Base functions and classes for CRISPR gRNA design

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Documentation for package ‘crisprBase’ version 1.2.0

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A B C E G H I M N P R S T W

-- A --

annotateMismatches Annotate mismatches between spacer and protospacer sequences
AsCas12a AsCas12a CrisprNuclease object

-- B --

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

-- C --

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.

-- E --

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

-- G --

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

-- H --

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.

-- I --

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.

-- M --

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.

-- N --

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.

-- P --

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.

-- R --

restrictionEnzymes List of Nuclease objects representing common restriction enzymes

-- S --

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

-- T --

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.

-- W --

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.