Man pages for benjjneb/dada2
Accurate, high-resolution sample inference from amplicon sequencing 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 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... |
