# Generated by roxygen2: do not edit by hand

export(calculateKmerEnrichment)
export(calculateKmerScores)
export(calculateLocalConsistency)
export(calculateMotifEnrichment)
export(calculateTranscriptMC)
export(checkKmers)
export(computeKmerEnrichment)
export(createKmerMotif)
export(createMatrixMotif)
export(drawVolcanoPlot)
export(empiricalEnrichmentMeanCDF)
export(generateIUPACByKmers)
export(generateIUPACByMatrix)
export(generateKmers)
export(generateKmersFromIUPAC)
export(generatePermutedEnrichments)
export(geometricMean)
export(getMotifById)
export(getMotifByRBP)
export(getMotifs)
export(getPPM)
export(initIUPAClookupTable)
export(motifsMetaInfo)
export(pCombine)
export(permTestGeometricMean)
export(runKmerSPMA)
export(runKmerTSMA)
export(runMatrixSPMA)
export(runMatrixTSMA)
export(scoreSequences)
export(scoreSpectrum)
export(scoreTranscripts)
export(setMotifs)
export(spectrumClassifier)
export(subdivideData)
exportClasses(RBPMotif)
exportClasses(SpectrumScore)
exportMethods(motifHeptamers)
exportMethods(motifHexamers)
exportMethods(motifIUPAC)
exportMethods(motifId)
exportMethods(motifLength)
exportMethods(motifMatrix)
exportMethods(motifRbps)
exportMethods(motifSource)
exportMethods(motifSpecies)
exportMethods(motifType)
exportMethods(plot)
exportMethods(spectrumAdjRSquared)
exportMethods(spectrumConsistencyScore)
exportMethods(spectrumConsistencyScoreN)
exportMethods(spectrumConsistencyScorePValue)
exportMethods(spectrumDegree)
exportMethods(spectrumFStatistic)
exportMethods(spectrumFStatisticPValue)
exportMethods(spectrumResiduals)
exportMethods(spectrumSlope)
importFrom(BiocGenerics,width)
importFrom(Biostrings,BString)
importFrom(Biostrings,DNAStringSet)
importFrom(Biostrings,IUPAC_CODE_MAP)
importFrom(Biostrings,RNAStringSet)
importFrom(Biostrings,maskMotif)
importFrom(Biostrings,maxScore)
importFrom(Biostrings,oligonucleotideFrequency)
importFrom(GenomicRanges,gaps)
importFrom(Rcpp,sourceCpp)
importFrom(TFMPvalue,TFMpv2sc)
importFrom(dplyr,arrange)
importFrom(dplyr,filter)
importFrom(dplyr,select)
importFrom(ggplot2,aes)
importFrom(ggplot2,aes_string)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_line)
importFrom(ggplot2,element_text)
importFrom(ggplot2,geom_density)
importFrom(ggplot2,geom_histogram)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_smooth)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,geom_tile)
importFrom(ggplot2,geom_vline)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggplot_build)
importFrom(ggplot2,ggplot_gtable)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_alpha_manual)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_fill_gradient)
importFrom(ggplot2,scale_fill_gradient2)
importFrom(ggplot2,scale_size_manual)
importFrom(ggplot2,scale_x_discrete)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,xlab)
importFrom(ggplot2,ylab)
importFrom(ggseqlogo,ggseqlogo)
importFrom(gridExtra,arrangeGrob)
importFrom(methods,as)
importFrom(methods,is)
importFrom(methods,new)
importFrom(methods,setClass)
importFrom(methods,setClassUnion)
importFrom(methods,setGeneric)
importFrom(methods,setMethod)
importFrom(methods,signature)
importFrom(parallel,clusterExport)
importFrom(parallel,makeCluster)
importFrom(parallel,parLapply)
importFrom(scales,squish)
importFrom(stats,binom.test)
importFrom(stats,chisq.test)
importFrom(stats,fisher.test)
importFrom(stats,lm)
importFrom(stats,p.adjust)
importFrom(stats,pchisq)
importFrom(stats,pf)
importFrom(stats,pnorm)
importFrom(stats,poly)
importFrom(stats,predict)
importFrom(stats,pt)
importFrom(stats,qnorm)
importFrom(stats,sd)
importFrom(utils,data)
useDynLib(transite)
