NAMESPACE

# Generated by roxygen2: do not edit by hand

export(binContinuousListsAsDiscrete)
export(bootstrapFasta)
export(callPartis)
export(checkColumn)
export(collapseAlleles)
export(compareAcidityDistributions)
export(compareAliphaticIndexDistributions)
export(compareAromaticityDistributions)
export(compareAtchleyFactorDistributions)
export(compareBasicityDistributions)
export(compareBulkinessDistributions)
export(compareCDR3LengthDistributions)
export(compareCDR3PairwiseDistanceDistributions)
export(compareCategoricalDistributions)
export(compareChargeDistributions)
export(compareColdspotCountDistributions)
export(compareCollessLikeIndices)
export(compareCopheneticIndices)
export(compareDGene3PrimeDeletionLengthDistributions)
export(compareDGene5PrimeDeletionLengthDistributions)
export(compareDGeneDistributions)
export(compareDJInsertionMatrices)
export(compareDeletionLengths)
export(compareDistanceFromGermlineToSequenceDistributions)
export(compareGCContentDistributions)
export(compareGRAVYDistributions)
export(compareGeneUsage)
export(compareGermlineGeneDistributions)
export(compareHillNumbers)
export(compareHotspotCountDistributions)
export(compareInFramePercentages)
export(compareJGene5PrimeDeletionLengthDistributions)
export(compareJGeneDistributions)
export(compareJointGeneDistributions)
export(compareKideraFactorDistributions)
export(compareMutabilityModels)
export(compareNNDistanceDistributions)
export(comparePairwiseDistanceDistributions)
export(comparePerGeneMutationRates)
export(comparePerGenePerPositionMutationRates)
export(comparePolarityDistributions)
export(comparePositionalDistanceBetweenMutationsDistributions)
export(compareRepertoires)
export(compareSackinIndices)
export(compareSelectionEstimates)
export(compareSubstitutionAndMutabilityModels)
export(compareVDInsertionMatrices)
export(compareVDJDistributions)
export(compareVGene3PrimeDeletionLengthDistributions)
export(compareVGeneDistributions)
export(compareVJInsertionMatrices)
export(convertNucleobasesToAminoAcids)
export(convertNucleobasesToAminoAcidsBySequence)
export(determineComparisonMethod)
export(doComparison)
export(doNNSubsamplingBatchStep)
export(extractCDR3CodonStartPositions)
export(filterAminoAcidSequences)
export(getAcidityDistribution)
export(getAliphaticIndex)
export(getAliphaticIndexDistribution)
export(getAminoAcidDistribution)
export(getAminoAcidProperties)
export(getAndPrintComparison)
export(getApproximateDistribution)
export(getApproximateNearestNeighborDistribution)
export(getAromaticityDistribution)
export(getAtchleyFactorDistribution)
export(getAtchleyFactorDistributions)
export(getAutomaticAverageDivergence)
export(getAverageDivergence)
export(getBasicityDistribution)
export(getBulkinessDistribution)
export(getCDR3LengthDistribution)
export(getCDR3PairwiseDistanceDistribution)
export(getChargeDistribution)
export(getColdspotCount)
export(getColdspotCountDistribution)
export(getCollessLikeIndex)
export(getColumnSequences)
export(getColumnValues)
export(getContinuousJSDivergenceByIntegration)
export(getCopheneticIndex)
export(getDGene3PrimeDeletionLengthDistribution)
export(getDGene5PrimeDeletionLengthDistribution)
export(getDJInsertionLengthDistribution)
export(getDJInsertionMatrix)
export(getDeletionLengths)
export(getDistanceFromGermlineToSequenceDistribution)
export(getDistanceMatrix)
export(getDistanceVector)
export(getDistancesFromGermlineToSequence)
export(getFullPartisAnnotation)
export(getGCContent)
export(getGCContentDistribution)
export(getGRAVYDistribution)
export(getGridDims)
export(getHotspotCount)
export(getHotspotCountDistribution)
export(getIgBlastAnnotations)
export(getInFramePercentage)
export(getInsertionLengths)
export(getInsertionMatrix)
export(getJGene3PrimeDeletionLengthDistribution)
export(getJGene5PrimeDeletionLengthDistribution)
export(getJSDivergence)
export(getJointGeneTable)
export(getKideraFactorDistributions)
export(getKideraFactorsBySequence)
export(getMarkovMatrix)
export(getMotifCount)
