Files in benjjneb/dada2
Accurate, high-resolution sample inference from amplicon sequencing data
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
LICENSE
NAMESPACE
NEWS
R/RcppExports.R
R/allClasses.R
R/allPackage.R
R/chimeras.R
R/dada.R
R/errorModels.R
R/filter.R
R/misc.R
R/multiSample.R
R/paired.R
R/plot-methods.R
R/sequenceIO.R
R/show-methods.R
R/taxonomy.R
README.md
data/errBalancedF.rda
data/errBalancedR.rda
data/tperr1.rda
inst/CITATION
inst/NEWS
inst/extdata/example_seqs.fa
inst/extdata/example_species_assignment.fa.gz
inst/extdata/example_train_set.fa.gz
inst/extdata/phix_genome.fa
inst/extdata/sam1F.fastq.gz
inst/extdata/sam1R.fastq.gz
inst/extdata/sam2F.fastq.gz
inst/extdata/sam2R.fastq.gz
inst/extdata/samPB.fastq.gz
inst/extdata/samPBprimers.fastq.gz
inst/extdata/ten_16s.100.fa.gz
inst/include/dada2.h
inst/include/dada2_RcppExports.h
man/PacBioErrfun.Rd
man/addSpecies.Rd
man/assignSpecies.Rd
man/assignTaxonomy.Rd
man/c-dada-method.Rd
man/c-derep-method.Rd
man/collapseNoMismatch.Rd
man/dada-class.Rd
man/dada.Rd
man/dada2-package.Rd
man/derep-class.Rd
man/derepFasta.Rd
man/derepFastq.Rd
man/errBalancedF.Rd
man/errBalancedR.Rd
man/fastqFilter.Rd
man/fastqPairedFilter.Rd
man/filterAndTrim.Rd
man/getDadaOpt.Rd
man/getErrors.Rd
man/getSequences.Rd
man/getUniques.Rd
man/inflateErr.Rd
man/isBimera.Rd
man/isBimeraDenovo.Rd
man/isBimeraDenovoTable.Rd
man/isPhiX.Rd
man/isShiftDenovo.Rd
man/learnErrors.Rd
man/loessErrfun.Rd
man/makeBinnedQualErrfun.Rd
man/makeSequenceTable.Rd
man/makeSpeciesFasta_RDP.Rd
man/makeSpeciesFasta_Silva.Rd
man/makeTaxonomyFasta_GG2.Rd
man/makeTaxonomyFasta_RDP.Rd
man/makeTaxonomyFasta_SilvaNR.Rd
man/mergePairs.Rd
man/mergeSequenceTables.Rd
man/names-set-dada-ANY-method.Rd
man/names-set-derep-ANY-method.Rd
man/noqualErrfun.Rd
man/nwalign.Rd
man/nwhamming.Rd
man/plotComplexity.Rd
man/plotErrors.Rd
man/plotQualityProfile.Rd
man/qtables2.Rd
man/rc.Rd
man/removeBimeraDenovo.Rd
man/removePrimers.Rd
man/seqComplexity.Rd
man/setDadaOpt.Rd
man/show-methods.Rd
man/tperr1.Rd
man/uniques-vector.Rd
man/uniquesToFasta.Rd
man/writeFasta.Rd
src/Makevars
src/Makevars.win
src/RcppExports.cpp
src/Rmain.cpp
src/chimera.cpp
src/cluster.cpp
src/containers.cpp
src/dada.h
src/error.cpp
src/evaluate.cpp
src/filter.cpp
src/kmers.cpp
src/misc.cpp
src/nwalign_endsfree.cpp
src/nwalign_vectorized.cpp
src/pval.cpp
src/taxonomy.cpp
vignettes/Clearness.css
vignettes/dada2-intro.Rmd
