dada2-package	dada2-package
addSpecies	addSpecies
assignSpecies	assignSpecies
assignTaxonomy	assignTaxonomy
c,dada-method	show-methods
c,derep-method	show-methods
collapseNoMismatch	collapseNoMismatch
dada	dada
dada-class	dada-class
dada_to_seq_table	dada_to_seq_table
derep-class	derep-class
derepFasta	derepFasta
derepFastq	derepFastq
errBalancedF	errBalancedF
errBalancedR	errBalancedR
errExtremeF	errExtremeF
errExtremeR	errExtremeR
errHmpF	errHmpF
errHmpR	errHmpR
evaluate_kmers	evaluate_kmers
fastqFilter	fastqFilter
fastqPairedFilter	fastqPairedFilter
getDadaOpt	getDadaOpt
getSequences	getSequences
getUniques	getUniques
inflateErr	inflateErr
isBimera	isBimera
isBimeraDenovo	isBimeraDenovo
isBimeraDenovoTable	isBimeraDenovoTable
isPhiX	isPhiX
isShiftDenovo	isShiftDenovo
loessErrfun	loessErrfun
makeSequenceTable	makeSequenceTable
makeSpeciesFasta_RDP	makeSpeciesFasta_RDP
makeSpeciesFasta_Silva	makeSpeciesFasta_Silva
mergePairs	mergePairs
mergePairsByID	mergePairsByID
mergeSequenceTables	mergeSequenceTables
names<-,dada,ANY-method	show-methods
names<-,derep,ANY-method	show-methods
nwalign	nwalign
nwhamming	nwhamming
plotComplementarySubstitutions	plotComplementarySubstitutions
plotErrors	plotErrors
plotQualityProfile	plotQualityProfile
qtables2	qtables2
removeBimeraDenovo	removeBimeraDenovo
setDadaOpt	setDadaOpt
show,dada-method	show-methods
show,derep-method	show-methods
tperr1	tperr1
uniques-vector	uniques-vector
uniquesToFasta	uniquesToFasta
