dada2-package |
DADA2 package |
assignTaxonomy |
assignTaxonomy assigns taxonomy to provided sequences. |
collapseNoMismatch |
Collapse 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' |
dada_to_seq_table |
Map denoised sequence to each read. |
derep-class |
derep - A class representing dereplicated sequences |
derepFastq |
Read 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. |
evaluate_kmers |
Generate the kmer-distance and the alignment distance from the given set of sequences. |
fastqFilter |
fastqFilter filters and trims fastq files. |
fastqPairedFilter |
fastqPairedFilter filters and trims paired forward and reverse fastq files. |
getDadaOpt |
Get DADA options |
getSequences |
Get vector of sequences. |
getUniques |
Get the "uniques vector": Integer vector named by sequence and valued by abundance. |
inflateErr |
Inflates an error rate matrix by a specified factor accounting for saturation. |
isBimera |
Determine if input sequence is a bimera of putative parent sequences. |
isBimeraDenovo |
Identify bimeras de-novo from collections of unique sequences. |
isShiftDenovo |
Identify sequences that are identical to a more abundant sequence up to an overall shift. |
loessErrfun |
Use a loess fit to estimate error rates from transition counts. |
makeSequenceTable |
Construct a sample-by-sequence observation matrix. |
mergePairs |
Merge paired forward and reverse reads after DADA denoising. |
mergePairsByID |
Merge forward and reverse reads after DADA denoising, even if reads were not originally ordered together. |
nwalign |
Needlman-Wunsch alignment with ends-free gapping. |
nwhamming |
Hamming distance after Needlman-Wunsch alignment with ends-free gapping. |
plotComplementarySubstitutions |
Plot Substitution Pairs from DADA Result |
plotErrors |
Plot error rates after dada processing. |
setDadaOpt |
Set DADA options |
show-method |
method extensions to show for dada2 objects. |
tperr1 |
An empirical error matrix. |
uniquesToFasta |
Write a uniques vector to a FASTA file |