Files in RIVM-IIV-Microbiome/biomeUtils
Utilities for microbiome analytics
.Rbuildignore
.github/workflows/rcmdcheck.yml
.gitignore
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
NEWS.md
R/biomeUtils.R
R/buildSeqTree.R
R/calculatePD.R
R/calculateQC.R
R/calculateTaxaFoldDifference.R
R/checkFilterEffect.R
R/checkPolyphyletic.R
R/cleanTaxonomy.R
R/comparePhyloseq.R
R/data.R
R/fetchSequence.R
R/filterPhyloseq.R
R/filterTaxaTotal.R
R/findTopTaxa.R
R/genericUtilities.R
R/getPhyloseqSlots.R
R/getPrevalence.R
R/getTaxaOverview.R
R/getTaxaSummary.R
R/getTibbles.R
R/getYCTheta.R
R/meltDistanceToTable.R
R/mutatePhyloseq.R
R/pullPhyloseq.R
R/readMergedMetaphlan.R
R/removeZeros.R
R/renameSampleVariables.R
R/saveData.R
R/saveSequence.R
R/separateSampleColumn.R
R/summarizeTaxonomicAssignments.R
R/transformPhyloseq.R
R/trendAbundanceAssignment.R
R/uniqueness.R
R/uniteGenusSpeciesNames.R
R/uniteSampleColumn.R
README.md
_pkgdown.yml
biomeUtils.Rproj
data-raw/tree_test.pdf
data-raw/tree_test_2.pdf
data/FuentesIliGutData.rda
data/SprockettTHData.rda
docs/404.html
docs/LICENSE-text.html
docs/LICENSE.html
docs/articles/Introduction.html
docs/articles/Introduction_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/Introduction_files/figure-html/unnamed-chunk-11-1.png
docs/articles/Introduction_files/figure-html/unnamed-chunk-12-1.png
docs/articles/Introduction_files/figure-html/unnamed-chunk-14-1.png
docs/articles/Introduction_files/figure-html/unnamed-chunk-9-1.png
docs/articles/Introduction_files/header-attrs-2.11/header-attrs.js
docs/articles/Introduction_files/header-attrs-2.8/header-attrs.js
docs/articles/index.html
docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/link.svg
docs/news/index.html
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/FuentesIliGutData.html
docs/reference/Rplot001.png
docs/reference/SprockettTHData.html
docs/reference/biomeUtils-package.html
docs/reference/buildSeqTree.html
docs/reference/calculatePD.html
docs/reference/calculateQC.html
docs/reference/calculateTaxaFoldDifference.html
docs/reference/checkFilterEffect.html
docs/reference/checkPolyphyletic.html
docs/reference/chekFilterEffect.html
docs/reference/cleanTaxonomy.html
docs/reference/clusterASVs.html
docs/reference/comparePhyloseq.html
docs/reference/dysbiosisScore.html
docs/reference/fetchSequence.html
docs/reference/filterPhyloseq.html
docs/reference/filterTaxaTotal.html
docs/reference/findTopTaxa.html
docs/reference/genericUtilities.html
docs/reference/getPhyloseqSlots.html
docs/reference/getPrevalence.html
docs/reference/getTaxaOverview.html
docs/reference/getTaxaSummary.html
docs/reference/getTibble.html
docs/reference/getYCTheta.html
docs/reference/index.html
docs/reference/meltDistanceToTable.html
docs/reference/mutatePhyloseq.html
docs/reference/pullPhyloseq.html
docs/reference/readMergedMetaphlan.html
docs/reference/removeZeros.html
docs/reference/renameSampleVariables.html
docs/reference/saveData.html
docs/reference/saveSequence.html
docs/reference/separateSampleColumn.html
docs/reference/summarizeTaxonomicAssignments.html
docs/reference/transformation.html
docs/reference/trendAbundanceAssignment-1.png
docs/reference/trendAbundanceAssignment.html
docs/reference/uniqueness.html
docs/reference/uniteGenusSpeciesNames.html
docs/reference/uniteSampleColumn.html
docs/sitemap.xml
inst/extras/sequences.fasta
man/FuentesIliGutData.Rd
man/SprockettTHData.Rd
man/biomeUtils-package.Rd
man/buildSeqTree.Rd
man/calculatePD.Rd
man/calculateQC.Rd
man/calculateTaxaFoldDifference.Rd
man/checkFilterEffect.Rd
man/checkPolyphyletic.Rd
man/cleanTaxonomy.Rd
man/comparePhyloseq.Rd
man/fetchSequence.Rd
man/filterPhyloseq.Rd
man/filterTaxaTotal.Rd
man/findTopTaxa.Rd
man/genericUtilities.Rd
man/getPhyloseqSlots.Rd
man/getPrevalence.Rd
man/getTaxaOverview.Rd
man/getTaxaSummary.Rd
man/getTibble.Rd
man/getYCTheta.Rd
man/meltDistanceToTable.Rd
man/mutatePhyloseq.Rd
man/pullPhyloseq.Rd
man/readMergedMetaphlan.Rd
man/removeZeros.Rd
man/renameSampleVariables.Rd
man/saveData.Rd
man/saveSequence.Rd
man/separateSampleColumn.Rd
man/summarizeTaxonomicAssignments.Rd
man/transformation.Rd
man/trendAbundanceAssignment.Rd
man/uniqueness.Rd
man/uniteGenusSpeciesNames.Rd
man/uniteSampleColumn.Rd
tests/testthat.R
tests/testthat/test-calculatePD.R
tests/testthat/test-calculateTaxaFoldChange.R
tests/testthat/test-getPrevalence.R
tests/testthat/test-getTaxaSummary.R
tests/testthat/test-trendAbundanceAssignment.R
tests/testthat/test-uniqueness.R
vignettes/.gitignore
vignettes/Introduction.Rmd
