addCompositeScores	addCompositeScores
addCompositeScores,GuideSet-method	addCompositeScores
addCompositeScores,NULL-method	addCompositeScores
addCompositeScores,PairedGuideSet-method	addCompositeScores
addConservationScores	addConservationScores
addConservationScores,GuideSet-method	addConservationScores
addConservationScores,NULL-method	addConservationScores
addConservationScores,PairedGuideSet-method	addConservationScores
addCutSites	GuideSet-class
addCutSites,GuideSet-method	GuideSet-class
addDistanceToTss	addDistanceToTss
addDistanceToTss,GuideSet-method	addDistanceToTss
addDistanceToTss,NULL-method	addIsoformAnnotation
addDistanceToTss,PairedGuideSet-method	addDistanceToTss
addEditedAlleles	addEditedAlleles
addEditingSites	addEditingSites
addEditingSites,GuideSet-method	addEditingSites
addEditingSites,NULL-method	addEditingSites
addEditingSites,PairedGuideSet-method	addEditingSites
addExonTable	addExonTable
addGeneAnnotation	addGeneAnnotation
addGeneAnnotation,GuideSet-method	addGeneAnnotation
addGeneAnnotation,NULL-method	addSNPAnnotation
addGeneAnnotation,PairedGuideSet-method	addGeneAnnotation
addIsoformAnnotation	addIsoformAnnotation
addIsoformAnnotation,GuideSet-method	addIsoformAnnotation
addIsoformAnnotation,NULL-method	addIsoformAnnotation
addIsoformAnnotation,PairedGuideSet-method	addIsoformAnnotation
addNtcs	addNtcs
addNtcs,GuideSet-method	addNtcs
addNtcs,NULL-method	addNtcs
addNtcs,PairedGuideSet-method	addNtcs
addOffTargetScores	addOffTargetScores
addOffTargetScores,GuideSet-method	addOffTargetScores
addOffTargetScores,NULL-method	addOffTargetScores
addOffTargetScores,PairedGuideSet-method	addOffTargetScores
addOnTargetScores	addOnTargetScores
addOnTargetScores,GuideSet-method	addOnTargetScores
addOnTargetScores,NULL-method	addOnTargetScores
addOnTargetScores,PairedGuideSet-method	addOnTargetScores
addOpsBarcodes	addOpsBarcodes
addPamScores	addPamScores
addPamScores,GuideSet-method	addPamScores
addPamScores,NULL-method	addPamScores
addPamScores,PairedGuideSet-method	addPamScores
addPfamDomains	addPfamDomains
addPfamDomains,GuideSet-method	addPfamDomains
addPfamDomains,NULL-method	addPfamDomains
addPfamDomains,PairedGuideSet-method	addPfamDomains
addReinitiationFlag	addReinitiationFlag
addRepeats	addRepeats
addRepeats,GuideSet-method	addRepeats
addRepeats,NULL-method	addRepeats
addRepeats,PairedGuideSet-method	addRepeats
addRestrictionEnzymes	addRestrictionEnzymes
addRestrictionEnzymes,GuideSet-method	addRestrictionEnzymes
addRestrictionEnzymes,NULL-method	addRestrictionEnzymes
addRestrictionEnzymes,PairedGuideSet-method	addRestrictionEnzymes
addSequenceFeatures	addSequenceFeatures
addSequenceFeatures,GuideSet-method	addSequenceFeatures
addSequenceFeatures,NULL-method	addSequenceFeatures
addSequenceFeatures,PairedGuideSet-method	addSequenceFeatures
addSNPAnnotation	addSNPAnnotation
addSNPAnnotation,GuideSet-method	addSNPAnnotation
addSNPAnnotation,NULL-method	addSNPAnnotation
addSNPAnnotation,PairedGuideSet-method	addSNPAnnotation
addSpacerAlignments	addSpacerAlignments
addSpacerAlignments,GuideSet-method	addSpacerAlignments
addSpacerAlignments,NULL-method	addSpacerAlignments
addSpacerAlignments,PairedGuideSet-method	addSpacerAlignments
addSpacerAlignmentsIterative	addSpacerAlignments
addSpacerAlignmentsIterative,GuideSet-method	addSpacerAlignments
addSpacerAlignmentsIterative,NULL-method	addSpacerAlignments
addSpacerAlignmentsIterative,PairedGuideSet-method	addSpacerAlignments
addTssAnnotation	addTssAnnotation
addTssAnnotation,GuideSet-method	addTssAnnotation
addTssAnnotation,NULL-method	addTssAnnotation
addTssAnnotation,PairedGuideSet-method	addTssAnnotation
addTxTable	addTxTable
alignments	GuideSet-class
alignments,GuideSet-method	GuideSet-class
alignments<-	GuideSet-class
alignments<-,GuideSet-method	GuideSet-class
bsgenome	GuideSet-class
bsgenome,GuideSet-method	GuideSet-class
completeSpacers	completeSpacers
convertToMinMaxGRanges	convertToMinMaxGRanges
convertToProtospacerGRanges	convertToProtospacerGRanges
