Comprehensive design of CRISPR gRNAs for nucleases and base editors


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Documentation for package ‘crisprDesign’ version 1.6.0

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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.
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