API for benjjneb/dada2
Accurate, high-resolution sample inference from amplicon sequencing data
| Global functions | |
|---|---|
| .nFilter | Source code |
| C_assign_taxonomy2 | Source code |
| C_eval_pair | Source code |
| C_isACGT | Source code |
| C_is_bimera | Source code |
| C_matchRef | Source code |
| C_matrixEE | Source code |
| C_nwalign | Source code |
| C_nwvec | Source code |
| C_pair_consensus | Source code |
| C_table_bimera2 | Source code |
| PacBioErrfun | Man page Source code |
| accumulateTrans | Source code |
| addSpecies | Man page Source code |
| assignSpecies | Man page Source code |
| assignTaxonomy | Man page Source code |
| bs1ham | Source code |
| c,dada-method | Man page |
| c,derep-method | Man page |
| checkConvergence | Source code |
| collapseNoMismatch | Man page Source code |
| combineDereps2 | Source code |
| dada | Man page Source code |
| dada-class | Man page |
| dada2 | Man page |
| dada2-package | Man page |
| dada_uniques | Source code |
| derep-class | Man page |
| derepFasta | Man page Source code |
| derepFastq | Man page Source code |
| errBalancedF | Man page |
| errBalancedR | Man page |
| fastqFilter | Man page Source code |
| fastqPairedFilter | Man page Source code |
| filt.print | Source code |
| filterAndTrim | Man page Source code |
| getAbund | Source code |
| getBadBases | Source code |
| getDadaOpt | Man page Source code |
| getDerep | Source code |
| getErrors | Man page Source code |
| getNseq | Source code |
| getSequences | Man page Source code |
| getUniques | Man page Source code |
| inflateErr | Man page Source code |
| is.list.of | Source code |
| is.sequence.table | Source code |
| isBadBaseFP | Source code |
| isBimera | Man page Source code |
| isBimeraDenovo | Man page Source code |
| isBimeraDenovoTable | Man page Source code |
| isMatch | Source code |
| isPhiX | Man page Source code |
| isShift | Source code |
| isShiftDenovo | Man page Source code |
| isShiftedPair | Source code |
| kdist_matches | Source code |
| kmer_dist | Source code |
| kmer_matches | Source code |
| kord_dist | Source code |
| learnErrors | Man page Source code |
| loessErrfun | Man page Source code |
| makeBinnedQualErrfun | Man page Source code |
| makeSequenceTable | Man page Source code |
| makeSpeciesFasta_RDP | Man page Source code |
| makeSpeciesFasta_Silva | Man page Source code |
| makeTaxonomyFasta_GG2 | Man page Source code |
| makeTaxonomyFasta_RDP | Man page Source code |
| makeTaxonomyFasta_SilvaNR | Man page Source code |
| mapHits | Source code |
| matchGenera | Source code |
| mergePairs | Man page Source code |
| mergeSequenceTables | Man page Source code |
| names<-,dada,ANY-method | Man page |
| names<-,derep,ANY-method | Man page |
| noqualErrfun | Man page Source code |
| nwalign | Man page Source code |
| nwextract | Source code |
| nwhamming | Man page |
| parseFastqDirectory | Source code |
| pfasta | Source code |
| plotComplexity | Man page Source code |
| plotErrors | Man page Source code |
| plotQualityProfile | Man page Source code |
| qtables2 | Man page Source code |
| rc | Man page Source code |
| removeBimeraDenovo | Man page Source code |
| removePrimers | Man page Source code |
| samdf_to_qiime2 | Source code |
| sameOrder | Source code |
| seqComplexity | Man page Source code |
| seqtab_to_mothur | Source code |
| seqtab_to_qiime | Source code |
| setDadaOpt | Man page Source code |
| show,dada-method | Man page |
| show,derep-method | Man page |
| sindex | Source code |
| strdiff | Source code |
| tax.check | Source code |
| tperr1 | Man page |
| uniques-vector | Man page |
| uniquesToFasta | Man page Source code |
| writeFasta,character-method | Man page |
