# Generated by roxygen2: do not edit by hand

export(addChr2Exclude)
export(addInPASEnsDb)
export(addInPASGenome)
export(addInPASOutputDirectory)
export(addInPASTxDb)
export(addLockName)
export(assemble_allCov)
export(extract_UTR3Anno)
export(filter_testOut)
export(find_minMSEDistr)
export(getChr2Exclude)
export(getInPASEnsDb)
export(getInPASGenome)
export(getInPASOutputDirectory)
export(getInPASSQLiteDb)
export(getInPASTxDb)
export(getLockName)
export(get_UTR3eSet)
export(get_chromosomes)
export(get_lastCDSUTR3)
export(get_regionCov)
export(get_ssRleCov)
export(get_usage4plot)
export(parse_TxDb)
export(plot_utr3Usage)
export(run_coverageQC)
export(run_limmaAnalysis)
export(search_CPs)
export(set_globals)
export(setup_CPsSearch)
export(setup_GSEA)
export(setup_parCPsSearch)
export(setup_sqlitedb)
export(test_dPDUI)
exportClasses(UTR3eSet)
import(BSgenome)
import(Biobase)
import(GenomicFeatures)
import(GenomicRanges)
import(RSQLite)
import(S4Vectors)
import(flock)
import(limma)
import(methods)
import(readr)
importFrom(AnnotationDbi,mapIds)
importFrom(BSgenome,getSeq)
importFrom(BSgenome,matchPWM)
importFrom(Biostrings,DNAString)
importFrom(Biostrings,alphabetFrequency)
importFrom(Biostrings,letterFrequencyInSlidingView)
importFrom(Biostrings,toString)
importFrom(GenomeInfoDb,mapSeqlevels)
importFrom(GenomeInfoDb,seqlengths)
importFrom(GenomeInfoDb,seqlevels)
importFrom(GenomeInfoDb,seqlevelsStyle)
importFrom(IRanges,IRanges)
importFrom(IRanges,Views)
importFrom(IRanges,viewApply)
importFrom(IRanges,viewMeans)
importFrom(batchtools,batchMap)
importFrom(batchtools,makeClusterFunctionsInteractive)
importFrom(batchtools,makeClusterFunctionsLSF)
importFrom(batchtools,makeClusterFunctionsMulticore)
importFrom(batchtools,makeClusterFunctionsOpenLava)
importFrom(batchtools,makeClusterFunctionsSGE)
importFrom(batchtools,makeClusterFunctionsSlurm)
importFrom(batchtools,makeClusterFunctionsSocket)
importFrom(batchtools,makeClusterFunctionsTORQUE)
importFrom(batchtools,makeRegistry)
importFrom(batchtools,reduceResultsList)
importFrom(batchtools,submitJobs)
importFrom(batchtools,waitForJobs)
importFrom(cleanUpdTSeq,buildFeatureVector)
importFrom(cleanUpdTSeq,predictTestSet)
importFrom(depmixS4,depmix)
importFrom(depmixS4,fit)
importFrom(depmixS4,getpars)
importFrom(depmixS4,posterior)
importFrom(dplyr,arrange)
importFrom(dplyr,as_tibble)
importFrom(dplyr,bind_cols)
importFrom(dplyr,bind_rows)
importFrom(dplyr,desc)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,n)
importFrom(dplyr,pull)
importFrom(dplyr,select)
importFrom(dplyr,summarise)
importFrom(dplyr,syms)
importFrom(future,multicore)
importFrom(future,multisession)
importFrom(future,plan)
importFrom(future.apply,future_lapply)
importFrom(future.apply,future_mapply)
importFrom(ggplot2,aes)
importFrom(ggplot2,element_text)
importFrom(ggplot2,facet_grid)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_vline)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,theme)
importFrom(ggplot2,vars)
importFrom(ggplot2,ylab)
importFrom(grDevices,dev.off)
importFrom(grDevices,pdf)
importFrom(grDevices,rainbow)
importFrom(graphics,abline)
importFrom(graphics,hist)
importFrom(graphics,legend)
importFrom(graphics,lines)
importFrom(magrittr,"%>%")
importFrom(parallelly,availableCores)
importFrom(plyranges,as_granges)
importFrom(plyranges,complement_ranges)
importFrom(plyranges,disjoin_ranges)
importFrom(plyranges,filter)
importFrom(plyranges,group_by)
importFrom(plyranges,mutate)
importFrom(plyranges,reduce_ranges)
importFrom(plyranges,reduce_ranges_directed)
importFrom(plyranges,remove_names)
importFrom(plyranges,select)
importFrom(plyranges,set_genome_info)
importFrom(plyranges,shift_downstream)
importFrom(plyranges,summarise)
importFrom(preprocessCore,colSummarizeAvg)
importFrom(preprocessCore,colSummarizeMedian)
importFrom(preprocessCore,normalize.quantiles)
importFrom(preprocessCore,normalize.quantiles.robust)
importFrom(reshape2,melt)
importFrom(stats,BIC)
importFrom(stats,density)
importFrom(stats,fft)
importFrom(stats,fisher.test)
importFrom(stats,loess.smooth)
importFrom(stats,model.matrix)
importFrom(stats,p.adjust)
importFrom(stats,pnorm)
importFrom(stats,poisson)
importFrom(stats,smooth.spline)
importFrom(stats,t.test)
importFrom(utils,packageVersion)
importFrom(utils,read.delim)
importFrom(utils,write.table)
