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 of dada-class objects to list... |
c-derep-method | Change concatenation of derep-class objects to list... |
collapseNoMismatch | Combine together sequences that are identical up to shifts... |
dada | High resolution sample inference from amplicon data. |
dada2-package | DADA2 package |
dada-class | The object class returned by 'dada' |
derep-class | A class representing dereplicated sequences |
derepFasta | derepFasta creates a derep-class object from a fasta file, by... |
derepFastq | Read in and dereplicate a fastq file. |
errBalancedF | An empirical error matrix. |
errBalancedR | 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... |
isBimera | Determine if input sequence is a bimera of putative parent... |
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... |
learnErrors | Learns the error rates from an input list, or vector, of file... |
loessErrfun | Use a loess fit to estimate error rates from transition... |
makeSequenceTable | Construct a sample-by-sequence observation matrix. |
makeSpeciesFasta_RDP | This function creates the dada2 assignSpecies fasta file for... |
makeSpeciesFasta_Silva | This function creates the dada2 assignSpecies fasta file for... |
makeTaxonomyFasta_RDP | This function creates the dada2 assignTaxonomy training fasta... |
makeTaxonomyFasta_Silva | DEPRECATED in favor of 'makeTaxonomyFasta_SilvaNR" |
makeTaxonomyFasta_SilvaNR | This function creates the dada2 assignTaxonomy training fasta... |
mergePairs | Merge denoised forward and reverse reads. |
mergeSequenceTables | Merge two or more sample-by-sequence observation matrices. |
names-set-dada-ANY-method | Deactivate renaming of dada-class objects. |
names-set-derep-ANY-method | Deactivate renaming of derep-class objects. |
noqualErrfun | Estimate error rates for each type of transition while... |
nwalign | Needleman-Wunsch alignment. |
nwhamming | Hamming distance after Needlman-Wunsch alignment. |
PacBioErrfun | Estimate error rates from transition counts in PacBio CCS... |
plotComplexity | Plot sequence complexity profile of a fastq file. |
plotErrors | Plot observed and estimated error rates. |
plotQualityProfile | Plot quality profile of a fastq file. |
qtables2 | Internal tables function |
rc | Reverse complement DNA sequences. |
removeBimeraDenovo | Remove bimeras from collections of unique sequences. |
removePrimers | Removes primers and orients reads in a consistent direction. |
seqComplexity | Determine if input sequence(s) are low complexity. |
setDadaOpt | Set DADA options |
show-methods | method extensions to show for dada2 objects. |
tperr1 | An empirical error matrix. |
uniquesToFasta | Write a uniques vector to a FASTA file |
uniques-vector | The named integer vector format used to represent collections... |
writeFasta | Writes a named character vector of DNA sequences to a fasta... |
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