# Comprehensive design of CRISPR gRNAs for nucleases and base editors

## Documentation for package ‘crisprDesign’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G O P Q R S T U V

## -- 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.
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
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
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 storing the range of all 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.

## -- 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
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.
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

## -- U --

updateOpsLibrary | Update OPS library with additional gRNAs

## -- V --

validateOpsLibrary | Validate gRNA library for optical pooled screening