export(getMutabilityModel)
export(getMutationInfo)
export(getNearestNeighborDistances)
export(getNearestNeighborDistribution)
export(getPairwiseDistanceDistribution)
export(getPartisAnnotations)
export(getPartisAnnotationsFromStrings)
export(getPartisPartitions)
export(getPartisSimulation)
export(getPerGeneMutationRates)
export(getPerGenePerPositionMutationRates)
export(getPolarityDistribution)
export(getPositionalDistanceBetweenMutationsDistribution)
export(getPositionalDistancesBetweenMutationsBySequence)
export(getSackinIndex)
export(getSelectionEstimate)
export(getSequenceListFromFasta)
export(getSpotCount)
export(getSubstitutionModel)
export(getSumOfAbsoluteDifferences)
export(getUnivariateDistributionDataTable)
export(getUsageTableFromFullList)
export(getVDInsertionLengthDistribution)
export(getVDInsertionMatrix)
export(getVGene3PrimeDeletionLengthDistribution)
export(getVGene5PrimeDeletionLengthDistribution)
export(getVJInsertionLengthDistribution)
export(getVJInsertionMatrix)
export(hasStopCodon)
export(hasUnrecognizedAminoAcids)
export(loadNewDatasets)
export(multiplot)
export(parsePythonDictionary)
export(plotAcidityDistribution)
export(plotAliphaticIndexDistribution)
export(plotAromaticityDistribution)
export(plotBasicityDistribution)
export(plotBulkinessDistribution)
export(plotCDR3LengthDistribution)
export(plotCDR3PairwiseDistanceDistribution)
export(plotChargeDistribution)
export(plotClusterSizeDistribution)
export(plotColdspotCountDistribution)
export(plotDGene3PrimeDeletionLengthDistribution)
export(plotDGene5PrimeDeletionLengthDistribution)
export(plotDJInsertionLengthDistribution)
export(plotDistanceFromGermlineToSequenceDistribution)
export(plotDistribution)
export(plotGCContentDistribution)
export(plotGRAVYDistribution)
export(plotHotspotCountDistribution)
export(plotJGene3PrimeDeletionLengthDistribution)
export(plotJGene5PrimeDeletionLengthDistribution)
export(plotNearestNeighborDistribution)
export(plotPairwiseDistanceDistribution)
export(plotPolarityDistribution)
export(plotPositionalDistanceBetweenMutationsDistribution)
export(plotUnivariateDistributions)
export(plotVDInsertionLengthDistribution)
export(plotVGene3PrimeDeletionLengthDistribution)
export(plotVGene5PrimeDeletionLengthDistribution)
export(plotVJInsertionLengthDistribution)
export(preventOutputOverwrite)
export(readPartisAnnotations)
export(removeEmptyStrings)
export(resampleData)
export(standardizeList)
export(subsample)
export(subsampleVector)
export(subsetToQuantileRange)
import(ggplot2)
import(methods)
import(stats)
import(utils)
importFrom(Biostrings,DNAStringSet)
importFrom(Biostrings,vcountPattern)
importFrom(CollessLike,colless.like.index)
importFrom(CollessLike,cophen.index)
importFrom(CollessLike,sackin.index)
importFrom(Peptides,aIndex)
importFrom(Peptides,kideraFactors)
importFrom(alakazam,aminoAcidProperties)
importFrom(alakazam,calcDiversity)
importFrom(alakazam,checkColumns)
importFrom(alakazam,gravy)
importFrom(ape,GC.content)
importFrom(ape,as.DNAbin)
importFrom(crayon,green)
importFrom(crayon,yellow)
importFrom(data.table,as.data.table)
importFrom(data.table,data.table)
importFrom(data.table,fread)
importFrom(data.table,fwrite)
importFrom(dplyr,last)
importFrom(entropy,KL.empirical)
importFrom(grid,grid.layout)
importFrom(grid,grid.newpage)
importFrom(grid,pushViewport)
importFrom(grid,viewport)
importFrom(jsonlite,fromJSON)
importFrom(magrittr,"%$%")
importFrom(magrittr,"%>%")
importFrom(magrittr,extract)
importFrom(seqinr,read.fasta)
importFrom(seqinr,translate)
importFrom(seqinr,write.fasta)
importFrom(shazam,calcBaseline)
importFrom(shazam,createMutabilityMatrix)
importFrom(shazam,createSubstitutionMatrix)
importFrom(shazam,distToNearest)
importFrom(shazam,findThreshold)
importFrom(shazam,summarizeBaseline)
importFrom(stringdist,stringdistmatrix)
importFrom(stringr,str_split)
importFrom(stringr,str_sub)
importFrom(textmineR,CalcJSDivergence)
importFrom(yaml,yaml.load)
importFrom(yaml,yaml.load_file)