# Generated by roxygen2: do not edit by hand

export("envExp<-")
export(DEG.analysis)
export(DEG.plot.static)
export(DTEG.analysis)
export(DTEG.plot)
export(ORFik.template.experiment)
export(ORFik.template.experiment.zf)
export(ORFikQC)
export(QCfolder)
export(QCreport)
export(QCstats)
export(QCstats.plot)
export(RiboQC.plot)
export(STAR.align.folder)
export(STAR.align.single)
export(STAR.allsteps.multiQC)
export(STAR.index)
export(STAR.install)
export(STAR.multiQC)
export(STAR.remove.crashed.genome)
export(TOP.Motif.ecdf)
export(artificial.orfs)
export(asTX)
export(assignTSSByCage)
export(bamVarName)
export(collapse.fastq)
export(collapseDuplicatedReads)
export(combn.pairs)
export(computeFeatures)
export(config)
export(config.exper)
export(config.save)
export(convertLibs)
export(convertToOneBasedRanges)
export(convert_bam_to_ofst)
export(convert_to_bigWig)
export(convert_to_covRle)
export(convert_to_covRleList)
export(countOverlapsW)
export(countTable)
export(countTable_regions)
export(covRle)
export(covRleFromGR)
export(covRleList)
export(coverageHeatMap)
export(coveragePerTiling)
export(coverageScorings)
export(create.experiment)
export(defineTrailer)
export(detectRibosomeShifts)
export(disengagementScore)
export(distToCds)
export(distToTSS)
export(download.SRA)
export(download.SRA.metadata)
export(entropy)
export(envExp)
export(experiment)
export(experiment.colors)
export(export.bed12)
export(export.bedoc)
export(export.bigWig)
export(export.fstwig)
export(export.ofst)
export(export.wiggle)
export(extendLeaders)
export(extendTrailers)
export(f)
export(filepath)
export(filterExtremePeakGenes)
export(filterTranscripts)
export(fimport)
export(findFa)
export(findMapORFs)
export(findORFs)
export(findORFsFasta)
export(findPeaksPerGene)
export(findUORFs)
export(firstEndPerGroup)
export(firstExonPerGroup)
export(firstStartPerGroup)
export(flankPerGroup)
export(floss)
export(fpkm)
export(fractionLength)
export(fread.bed)
export(gcContent)
export(geneToSymbol)
export(getGenomeAndAnnotation)
export(get_bioproject_candidates)
export(get_silva_rRNA)
export(groupGRangesBy)
export(groupings)
export(heatMapRegion)
export(heatMap_single)
export(import.bedo)
export(import.bedoc)
export(import.fstwig)
export(import.ofst)
export(initiationScore)
export(insideOutsideORF)
export(install.fastp)
export(install.sratoolkit)
export(isInFrame)
export(isOverlapping)
export(kozakHeatmap)
export(kozakSequenceScore)
export(kozak_IR_ranking)
export(lastExonEndPerGroup)
export(lastExonPerGroup)
export(lastExonStartPerGroup)
export(libFolder)
export(libraryTypes)
export(list.experiments)
export(list.genomes)
export(loadRegion)
export(loadRegions)
export(loadTranscriptType)
export(loadTxdb)
export(longestORFs)
export(makeORFNames)
export(makeSummarizedExperimentFromBam)
export(makeTxdbFromGenome)
export(mergeFastq)
export(mergeLibs)
export(metaWindow)
export(name)
export(numExonsPerGroup)
export(optimizedTranscriptLengths)
export(orfFrameDistributions)
export(orfScore)
export(outputLibs)
export(pSitePlot)
export(pcaExperiment)
export(pmapFromTranscriptF)
export(pmapToTranscriptF)
export(r)
export(rankOrder)
export(read.experiment)
export(readBam)
export(readWidths)
export(reassignTSSbyCage)
export(reassignTxDbByCage)
export(reduceKeepAttr)
export(regionPerReadLength)
export(remove.experiments)
export(ribo_fft)
export(ribo_fft_plot)
export(ribosomeReleaseScore)
export(ribosomeStallingScore)
export(rnaNormalize)
export(save.experiment)
export(scaledWindowPositions)
export(scoreSummarizedExperiment)
export(seqnamesPerGroup)
export(shiftFootprints)
export(shiftFootprintsByExperiment)
export(shiftPlots)
export(shifts.load)
export(simpleLibs)
export(sortPerGroup)
export(startCodons)
export(startDefinition)
export(startRegion)
export(startRegionString)
export(startSites)
export(stopCodons)
export(stopDefinition)
export(stopRegion)
export(stopSites)
export(strandBool)
export(strandPerGroup)
