addCompositeScores      Add on-target composite score to a GuideSet
                        object.
addConservationScores   Add on-target composite score to a GuideSet
                        object.
addDistanceToTss        Add distance to TSS for a specificed TSS id
addEditedAlleles        To add edited alleles for a CRISPR base editing
                        GuideSet
addEditingSites         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
addIsoformAnnotation    Add isoform-specific annotation to a GuideSet
                        object
addNtcs                 Add non-targeting control (NTC) sequences to
                        GuideSet
addOffTargetScores      Add CFD and MIT scores to a GuideSet object.
addOnTargetScores       Add on-target scores to a GuideSet object.
addOpsBarcodes          Add optical pooled screening (OPS) barcodes
addPamScores            Add PAM scores to a GuideSet object.
addPfamDomains          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
addRestrictionEnzymes   Restriction enzyme recognition sites in spacer
                        sequences
addSequenceFeatures     Add spacer sequence feature annotation columns
                        to a GuideSet object
addSNPAnnotation        Add SNP annotation to a GuideSet object
addSpacerAlignments     Functions for finding and characterizing on-
                        and off-targets of spacer sequences.
addTssAnnotation        Add TSS context annotation to a GuideSet object
addTxTable              Add a gene-specific transcript table to a
                        GuideSet object.
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.
designCompleteAnnotation
                        One-step gRNA design and annotation function
designOpsLibrary        Design gRNA library for optical pooled
                        screening
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
getBarcodeDistanceMatrix
                        Get distance between query and target sets of
                        barcodes
getConsensusIsoform     Get the genomic ranges of a consensus isoform
getMrnaSequences        Retrieve mRNA sequences
getPreMrnaSequences     Retrieve pre-mRNA sequences
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
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.
pamOrientation          An S4 class to store pairs of CRISPR gRNA
                        sequences.
preparePfamTable        Obtain Pfam domains from biomaRt
queryTss                Convenience function to search for TSS
                        coordinates.
queryTxObject           Convenience function to search for gene
                        coordinates.
rankSpacers             Recommended gRNA ranking
removeRepeats           Remove GuideSet gRNAs that overlap repeat
                        elements
removeSpacersWithSecondaryTargets
                        Remove gRNAs targeting secondary targets
snpObjectExample        Example of a GRanges object containing SNPs
tssObjectExample        Example of a GRanges object containing TSS
                        coordinates
TxDb2GRangesList        Convert a TxDb object into a GRangesList
updateOpsLibrary        Update OPS library with additional gRNAs
validateOpsLibrary      Validate gRNA library for optical pooled
                        screening
