Files in derele/MultiAmplicon
Metabarcoding and microbiome analysis using multiple amplicons
.Rbuildignore
.gitattributes
.github/.gitignore
.github/workflows/pkgdown.yaml
.gitignore
.travis.yml
DESCRIPTION
Meta/vignette.rds
MultiAmplicon.Rproj
NAMESPACE
R/allClasses.R
R/annotateTaxa.R
R/concatenate-methods.R
R/data.R
R/pipeline.R
R/pipeline_track.R
R/plot-methods.R
R/show-methods.R
R/sortAmplicons.R
R/subset-methods.R
R/toPhyloseq.R
README.md
appveyor.yml
codecov.yml
data/carnivoreSeqRuns.rda
doc/MultiAmplicon-real-world-example.R
doc/MultiAmplicon-real-world-example.Rmd
doc/MultiAmplicon-real-world-example.html
doc/MultiAmplicon-small-example.R
doc/MultiAmplicon-small-example.Rmd
doc/MultiAmplicon-small-example.html
docs/articles/MultiAmplicon-real-world-example.html
docs/articles/MultiAmplicon-real-world-example_files/anchor-sections-1.0/anchor-sections.css
docs/articles/MultiAmplicon-real-world-example_files/anchor-sections-1.0/anchor-sections.js
docs/articles/MultiAmplicon-real-world-example_files/figure-html/phydiversity-1.png
docs/articles/MultiAmplicon-real-world-example_files/figure-html/plottrack-1.png
docs/articles/MultiAmplicon-real-world-example_files/figure-html/tracking-1.png
docs/articles/MultiAmplicon-small-example.html
docs/articles/MultiAmplicon-small-example_files/figure-html/plotAmpliconNumbers-1.png
docs/articles/index.html
docs/authors.html
docs/index.html
docs/reference/MultiAmplicon-class.html
docs/reference/PairedDada-class.html
docs/reference/PairedDerep-class.html
docs/reference/PairedReadFileSet-class.html
docs/reference/PrimerPairsSet-class.html
docs/reference/Rplot001.png
docs/reference/addSampleData.html
docs/reference/blastTaxAnnot.html
docs/reference/calcPropMerged.html
docs/reference/carnivoreSeqRuns.html
docs/reference/concatenateMultiAmplicon.html
docs/reference/dadaMulti.html
docs/reference/derepMulti.html
docs/reference/dot-fillSampleTables.html
docs/reference/getPipelineSummary.html
docs/reference/index.html
docs/reference/makeSequenceTableMulti.html
docs/reference/mergeMulti.html
docs/reference/plotAmpliconNumbers.html
docs/reference/plotPipelineSummary.html
docs/reference/removeChimeraMulti.html
docs/reference/sortAmplicons.html
docs/reference/toPhyloseq.html
inst/doc/MultiAmplicon-real-world-example.pdf
inst/doc/MultiAmplicon-small-example.pdf
inst/extdata/fastq/S00_F_filt.fastq.gz
inst/extdata/fastq/S00_R_filt.fastq.gz
inst/extdata/fastq/S01_F_filt.fastq.gz
inst/extdata/fastq/S01_R_filt.fastq.gz
inst/extdata/fastq/S02_F_filt.fastq.gz
inst/extdata/fastq/S02_R_filt.fastq.gz
inst/extdata/fastq/S03_F_filt.fastq.gz
inst/extdata/fastq/S03_R_filt.fastq.gz
inst/extdata/fastq/S04_F_filt.fastq.gz
inst/extdata/fastq/S04_R_filt.fastq.gz
inst/extdata/fastq/S05D_F_filt.fastq.gz
inst/extdata/fastq/S05D_R_filt.fastq.gz
inst/extdata/fastq/S05_F_filt.fastq.gz
inst/extdata/fastq/S05_R_filt.fastq.gz
inst/extdata/fastq/S06_F_filt.fastq.gz
inst/extdata/fastq/S06_R_filt.fastq.gz
inst/extdata/in.fasta
inst/extdata/out.blt
inst/extdata/real_world_primers.csv
man/MultiAmplicon-class.Rd
man/PairedReadFileSet-class.Rd
man/PrimerPairsSet-class.Rd
man/addSampleData.Rd
man/blastTaxAnnot.Rd
man/calcPropMerged.Rd
man/carnivoreSeqRuns.Rd
man/concatenateMultiAmplicon.Rd
man/dadaMulti.Rd
man/derepMulti.Rd
man/dot-fillSampleTables.Rd
man/dot-sumThingsOrNull.Rd
man/getCounts.Rd
man/getPipelineSummary.Rd
man/makeSequenceTableMulti.Rd
man/mergeMulti.Rd
man/plotAmpliconNumbers.Rd
man/plotPipelineSummary.Rd
man/removeChimeraMulti.Rd
man/sortAmplicons.Rd
man/toPhyloseq.Rd
testdraft/left_over_tests.R
testdraft/scribble.R
testdraft/test_track_read.R
tests/testthat.R
tests/testthat/test_MultiAmplicon.R
vignettes/MultiAmplicon-real-world-example.Rmd
vignettes/MultiAmplicon-real-world-example.html
vignettes/MultiAmplicon-real-world-example.pdf
vignettes/MultiAmplicon-real-world-example_files/figure-html/phydiversity-1.png
vignettes/MultiAmplicon-real-world-example_files/figure-html/plottrack-1.png
vignettes/MultiAmplicon-real-world-example_files/figure-html/tracking-1.png
vignettes/MultiAmplicon-real-world-example_files/figure-latex/phydiversity-1.pdf
vignettes/MultiAmplicon-real-world-example_files/figure-latex/plottrack-1.pdf
vignettes/MultiAmplicon-real-world-example_files/figure-latex/tracking-1.pdf
vignettes/MultiAmplicon-small-example.R
vignettes/MultiAmplicon-small-example.Rmd
vignettes/MultiAmplicon-small-example.aux
vignettes/MultiAmplicon-small-example.html
vignettes/MultiAmplicon-small-example.out
vignettes/MultiAmplicon-small-example.pdf
vignettes/MultiAmplicon-small-example_files/figure-html/plotAmpliconNumbers-1.png
vignettes/MultiAmplicon-small-example_files/figure-latex/plotAmpliconNumbers-1.pdf
