NAMESPACE

# Generated by roxygen2: do not edit by hand

export(addFeature)
export(addListNameToReads)
export(annotateSites)
export(blatListedSet)
export(blatSeqs)
export(chunkize)
export(clusterSites)
export(crossOverCheck)
export(decodeByBarcode)
export(dereplicateReads)
export(doRCtest)
export(extractFeature)
export(extractSeqs)
export(findAndRemoveVector)
export(findAndTrimSeq)
export(findBarcodes)
export(findIntegrations)
export(findLTRs)
export(findLinkers)
export(findPrimers)
export(findVector)
export(getIntegrationSites)
export(getSectorsForSamples)
export(getSonicAbund)
export(isuSites)
export(otuSites)
export(pairUpAlignments)
export(pairwiseAlignSeqs)
export(primerIDAlignSeqs)
export(pslCols)
export(pslToRangedObject)
export(read.BAMasPSL)
export(read.SeqFolder)
export(read.blast8)
export(read.psl)
export(read.sampleInfo)
export(read.seqsFromSector)
export(removeReadsWithNs)
export(replicateReads)
export(sampleSummary)
export(splitByBarcode)
export(splitSeqsToFiles)
export(startgfServer)
export(trimSeqs)
export(troubleshootLinkers)
export(vpairwiseAlignSeqs)
export(write.listedDNAStringSet)
export(write.psl)
import(BiocGenerics)
import(BiocParallel)
import(Biostrings)
import(GenomicAlignments)
import(GenomicRanges)
import(hiAnnotator)
import(sonicLength)
importFrom(dplyr,"%>%")
importFrom(dplyr,arrange)
importFrom(dplyr,bind_rows)
importFrom(dplyr,contains)
importFrom(dplyr,count)
importFrom(dplyr,desc)
importFrom(dplyr,group_by)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,n)
importFrom(dplyr,rename)
importFrom(dplyr,select)
importFrom(dplyr,summarise)
importFrom(dplyr,ungroup)
importFrom(methods,as)
importFrom(methods,is)
importFrom(readxl,read_excel)
importFrom(stats,aggregate)
importFrom(stats,ave)
importFrom(stats,filter)
importFrom(stats,na.omit)
importFrom(stats,runif)
importFrom(utils,count.fields)
importFrom(utils,read.delim)
importFrom(utils,write.table)