Files in microbiome/mia
Microbiome analysis
.Rbuildignore
.github/.gitignore
.github/ISSUE_TEMPLATE/Pull Request.md
.github/ISSUE_TEMPLATE/bug_report.md
.github/ISSUE_TEMPLATE/feature_request.md
.github/ISSUE_TEMPLATE/pull-request.md
.github/ISSUE_TEMPLATE/user-support.md
.github/workflows/rworkflows.yml
.gitignore
CONTRIBUTING.md
DESCRIPTION
LICENSE
NAMESPACE
NEWS
R/addAlpha.R
R/addDissimilarity.R
R/addLDA.R
R/addNMF.R
R/agglomerate.R
R/calculateDMM.R
R/calculateJSD.R
R/calculateOverlap.R
R/calculateUnifrac.R
R/cluster.R
R/convertFromBIOM.R
R/convertFromDADA2.R
R/convertFromPhyloseq.R
R/convertToPhyloseq.R
R/decontam.R
R/deprecate.R
R/estimateDivergence.R
R/estimateDiversity.R
R/estimateDominance.R
R/estimateEvenness.R
R/estimateRichness.R
R/getCrossAssociation.R
R/getDominant.R
R/getPrevalence.R
R/importHumann.R
R/importMetaphlan.R
R/importMothur.R
R/importQIIME2.R
R/importTaxpasta.R
R/mediate.R
R/meltAssay.R
R/merge.R
R/mergeSEs.R
R/mia.R
R/rarefyAssay.R
R/runCCA.R
R/runDPCoA.R
R/runNMDS.R
R/splitByRanks.R
R/splitOn.R
R/subset.R
R/summaries.R
R/taxonomy.R
R/transformCounts.R
R/utils.R
README.md
data/GlobalPatterns.rda
data/HintikkaXOData.rda
data/Tengeler2020.rda
data/Tito2024QMP.rda
data/dmn_se.rda
data/enterotype.rda
data/esophagus.rda
data/peerj13075.rda
inst/extdata/Aggregated_humanization2.biom
inst/extdata/Data_humanization_phylo_aggregation.tre
inst/extdata/Mapping_file_ADHD_aggregated.csv
inst/extdata/complete.biom
inst/extdata/humann_output.tsv
inst/extdata/less_ranks.biom
inst/extdata/merged_abundance_table.txt
inst/extdata/more_ranks.biom
inst/extdata/mothur_example.cons.taxonomy
inst/extdata/mothur_example.design
inst/extdata/mothur_example.shared
inst/extdata/mothur_example.taxonomy
inst/extdata/refseq.qza
inst/extdata/sample-metadata.tsv
inst/extdata/simple.biom
inst/extdata/table-rownamesInSeq.qza
inst/extdata/table.qza
inst/extdata/taxonomy.qza
inst/extdata/taxpasta_no_type.biom
inst/extdata/tree.qza
inst/scripts/Tito2024QMP.R
inst/scripts/biom_test_data.py
inst/scripts/import.R
man/GlobalPatterns.Rd
man/HintikkaXOData.Rd
man/Tengeler2020.Rd
man/Tito2024QMP.Rd
man/addAlpha.Rd
man/addCluster.Rd
man/addDivergence.Rd
man/addLDA.Rd
man/addNMF.Rd
man/agglomerate-methods.Rd
man/agglomerateByPrevalence.Rd
man/calculateDMN.Rd
man/convertFromDADA2.Rd
man/convertFromPhyloseq.Rd
man/deprecate.Rd
man/dmn_se.Rd
man/enterotype.Rd
man/esophagus.Rd
man/figures/mia_logo.png
man/getCrossAssociation.Rd
man/getDissimilarity.Rd
man/getDominant.Rd
man/getMediation.Rd
man/getPrevalence.Rd
man/hierarchy-tree.Rd
man/importBIOM.Rd
man/importHUMAnN.Rd
man/importMetaPhlAn.Rd
man/importMothur.Rd
man/importQIIME2.Rd
man/importTaxpasta.Rd
man/isContaminant.Rd
man/meltSE.Rd
man/mergeSEs.Rd
man/mia-datasets.Rd
man/mia-package.Rd
man/peerj13075.Rd
man/rarefyAssay.Rd
man/runCCA.Rd
man/runDPCoA.Rd
man/runNMDS.Rd
man/splitOn.Rd
man/summaries.Rd
man/taxonomy-methods.Rd
man/transformAssay.Rd
pkgdown/_pkgdown.yml
tests/testthat.R
tests/testthat/test-0divergence.R
tests/testthat/test-0diversity.R
tests/testthat/test-0utilites.R
tests/testthat/test-2merge.R
tests/testthat/test-2mergeSEs.R
tests/testthat/test-2taxonomy.R
tests/testthat/test-3agglomerate.R
tests/testthat/test-4IO.R
tests/testthat/test-4splitByRanks.R
tests/testthat/test-4splitOn.R
tests/testthat/test-5Unifrac.R
tests/testthat/test-5addLDA.R
tests/testthat/test-5addNMF.R
tests/testthat/test-5calculateOverlap.R
tests/testthat/test-5dominance.R
tests/testthat/test-5dominantTaxa.R
tests/testthat/test-5evenness.R
tests/testthat/test-5getCrossAssociation.R
tests/testthat/test-5getDissimilarity.R
tests/testthat/test-5prevalence.R
tests/testthat/test-5richness.R
tests/testthat/test-5runDPCoA.R
tests/testthat/test-5runNMDS.R
tests/testthat/test-5transformCounts.R
tests/testthat/test-6cca.R
tests/testthat/test-7decontam.R
tests/testthat/test-8subsample.R
tests/testthat/test-8summaries.R
tests/testthat/test-9cluster.R
tests/testthat/test-addAlpha.R
tests/testthat/test-importTaxpasta.R
tests/testthat/test-mediate.R
vignettes/mia.Rmd
vignettes/references.bib