crisprNuclease	GuideSet-class
crisprNuclease,GuideSet-method	GuideSet-class
crisprNuclease,PairedGuideSet-method	PairedGuideSet-class
customSequences	GuideSet-class
customSequences,GuideSet-method	GuideSet-class
cutLength	PairedGuideSet-class
cutLength,PairedGuideSet-method	PairedGuideSet-class
cutSites,GuideSet-method	GuideSet-class
cutSites,PairedGuideSet-method	PairedGuideSet-class
designCompleteAnnotation	designCompleteAnnotation
designOpsLibrary	designOpsLibrary
editedAlleles	GuideSet-class
editedAlleles,GuideSet-method	GuideSet-class
enzymeAnnotation	GuideSet-class
enzymeAnnotation,GuideSet-method	GuideSet-class
enzymeAnnotation<-	GuideSet-class
enzymeAnnotation<-,GuideSet-method	GuideSet-class
exonTable	GuideSet-class
exonTable,GuideSet-method	GuideSet-class
findSpacerPairs	findSpacerPairs
findSpacers	findSpacers
flattenGuideSet	flattenGuideSet
geneAnnotation	GuideSet-class
geneAnnotation,GuideSet-method	GuideSet-class
geneAnnotation<-	GuideSet-class
geneAnnotation<-,GuideSet-method	GuideSet-class
getBarcodeDistanceMatrix	getBarcodeDistanceMatrix
getConsensusIsoform	getConsensusIsoform
getMrnaSequences	getMrnaSequences
getPAMSequence	completeSpacers
getPAMSiteFromStartAndEnd	completeSpacers
getPreMrnaSequences	getPreMrnaSequences
getSpacerAlignments	addSpacerAlignments
getSpacerSequence	completeSpacers
getTssObjectFromTxObject	getTssObjectFromTxObject
getTxDb	getTxDb
getTxInfoDataFrame	getTxInfoDataFrame
grListExample	grListExample
grRepeatsExample	grRepeatsExample
GuideSet	GuideSet-class
GuideSet-class	GuideSet-class
GuideSet2DataFrames	GuideSet2DataFrames
guideSetExample	guideSetExample
guideSetExampleFullAnnotation	guideSetExampleFullAnnotation
guideSetExampleWithAlignments	guideSetExampleWithAlignments
mcols	reexports
offTargets	GuideSet-class
offTargets,GuideSet-method	GuideSet-class
onTargets	GuideSet-class
onTargets,GuideSet-method	GuideSet-class
PairedGuideSet	PairedGuideSet-class
PairedGuideSet-class	PairedGuideSet-class
pamDistance	PairedGuideSet-class
pamDistance,PairedGuideSet-method	PairedGuideSet-class
pamLength,GuideSet-method	GuideSet-class
pamLength,PairedGuideSet-method	PairedGuideSet-class
pamOrientation	PairedGuideSet-class
pamOrientation,PairedGuideSet-method	PairedGuideSet-class
pams,GuideSet-method	GuideSet-class
pams,PairedGuideSet-method	PairedGuideSet-class
pamSide,GuideSet-method	GuideSet-class
pamSide,PairedGuideSet-method	PairedGuideSet-class
pamSites	GuideSet-class
pamSites,GuideSet-method	GuideSet-class
pamSites,PairedGuideSet-method	PairedGuideSet-class
preparePfamTable	preparePfamTable
protospacers	GuideSet-class
protospacers,GuideSet-method	GuideSet-class
protospacers,PairedGuideSet-method	PairedGuideSet-class
prototypeSequence,GuideSet-method	GuideSet-class
queryTss	queryTss
queryTxObject	queryTxObject
rankSpacers	rankSpacers
reexports	reexports
removeRepeats	removeRepeats
removeRepeats,GuideSet-method	removeRepeats
removeRepeats,NULL-method	removeRepeats
removeRepeats,PairedGuideSet-method	removeRepeats
removeSpacersWithSecondaryTargets	removeSpacersWithSecondaryTargets
seqnames	reexports
snpObjectExample	snpObjectExample
snps	GuideSet-class
snps,GuideSet-method	GuideSet-class
snps<-	GuideSet-class
snps<-,GuideSet-method	GuideSet-class
spacerDistance	PairedGuideSet-class
spacerDistance,PairedGuideSet-method	PairedGuideSet-class
spacerLength,GuideSet-method	GuideSet-class
spacerLength,PairedGuideSet-method	PairedGuideSet-class
spacers	GuideSet-class
spacers,GuideSet-method	GuideSet-class
spacers,PairedGuideSet-method	PairedGuideSet-class
targetOrigin	GuideSet-class
targetOrigin,GuideSet-method	GuideSet-class
tssAnnotation	GuideSet-class
tssAnnotation,GuideSet-method	GuideSet-class
tssAnnotation<-	GuideSet-class
tssAnnotation<-,GuideSet-method	GuideSet-class
tssObjectExample	tssObjectExample
TxDb2GRangesList	TxDb2GRangesList
txTable	GuideSet-class
txTable,GuideSet-method	GuideSet-class
updateOpsLibrary	updateOpsLibrary
validateOpsLibrary	validateOpsLibrary
