Comprehensive design of CRISPR gRNAs for nucleases and base editors

Documentation for package ‘crisprDesign’ version 1.11.0

Help Pages

-- A --

addCompositeScores	Add on-target composite score to a GuideSet object.
addCompositeScores-method	Add on-target composite score to a GuideSet object.
addConservationScores	Add on-target composite score to a GuideSet object.
addConservationScores-method	Add on-target composite score to a GuideSet object.
addCrispraiScores	Add CRISPRa/CRISPRi on-target scores to a GuideSet object.
addCrispraiScores-method	Add CRISPRa/CRISPRi on-target scores to a GuideSet object.
addCutSites	An S4 class to store CRISPR gRNA sequences with modular annotations.
addCutSites-method	An S4 class to store CRISPR gRNA sequences with modular annotations.
addDistanceToTss	Add distance to TSS for a specificed TSS id
addDistanceToTss-method	Add distance to TSS for a specificed TSS id
addDistanceToTss-method	Add isoform-specific annotation to a GuideSet object
addEditedAlleles	To add edited alleles for a CRISPR base editing GuideSet
addEditingSites	Add optimal editing site for base editing gRNAs.
addEditingSites-method	Add optimal editing site for base editing gRNAs.
addExonTable	Add a gene-specific exon table to a GuideSet object.
addGeneAnnotation	Add gene context annotation to a GuideSet object
addGeneAnnotation-method	Add gene context annotation to a GuideSet object
addGeneAnnotation-method	Add SNP annotation to a GuideSet object
addIsoformAnnotation	Add isoform-specific annotation to a GuideSet object
addIsoformAnnotation-method	Add isoform-specific annotation to a GuideSet object
addNtcs	Add non-targeting control (NTC) sequences to GuideSet
addNtcs-method	Add non-targeting control (NTC) sequences to GuideSet
addOffTargetScores	Add CFD and MIT scores to a GuideSet object.
addOffTargetScores-method	Add CFD and MIT scores to a GuideSet object.
addOnTargetScores	Add on-target scores to a GuideSet object.
addOnTargetScores-method	Add on-target scores to a GuideSet object.
addOpsBarcodes	Add optical pooled screening (OPS) barcodes
addPamScores	Add PAM scores to a GuideSet object.
addPamScores-method	Add PAM scores to a GuideSet object.
addPfamDomains	Add Pfam domains annotation to GuideSet object
addPfamDomains-method	Add Pfam domains annotation to GuideSet object
addReinitiationFlag	Add a logical flag for gRNAs leading to potential reinitiation
addRepeats	Annotate a GuideSet object with repeat elements
addRepeats-method	Annotate a GuideSet object with repeat elements
addRestrictionEnzymes	Restriction enzyme recognition sites in spacer sequences
addRestrictionEnzymes-method	Restriction enzyme recognition sites in spacer sequences
addSequenceFeatures	Add spacer sequence feature annotation columns to a GuideSet object
addSequenceFeatures-method	Add spacer sequence feature annotation columns to a GuideSet object
addSNPAnnotation	Add SNP annotation to a GuideSet object
addSNPAnnotation-method	Add SNP annotation to a GuideSet object
addSpacerAlignments	Functions for finding and characterizing on- and off-targets of spacer sequences.
addSpacerAlignments-method	Functions for finding and characterizing on- and off-targets of spacer sequences.
addSpacerAlignmentsIterative	Functions for finding and characterizing on- and off-targets of spacer sequences.
addSpacerAlignmentsIterative-method	Functions for finding and characterizing on- and off-targets of spacer sequences.
addTssAnnotation	Add TSS context annotation to a GuideSet object
addTssAnnotation-method	Add TSS context annotation to a GuideSet object
addTxTable	Add a gene-specific transcript table to a GuideSet object.
alignments	An S4 class to store CRISPR gRNA sequences with modular annotations.
alignments-method	An S4 class to store CRISPR gRNA sequences with modular annotations.
alignments<-	An S4 class to store CRISPR gRNA sequences with modular annotations.
alignments<--method	An S4 class to store CRISPR gRNA sequences with modular annotations.

-- B --

bsgenome	An S4 class to store CRISPR gRNA sequences with modular annotations.
bsgenome-method	An S4 class to store CRISPR gRNA sequences with modular annotations.

