# Generated by roxygen2: do not edit by hand

export("getContrasts<-")
export("getDOU<-")
export("getDTE<-")
export(.PostHoc)
export(DOTSeq)
export(DOTSeqDataSetsFromFeatureCounts)
export(DOTSeqDataSetsFromSummarizeOverlaps)
export(PostHoc)
export(calculateUsage)
export(countReads)
export(fitDOU)
export(fitResults)
export(getContrasts)
export(getDOU)
export(getDTE)
export(getExonicReads)
export(getORFs)
export(mapIDs)
export(modelType)
export(plotDOT)
export(posthoc)
export(simDOT)
export(testDOU)
exportClasses(DOTSeqDataSets)
exportClasses(DOUData)
exportClasses(DTEData)
exportClasses(PostHoc)
exportMethods("getContrasts<-")
exportMethods("getDOU<-")
exportMethods("getDTE<-")
exportMethods(fitResults)
exportMethods(getContrasts)
exportMethods(getDOU)
exportMethods(getDTE)
exportMethods(modelType)
exportMethods(posthoc)
exportMethods(show)
import(GenomeInfoDb)
import(GenomeInfoDbData)
import(GenomicAlignments)
import(GenomicRanges)
import(SummarizedExperiment)
importFrom(AnnotationDbi,keys)
importFrom(AnnotationDbi,loadDb)
importFrom(AnnotationDbi,saveDb)
importFrom(AnnotationDbi,select)
importFrom(BSgenome,getSeq)
importFrom(BiocGenerics,unlist)
importFrom(Biostrings,readDNAStringSet)
importFrom(DESeq2,"design<-")
importFrom(DESeq2,DESeq)
importFrom(DESeq2,DESeqDataSet)
importFrom(DESeq2,DESeqDataSetFromMatrix)
importFrom(DESeq2,design)
importFrom(DESeq2,lfcShrink)
importFrom(DESeq2,resultsNames)
importFrom(DESeq2,varianceStabilizingTransformation)
importFrom(GenomeInfoDb,isCircular)
importFrom(GenomeInfoDb,keepSeqlevels)
importFrom(GenomicAlignments,summarizeOverlaps)
importFrom(GenomicFeatures,cdsBy)
importFrom(GenomicFeatures,exonsBy)
importFrom(GenomicFeatures,genes)
importFrom(GenomicFeatures,mapFromTranscripts)
importFrom(GenomicFeatures,transcripts)
importFrom(IRanges,IRanges)
importFrom(IRanges,PartitioningByEnd)
importFrom(IRanges,heads)
importFrom(IRanges,tails)
importFrom(Rcpp,sourceCpp)
importFrom(Rsamtools,BamFile)
importFrom(Rsamtools,BamFileList)
importFrom(Rsamtools,ScanBamParam)
importFrom(Rsamtools,filterBam)
importFrom(Rsamtools,indexBam)
importFrom(Rsamtools,scanBam)
importFrom(Rsamtools,scanBamHeader)
importFrom(Rsamtools,sortBam)
importFrom(S4Vectors,"mcols<-")
importFrom(S4Vectors,"metadata<-")
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,Rle)
importFrom(S4Vectors,mcols)
importFrom(S4Vectors,metadata)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,subjectHits)
importFrom(ashr,ash)
importFrom(ashr,get_lfdr)
importFrom(ashr,get_lfsr)
importFrom(ashr,get_pm)
importFrom(ashr,get_qvalue)
importFrom(boot,inv.logit)
importFrom(data.table,":=")
importFrom(data.table,as.data.table)
importFrom(data.table,data.table)
importFrom(emmeans,contrast)
importFrom(emmeans,emmeans)
importFrom(glmmTMB,betabinomial)
importFrom(glmmTMB,fixef)
importFrom(glmmTMB,glmmTMB)
importFrom(glmmTMB,glmmTMBControl)
importFrom(grDevices,adjustcolor)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,dev.cur)
importFrom(grDevices,dev.new)
importFrom(grDevices,dev.off)
importFrom(grDevices,dev.size)
importFrom(graphics,abline)
importFrom(graphics,axis)
importFrom(graphics,barplot)
importFrom(graphics,hist)
importFrom(graphics,image)
importFrom(graphics,layout)
importFrom(graphics,legend)
importFrom(graphics,lines)
importFrom(graphics,mtext)
importFrom(graphics,par)
importFrom(graphics,plot)
importFrom(graphics,plot.new)
importFrom(graphics,plot.window)
importFrom(graphics,points)
importFrom(graphics,rect)
importFrom(graphics,strwidth)
importFrom(graphics,text)
importFrom(grid,grid.draw)
importFrom(grid,grid.newpage)
importFrom(methods,is)
importFrom(methods,new)
importFrom(methods,validObject)
importFrom(pbapply,pblapply)
importFrom(rtracklayer,import)
importFrom(stats,AIC)
importFrom(stats,aggregate)
importFrom(stats,anova)
importFrom(stats,as.dendrogram)
importFrom(stats,as.formula)
importFrom(stats,ave)
importFrom(stats,complete.cases)
importFrom(stats,cor.test)
importFrom(stats,density)
importFrom(stats,df)
importFrom(stats,dist)
importFrom(stats,hclust)
importFrom(stats,median)
importFrom(stats,model.matrix)
importFrom(stats,na.omit)
importFrom(stats,order.dendrogram)
importFrom(stats,p.adjust)
importFrom(stats,pnorm)
importFrom(stats,prcomp)
importFrom(stats,predict)
importFrom(stats,rbinom)
importFrom(stats,relevel)
importFrom(stats,rgamma)
importFrom(stats,rnbinom)
importFrom(stats,runif)
importFrom(stats,setNames)
importFrom(stats,smooth.spline)
importFrom(stats,var)
importFrom(txdbmaker,makeTxDbFromGFF)
importFrom(utils,combn)
importFrom(utils,head)
importFrom(utils,modifyList)
importFrom(utils,read.table)
importFrom(utils,tail)
useDynLib(DOTSeq, .registration = TRUE)