export(subsetToFrame)
export(symbols)
export(te.plot)
export(te.table)
export(te_rna.plot)
export(tile1)
export(topMotif)
export(transcriptWindow)
export(translationalEff)
export(trimming.table)
export(txNames)
export(txNamesToGeneNames)
export(txSeqsFromFa)
export(uORFSearchSpace)
export(uniqueGroups)
export(uniqueOrder)
export(unlistGrl)
export(widthPerGroup)
export(windowCoveragePlot)
export(windowPerGroup)
export(windowPerReadLength)
exportClasses(covRle)
exportClasses(covRleList)
exportClasses(experiment)
exportMethods(design)
exportMethods(length)
exportMethods(lengths)
exportMethods(organism)
exportMethods(seqinfo)
exportMethods(seqlevels)
exportMethods(show)
exportMethods(strandMode)
import(DESeq2)
import(GenomeInfoDb)
import(GenomicAlignments)
import(GenomicFeatures)
import(GenomicRanges)
import(IRanges)
import(SummarizedExperiment)
import(ggplot2)
importFrom(AnnotationDbi,loadDb)
importFrom(AnnotationDbi,metadata)
importFrom(AnnotationDbi,saveDb)
importFrom(BSgenome,getSeq)
importFrom(BiocGenerics,Reduce)
importFrom(BiocGenerics,basename)
importFrom(BiocGenerics,weights)
importFrom(BiocParallel,bplapply)
importFrom(BiocParallel,bpparam)
importFrom(Biostrings,DNAStringSet)
importFrom(Biostrings,PWM)
importFrom(Biostrings,alphabetFrequency)
importFrom(Biostrings,readDNAStringSet)
importFrom(Biostrings,writeXStringSet)
importFrom(DESeq2,DESeqDataSet)
importFrom(GenomicAlignments,first)
importFrom(GenomicAlignments,last)
importFrom(IRanges,heads)
importFrom(IRanges,quantile)
importFrom(IRanges,tails)
importFrom(R.utils,gunzip)
importFrom(Rcpp,sourceCpp)
importFrom(Rsamtools,BamFile)
importFrom(Rsamtools,FaFile)
importFrom(Rsamtools,ScanBamParam)
importFrom(Rsamtools,indexFa)
importFrom(Rsamtools,scanBam)
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,List)
importFrom(S4Vectors,Rle)
importFrom(S4Vectors,isTRUEorFALSE)
importFrom(S4Vectors,new2)
importFrom(S4Vectors,nrun)
importFrom(S4Vectors,pc)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,runValue)
importFrom(S4Vectors,subjectHits)
importFrom(S4Vectors,wmsg)
importFrom(biomaRt,getBM)
importFrom(biomaRt,useEnsembl)
importFrom(biomartr,getENSEMBLInfo)
importFrom(biomartr,getGTF)
importFrom(biomartr,getGenome)
importFrom(cowplot,plot_grid)
importFrom(data.table,":=")
importFrom(data.table,.I)
importFrom(data.table,.N)
importFrom(data.table,.SD)
importFrom(data.table,as.data.table)
importFrom(data.table,chmatch)
importFrom(data.table,copy)
importFrom(data.table,data.table)
importFrom(data.table,fread)
importFrom(data.table,fwrite)
importFrom(data.table,melt)
importFrom(data.table,melt.data.table)
importFrom(data.table,merge.data.table)
importFrom(data.table,rbindlist)
importFrom(data.table,setDF)
importFrom(data.table,setDT)
importFrom(data.table,setcolorder)
importFrom(data.table,setkey)
importFrom(data.table,setkeyv)
importFrom(data.table,setnames)
importFrom(data.table,setorder)
importFrom(fst,fst)
importFrom(fst,read_fst)
importFrom(fst,write_fst)
importFrom(ggplot2,theme)
importFrom(gridExtra,arrangeGrob)
importFrom(gridExtra,grid.arrange)
importFrom(httr,http_error)
importFrom(jsonlite,fromJSON)
importFrom(methods,as)
importFrom(methods,is)
importFrom(methods,new)
importFrom(rtracklayer,export.bed)
importFrom(rtracklayer,export.bw)
importFrom(rtracklayer,export.wig)
importFrom(rtracklayer,import)
importFrom(rtracklayer,import.bed)
importFrom(rtracklayer,import.bw)
importFrom(rtracklayer,import.wig)
importFrom(stats,as.formula)
importFrom(stats,fft)
importFrom(stats,spec.pgram)
importFrom(tools,file_ext)
importFrom(tools,file_path_sans_ext)
importFrom(utils,View)
importFrom(utils,combn)
importFrom(utils,download.file)
importFrom(utils,packageVersion)
importFrom(utils,read.csv2)
importFrom(utils,read.table)
importFrom(utils,tar)
importFrom(utils,untar)
importFrom(utils,unzip)
importFrom(utils,write.csv)
importFrom(utils,write.table)
importFrom(xml2,as_list)
importFrom(xml2,read_xml)
useDynLib(ORFik)
