Files in microbiome/mia

Microbiome analysis

.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 CONTRIBUTING.md R/addAlpha.R R/addDissimilarity.R R/addDivergence.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/estimateDiversity.R R/estimateDominance.R R/estimateEvenness.R R/estimateRichness.R R/getCrossAssociation.R R/getDominant.R R/getPERMANOVA.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 inst/scripts/Tito2024QMP.R 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/getCrossAssociation.Rd man/getDissimilarity.Rd man/getDominant.Rd man/getMediation.Rd man/getPERMANOVA.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 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-getPERMANOVA.R tests/testthat/test-importTaxpasta.R tests/testthat/test-mediate.R vignettes/mia.Rmd