dada2-package	dada2-package
addSpecies	addSpecies
assignSpecies	assignSpecies
assignTaxonomy	assignTaxonomy
c,dada-method	c-dada-method
c,derep-method	c-derep-method
collapseNoMismatch	collapseNoMismatch
dada	dada
dada-class	dada-class
dada2	dada2-package
derep-class	derep-class
derepFasta	derepFasta
derepFastq	derepFastq
errBalancedF	errBalancedF
errBalancedR	errBalancedR
fastqFilter	fastqFilter
fastqPairedFilter	fastqPairedFilter
filterAndTrim	filterAndTrim
getDadaOpt	getDadaOpt
getErrors	getErrors
getSequences	getSequences
getUniques	getUniques
inflateErr	inflateErr
isBimera	isBimera
isBimeraDenovo	isBimeraDenovo
isBimeraDenovoTable	isBimeraDenovoTable
isPhiX	isPhiX
isShiftDenovo	isShiftDenovo
learnErrors	learnErrors
loessErrfun	loessErrfun
makeBinnedQualErrfun	makeBinnedQualErrfun
makeSequenceTable	makeSequenceTable
makeSpeciesFasta_RDP	makeSpeciesFasta_RDP
makeSpeciesFasta_Silva	makeSpeciesFasta_Silva
makeTaxonomyFasta_GG2	makeTaxonomyFasta_GG2
makeTaxonomyFasta_RDP	makeTaxonomyFasta_RDP
makeTaxonomyFasta_SilvaNR	makeTaxonomyFasta_SilvaNR
mergePairs	mergePairs
mergeSequenceTables	mergeSequenceTables
names<-,dada,ANY-method	names-set-dada-ANY-method
names<-,derep,ANY-method	names-set-derep-ANY-method
noqualErrfun	noqualErrfun
nwalign	nwalign
nwhamming	nwhamming
PacBioErrfun	PacBioErrfun
plotComplexity	plotComplexity
plotErrors	plotErrors
plotQualityProfile	plotQualityProfile
qtables2	qtables2
rc	rc
removeBimeraDenovo	removeBimeraDenovo
removePrimers	removePrimers
seqComplexity	seqComplexity
setDadaOpt	setDadaOpt
show,dada-method	show-methods
show,derep-method	show-methods
tperr1	tperr1
uniques-vector	uniques-vector
uniquesToFasta	uniquesToFasta
writeFasta,character-method	writeFasta