-- C --

completeSpacers	Get complete spacer information
convertToMinMaxGRanges	Convert a GuideSet object into a GRanges containing the range of all targeting gRNAs.
convertToProtospacerGRanges	Convert PAM site coordinates to protospacer start and end coordinates
crisprNuclease	An S4 class to store CRISPR gRNA sequences with modular annotations.
crisprNuclease-method	An S4 class to store CRISPR gRNA sequences with modular annotations.
crisprNuclease-method	An S4 class to store pairs of CRISPR gRNA sequences.
customSequences	An S4 class to store CRISPR gRNA sequences with modular annotations.
customSequences-method	An S4 class to store CRISPR gRNA sequences with modular annotations.
cutLength	An S4 class to store pairs of CRISPR gRNA sequences.
cutLength-method	An S4 class to store pairs of CRISPR gRNA sequences.
cutSites-method	An S4 class to store CRISPR gRNA sequences with modular annotations.
cutSites-method	An S4 class to store pairs of CRISPR gRNA sequences.

-- D --

designCompleteAnnotation	One-step gRNA design and annotation function
designOpsLibrary	Design gRNA library for optical pooled screening

-- E --

editedAlleles	An S4 class to store CRISPR gRNA sequences with modular annotations.
editedAlleles-method	An S4 class to store CRISPR gRNA sequences with modular annotations.
enzymeAnnotation	An S4 class to store CRISPR gRNA sequences with modular annotations.
enzymeAnnotation-method	An S4 class to store CRISPR gRNA sequences with modular annotations.
enzymeAnnotation<-	An S4 class to store CRISPR gRNA sequences with modular annotations.
enzymeAnnotation<--method	An S4 class to store CRISPR gRNA sequences with modular annotations.
exonTable	An S4 class to store CRISPR gRNA sequences with modular annotations.
exonTable-method	An S4 class to store CRISPR gRNA sequences with modular annotations.

-- F --

findSpacerPairs	Find pairs of CRISPR gRNA spacers from a pair of genomic regions.
findSpacers	Find CRISPR gRNA spacer sequences from a set of DNA sequences.
flattenGuideSet	Create a list of annotation tables from a GuideSet object

-- G --

geneAnnotation	An S4 class to store CRISPR gRNA sequences with modular annotations.
geneAnnotation-method	An S4 class to store CRISPR gRNA sequences with modular annotations.
geneAnnotation<-	An S4 class to store CRISPR gRNA sequences with modular annotations.
geneAnnotation<--method	An S4 class to store CRISPR gRNA sequences with modular annotations.
getBarcodeDistanceMatrix	Get distance between query and target sets of barcodes
getConsensusIsoform	Get the genomic ranges of a consensus isoform
getMrnaSequences	Retrieve mRNA sequences
getPAMSequence	Get complete spacer information
getPAMSiteFromStartAndEnd	Get complete spacer information
getPreMrnaSequences	Retrieve pre-mRNA sequences
getSpacerAlignments	Functions for finding and characterizing on- and off-targets of spacer sequences.
getSpacerSequence	Get complete spacer information
getTssObjectFromTxObject	Extract TSS coordinates from a gene model object
getTxDb	getTxDb
getTxInfoDataFrame	To obtain a DataFrame of transcript-specific CDS and mRNA coordinates
grListExample	Example of a TxDb object converted to a GRangesList
grRepeatsExample	Example of a GRanges object containing repeat elements
GuideSet	An S4 class to store CRISPR gRNA sequences with modular annotations.
GuideSet-class	An S4 class to store CRISPR gRNA sequences with modular annotations.
GuideSet2DataFrames	Create a list of annotation tables from a GuideSet object
guideSetExample	Example of a GuideSet object storing gRNA sequences targeting the CDS of IQSEC3
guideSetExampleFullAnnotation	Example of a fully-annotated GuideSet object storing gRNA sequences targeting the CDS of IQSEC3
guideSetExampleWithAlignments	Example of a GuideSet object storing gRNA sequences targeting the CDS of IQSEC3 with off-target alignments.

