Package: crisprBase 1.9.0

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:Jean-Philippe Fortin [aut, cre]

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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

Datasets:

AsCas12a - AsCas12a CrisprNuclease object
BE4max - BE4max BaseEditor object
CasRx - CasRx 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-1.9.0(bioc 3.20)crisprBase-1.8.0(bioc 3.19)

bioconductor-package

54 exports 1.90 score 27 dependencies 6 dependents

Last updated 2 months agofrom:1cc9791a89

Exports:annotateMismatches BaseEditor baseEditorName baseEditorName<-CrisprNickase CrisprNuclease cutSites editingStrand editingStrand<-editingWeights editingWeights<-extractPamFromTarget extractProtospacerFromTarget getAvailableCrisprNucleases getCutSiteFromPamSite getCutSiteRanges getEditingSiteFromPamSite getPamRanges getProtospacerRanges getTargetRanges hasSpacerGap isCutting isDnase isRnase metadata metadata<-motifLength motifs Nickase nickaseName nickaseName<-nickingStrand nickingStrand<-Nuclease nucleaseName nucleaseName<-pamIndices pamLength pams pamSide pamSide<-plotEditingWeights prototypeSequence show spacerGap spacerGap<-spacerIndices spacerLength spacerLength<-targetLength targetType targetType<-weights weights<-

Dependencies:askpass BiocGenerics Biostrings cli crayon curl GenomeInfoDb GenomeInfoDbData GenomicRanges glue httr IRanges jsonlite lifecycle magrittr mime openssl R6 rlang S4Vectors stringi stringr sys UCSC.utils vctrs XVector zlibbioc

Base functions and classes for CRISPR gRNA design

Jean-Philippe Fortin

Rendered fromcrisprBase.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2022-10-17
Started: 2021-09-21

Citation

Development and contributors

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
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