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. |
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. |
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. |
designCompleteAnnotation | One-step gRNA design and annotation function |
designOpsLibrary | Design gRNA library for optical pooled screening |
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. |
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 |
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. |
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. |
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. |
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 |
removeRepeats-method | Remove GuideSet gRNAs that overlap repeat elements |
removeSpacersWithSecondaryTargets | Remove gRNAs targeting secondary targets |
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. |
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. |
updateOpsLibrary | Update OPS library with additional gRNAs |
validateOpsLibrary | Validate gRNA library for optical pooled screening |