-- O --

offTargets	An S4 class to store CRISPR gRNA sequences with modular annotations.
offTargets-method	An S4 class to store CRISPR gRNA sequences with modular annotations.
onTargets	An S4 class to store CRISPR gRNA sequences with modular annotations.
onTargets-method	An S4 class to store CRISPR gRNA sequences with modular annotations.

-- P --

PairedGuideSet	An S4 class to store pairs of CRISPR gRNA sequences.
PairedGuideSet-class	An S4 class to store pairs of CRISPR gRNA sequences.
pamDistance	An S4 class to store pairs of CRISPR gRNA sequences.
pamDistance-method	An S4 class to store pairs of CRISPR gRNA sequences.
pamLength-method	An S4 class to store CRISPR gRNA sequences with modular annotations.
pamLength-method	An S4 class to store pairs of CRISPR gRNA sequences.
pamOrientation	An S4 class to store pairs of CRISPR gRNA sequences.
pamOrientation-method	An S4 class to store pairs of CRISPR gRNA sequences.
pams-method	An S4 class to store CRISPR gRNA sequences with modular annotations.
pams-method	An S4 class to store pairs of CRISPR gRNA sequences.
pamSide-method	An S4 class to store CRISPR gRNA sequences with modular annotations.
pamSide-method	An S4 class to store pairs of CRISPR gRNA sequences.
pamSites	An S4 class to store CRISPR gRNA sequences with modular annotations.
pamSites-method	An S4 class to store CRISPR gRNA sequences with modular annotations.
pamSites-method	An S4 class to store pairs of CRISPR gRNA sequences.
preparePfamTable	Obtain Pfam domains from biomaRt
protospacers	An S4 class to store CRISPR gRNA sequences with modular annotations.
protospacers-method	An S4 class to store CRISPR gRNA sequences with modular annotations.
protospacers-method	An S4 class to store pairs of CRISPR gRNA sequences.
prototypeSequence-method	An S4 class to store CRISPR gRNA sequences with modular annotations.

-- Q --

queryTss	Convenience function to search for TSS coordinates.
queryTxObject	Convenience function to search for gene coordinates.

-- R --

rankSpacers	Recommended gRNA ranking
removeRepeats	Remove GuideSet gRNAs that overlap repeat elements
removeRepeats-method	Remove GuideSet gRNAs that overlap repeat elements
removeSpacersWithSecondaryTargets	Remove gRNAs targeting secondary targets

-- S --

snps	An S4 class to store CRISPR gRNA sequences with modular annotations.
snps-method	An S4 class to store CRISPR gRNA sequences with modular annotations.
snps<-	An S4 class to store CRISPR gRNA sequences with modular annotations.
snps<--method	An S4 class to store CRISPR gRNA sequences with modular annotations.
spacerDistance	An S4 class to store pairs of CRISPR gRNA sequences.
spacerDistance-method	An S4 class to store pairs of CRISPR gRNA sequences.
spacerLength-method	An S4 class to store CRISPR gRNA sequences with modular annotations.
spacerLength-method	An S4 class to store pairs of CRISPR gRNA sequences.
spacers	An S4 class to store CRISPR gRNA sequences with modular annotations.
spacers-method	An S4 class to store CRISPR gRNA sequences with modular annotations.
spacers-method	An S4 class to store pairs of CRISPR gRNA sequences.

-- T --

targetOrigin	An S4 class to store CRISPR gRNA sequences with modular annotations.
targetOrigin-method	An S4 class to store CRISPR gRNA sequences with modular annotations.
tssAnnotation	An S4 class to store CRISPR gRNA sequences with modular annotations.
tssAnnotation-method	An S4 class to store CRISPR gRNA sequences with modular annotations.
tssAnnotation<-	An S4 class to store CRISPR gRNA sequences with modular annotations.
tssAnnotation<--method	An S4 class to store CRISPR gRNA sequences with modular annotations.
tssObjectExample	Example of a GRanges object containing TSS coordinates
TxDb2GRangesList	Convert a TxDb object into a GRangesList
txTable	An S4 class to store CRISPR gRNA sequences with modular annotations.
txTable-method	An S4 class to store CRISPR gRNA sequences with modular annotations.

-- U --

updateOpsLibrary

Update OPS library with additional gRNAs

-- V --

validateOpsLibrary

Validate gRNA library for optical pooled screening