PacBioErrfun            Estimate error rates from transition counts in
                        PacBio CCS data.
addSpecies              Add species-level annotation to a taxonomic
                        table.
assignSpecies           Taxonomic assignment to the species level by
                        exact matching.
assignTaxonomy          Classifies sequences against reference training
                        dataset.
c,dada-method           Change concatenation to list construction.
c,derep-method          Change concatenation to list construction.
collapseNoMismatch      Combine together sequences that are identical
                        up to shifts and/or length.
dada                    High resolution sample inference from amplicon
                        data.
dada-class              The object class returned by 'dada'
dada2-package           DADA2 package
derep-class             A class representing dereplicated sequences
derepFastq              Read in and dereplicate a fastq file.
errBalancedF            An empirical error matrix.
errBalancedR            An empirical error matrix.
errExtremeF             An empirical error matrix.
errExtremeR             An empirical error matrix.
errHmpF                 An empirical error matrix.
errHmpR                 An empirical error matrix.
fastqFilter             Filter and trim a fastq file.
fastqPairedFilter       Filters and trims paired forward and reverse
                        fastq files.
filterAndTrim           Filter and trim fastq file(s).
getDadaOpt              Get DADA options
getErrors               Extract already computed error rates.
getSequences            Get vector of sequences from input object.
getUniques              Get the uniques-vector from the input object.
inflateErr              Inflates an error rate matrix by a specified
                        factor, while accounting for saturation.
isBimera                Determine if input sequence is a bimera of
                        putative parent sequences.
isBimeraDenovo          Identify bimeras from collections of unique
                        sequences.
isBimeraDenovoTable     Identify bimeras in a sequence table.
isPhiX                  Determine if input sequence(s) match the phiX
                        genome.
isShiftDenovo           Identify sequences that are identical to a more
                        abundant sequence up to an overall shift.
learnErrors             Learns the error rates from an input list, or
                        vector, of file names or a list of
                        'derep-class' objects.
loessErrfun             Use a loess fit to estimate error rates from
                        transition counts.
makeSequenceTable       Construct a sample-by-sequence observation
                        matrix.
mergePairs              Merge denoised forward and reverse reads.
mergePairsByID          Merge forward and reverse reads after DADA
                        denoising, even if reads were not originally
                        ordered together.
mergeSequenceTables     Merge two or more sample-by-sequence
                        observation matrices.
names<-,dada,ANY-method
                        Deactivate renaming of dada-class objects.
names<-,derep,ANY-method
                        Deactivate renaming of derep-class objects.
noqualErrfun            Estimate error rates for each type of
                        transition while ignoring quality scores.
nwalign                 Needleman-Wunsch alignment.
nwhamming               Hamming distance after Needlman-Wunsch
                        alignment.
plotErrors              Plot observed and estimated error rates.
plotQualityProfile      Plot quality profile of a fastq file.
removeBimeraDenovo      Remove bimeras from collections of unique
                        sequences.
seqComplexity           Determine if input sequence(s) are low
                        complexity.
setDadaOpt              Set DADA options
show,derep-method       method extensions to show for dada2 objects.
tperr1                  An empirical error matrix.
uniques-vector          The named integer vector format used to
                        represent collections of unique DNA sequences.
uniquesToFasta          Write a uniques vector to a FASTA file
writeFasta,character-method
                        Writes a named character vector of DNA
                        sequences to a fasta file. Values are the
                        sequences, and names are used for the id lines.
