to represent a CRISPR nuclease. |
prototypeSequence-method | An S4 class to represent a CRISPR nickase. |
prototypeSequence-method | An S4 class to represent a CRISPR nuclease. |
restrictionEnzymes | List of Nuclease objects representing common restriction enzymes |
SaCas9 | SaCas9 CrisprNuclease object |
show-method | An S4 class to represent a base editor |
show-method | An S4 class to represent a CRISPR nickase. |
show-method | An S4 class to represent a CRISPR nuclease. |
show-method | An S4 class to represent a nickase |
show-method | An S4 class to represent a nuclease. |
spacerGap | An S4 class to represent a CRISPR nuclease. |
spacerGap-method | An S4 class to represent a CRISPR nickase. |
spacerGap-method | An S4 class to represent a CRISPR nuclease. |
spacerGap<- | An S4 class to represent a CRISPR nuclease. |
spacerGap<--method | An S4 class to represent a CRISPR nickase. |
spacerGap<--method | An S4 class to represent a CRISPR nuclease. |
spacerIndices | An S4 class to represent a CRISPR nuclease. |
spacerIndices-method | An S4 class to represent a CRISPR nickase. |
spacerIndices-method | An S4 class to represent a CRISPR nuclease. |
spacerLength | An S4 class to represent a CRISPR nuclease. |
spacerLength-method | An S4 class to represent a CRISPR nickase. |
spacerLength-method | An S4 class to represent a CRISPR nuclease. |
spacerLength<- | An S4 class to represent a CRISPR nuclease. |
spacerLength<--method | An S4 class to represent a CRISPR nickase. |
spacerLength<--method | An S4 class to represent a CRISPR nuclease. |
SpCas9 | SpCas9 CrisprNuclease object |
SpGCas9 | SpGCas9 CrisprNuclease object |
targetLength | An S4 class to represent a CRISPR nuclease. |
targetLength-method | An S4 class to represent a CRISPR nickase. |
targetLength-method | An S4 class to represent a CRISPR nuclease. |
targetType | An S4 class to represent a nuclease. |
targetType-method | An S4 class to represent a nuclease. |
targetType<- | An S4 class to represent a nuclease. |
targetType<--method | An S4 class to represent a nuclease. |
weights | An S4 class to represent a nuclease. |
weights-method | An S4 class to represent a nickase |
weights-method | An S4 class to represent a nuclease. |
weights<- | An S4 class to represent a nuclease. |
weights<--method | An S4 class to represent a nickase |
weights<--method | An S4 class to represent a nuclease. |