# Generated by roxygen2: do not edit by hand

export(PacBioErrfun)
export(addSpecies)
export(assignSpecies)
export(assignTaxonomy)
export(collapseNoMismatch)
export(dada)
export(derepFastq)
export(fastqFilter)
export(fastqPairedFilter)
export(filterAndTrim)
export(getDadaOpt)
export(getErrors)
export(getSequences)
export(getUniques)
export(inflateErr)
export(isBimera)
export(isBimeraDenovo)
export(isBimeraDenovoTable)
export(isPhiX)
export(isShiftDenovo)
export(learnErrors)
export(loessErrfun)
export(makeSequenceTable)
export(mergePairs)
export(mergeSequenceTables)
export(noqualErrfun)
export(nwalign)
export(nwhamming)
export(plotErrors)
export(plotQualityProfile)
export(removeBimeraDenovo)
export(seqComplexity)
export(setDadaOpt)
export(uniquesToFasta)
import(ggplot2)
importFrom(BiocGenerics,end)
importFrom(BiocGenerics,start)
importFrom(BiocGenerics,width)
importFrom(Biostrings,BStringSet)
importFrom(Biostrings,DNAString)
importFrom(Biostrings,DNAStringSet)
importFrom(Biostrings,PDict)
importFrom(Biostrings,end)
importFrom(Biostrings,oligonucleotideFrequency)
importFrom(Biostrings,quality)
importFrom(Biostrings,readDNAStringSet)
importFrom(Biostrings,readRNAStringSet)
importFrom(Biostrings,reverseComplement)
importFrom(Biostrings,vcountPDict)
importFrom(Biostrings,vmatchPattern)
importFrom(Biostrings,width)
importFrom(Biostrings,writeXStringSet)
importFrom(IRanges,narrow)
importFrom(Rcpp,evalCpp)
importFrom(RcppParallel,RcppParallelLibs)
importFrom(RcppParallel,setThreadOptions)
importFrom(ShortRead,FastqStreamer)
importFrom(ShortRead,ShortRead)
importFrom(ShortRead,ShortReadQ)
importFrom(ShortRead,append)
importFrom(ShortRead,encoding)
importFrom(ShortRead,id)
importFrom(ShortRead,nFilter)
importFrom(ShortRead,narrow)
importFrom(ShortRead,qa)
importFrom(ShortRead,readFasta)
importFrom(ShortRead,readFastq)
importFrom(ShortRead,reverseComplement)
importFrom(ShortRead,sread)
importFrom(ShortRead,srrank)
importFrom(ShortRead,srsort)
importFrom(ShortRead,trimTails)
importFrom(ShortRead,writeFasta)
importFrom(ShortRead,writeFastq)
importFrom(ShortRead,yield)
importFrom(XVector,rev)
importFrom(data.table,.N)
importFrom(data.table,data.table)
importFrom(data.table,key)
importFrom(data.table,setkey)
importFrom(data.table,setnames)
importFrom(data.table,uniqueN)
importFrom(methods,as)
importFrom(methods,is)
importFrom(parallel,detectCores)
importFrom(parallel,mclapply)
importFrom(parallel,mcmapply)
importFrom(reshape2,melt)
importFrom(stats,loess)
importFrom(stats,median)
importFrom(stats,ppois)
importFrom(stats,predict)
importFrom(utils,read.table)
useDynLib(dada2)
