# Base functions and classes for CRISPR gRNA design

## Documentation for package ‘crisprBase’ version 1.12.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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.
Csm | Csm CrisprNuclease object
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 --

MAD7 | MAD7 CrisprNuclease object
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.