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"agglomerateByModule", "agglomerateByModule,SummarizedExperiment-method", "agglomerateByRank", "agglomerateByRank,SingleCellExperiment-method", "agglomerateByRank,SummarizedExperiment-method", "agglomerateByRank,TreeSummarizedExperiment-method", "agglomerateByRanks", "agglomerateByRanks,SingleCellExperiment-method", "agglomerateByRanks,SummarizedExperiment-method", "agglomerateByRanks,TreeSummarizedExperiment-method", "agglomerateByVariable", "agglomerateByVariable,SummarizedExperiment-method", "agglomerateByVariable,TreeSummarizedExperiment-method", "splitByRanks", "unsplitByRanks", "unsplitByRanks,SingleCellExperiment-method", "unsplitByRanks,TreeSummarizedExperiment-method" ] }, { "page": "calculateDMN", "title": "Dirichlet-Multinomial Mixture Model: Machine Learning for Microbiome Data", "topics": [ "bestDMNFit", "bestDMNFit,SummarizedExperiment-method", "calculateDMN", "calculateDMN,ANY-method", "calculateDMN,SummarizedExperiment-method", "calculateDMNgroup", "calculateDMNgroup,ANY-method", "calculateDMNgroup,SummarizedExperiment-method", "getBestDMNFit", "getBestDMNFit,SummarizedExperiment-method", "getDMN", "getDMN,SummarizedExperiment-method", "performDMNgroupCV", "performDMNgroupCV,ANY-method", "performDMNgroupCV,SummarizedExperiment-method", "runDMN" ] }, { "page": "convertFromDADA2", "title": "Create a 'TreeSummarizedExperiment' object from 'DADA2' results", "topics": [ "convertFromDADA2" ] }, { "page": "importBIOM", "title": "Convert a 'TreeSummarizedExperiment' object to/from 'BIOM' results", "topics": [ "convertFromBIOM", "convertToBIOM", "convertToBIOM,SummarizedExperiment-method", "importBIOM" ] }, { "page": "convertFromPhyloseq", "title": "Create a 'TreeSummarizedExperiment' object from a phyloseq object", "topics": [ "convertFromPhyloseq", "convertToPhyloseq", "convertToPhyloseq,SummarizedExperiment-method", "convertToPhyloseq,TreeSummarizedExperiment-method" ] }, { "page": "deprecate", "title": "These functions will be deprecated. Please use other functions instead.", "topics": [ "addPerSampleDominantFeatures", "addPerSampleDominantFeatures,SummarizedExperiment-method", "addPerSampleDominantTaxa", "addPerSampleDominantTaxa,SummarizedExperiment-method", "addTaxonomyTree", "addTaxonomyTree,SummarizedExperiment-method", "calculateJSD", "calculateJSD,ANY-method", "calculateOverlap", "calculateOverlap,ANY-method", "calculateUnifrac", "calculateUnifrac,ANY-method", "cluster", "cluster,SummarizedExperiment-method", "countDominantFeatures", "countDominantFeatures,SummarizedExperiment-method", "countDominantTaxa", "countDominantTaxa,SummarizedExperiment-method", "deprecate", "estimateDivergence", "estimateDivergence,SummarizedExperiment-method", "estimateDiversity", "estimateDiversity,ANY-method", "estimateDominance", "estimateDominance,ANY-method", "estimateEvenness", "estimateEvenness,ANY-method", "estimateFaith", "estimateFaith,ANY-method", "estimateRichness", "estimateRichness,ANY-method", "full_join", "full_join,ANY-method", "getExperimentCrossAssociation", "getExperimentCrossAssociation,MultiAssayExperiment-method", "getExperimentCrossAssociation,SummarizedExperiment-method", "getExperimentCrossCorrelation", "getExperimentCrossCorrelation,ANY-method", "getPrevalentFeatures", "getPrevalentFeatures,ANY-method", "getPrevalentFeatures,SummarizedExperiment-method", "getPrevalentTaxa", "getPrevalentTaxa,ANY-method", "getPrevalentTaxa,SummarizedExperiment-method", "getRareFeatures", "getRareFeatures,ANY-method", "getRareFeatures,SummarizedExperiment-method", "getRareTaxa", "getRareTaxa,ANY-method", "getRareTaxa,SummarizedExperiment-method", "getTopFeatures", "getTopFeatures,SummarizedExperiment-method", "getTopTaxa", "getTopTaxa,SummarizedExperiment-method", "getUniqueFeatures", "getUniqueFeatures,SummarizedExperiment-method", "getUniqueTaxa", "getUniqueTaxa,SummarizedExperiment-method", "inner_join", "inner_join,ANY-method", "left_join", "left_join,ANY-method", "loadFromBiom", "loadFromHumann", "loadFromMetaphlan", "loadFromMothur", "loadFromQIIME2", "makePhyloseqFromTreeSE", "makePhyloseqFromTreeSE,SummarizedExperiment-method", "makePhyloseqFromTreeSE,TreeSummarizedExperiment-method", "makePhyloseqFromTreeSummarizedExperiment", "makePhyloseqFromTreeSummarizedExperiment,ANY-method", "makeTreeSEFromBiom", "makeTreeSEFromDADA2", "makeTreeSEFromPhyloseq", "makeTreeSummarizedExperimentFromBiom", "makeTreeSummarizedExperimentFromDADA2", "makeTreeSummarizedExperimentFromPhyloseq", "makeTreeSummarizedExperimentFromPhyloseq,ANY-method", "meltAssay", "meltAssay,SummarizedExperiment-method", "mergeCols", "mergeCols,SummarizedExperiment-method", "mergeCols,TreeSummarizedExperiment-method", "mergeFeatures", "mergeFeatures,SummarizedExperiment-method", "mergeFeatures,TreeSummarizedExperiment-method", "mergeFeaturesByPrevalence", "mergeFeaturesByPrevalence,SummarizedExperiment-method", "mergeFeaturesByRank", "mergeFeaturesByRank,SingleCellExperiment-method", "mergeFeaturesByRank,SummarizedExperiment-method", "mergeFeaturesByRank,TreeSummarizedExperiment-method", "mergeRows", "mergeRows,SummarizedExperiment-method", "mergeRows,TreeSummarizedExperiment-method", "mergeSamples", "mergeSamples,SummarizedExperiment-method", "mergeSamples,TreeSummarizedExperiment-method", "perSampleDominantFeatures", "perSampleDominantFeatures,SummarizedExperiment-method", "perSampleDominantTaxa", "perSampleDominantTaxa,SummarizedExperiment-method", "plotNMDS", "readQZA", "relabundance", "relabundance,SummarizedExperiment-method", "relabundance<-", "relabundance<-,SummarizedExperiment-method", "relAbundanceCounts", "relAbundanceCounts,SummarizedExperiment-method", "right_join", "right_join,ANY-method", "runJSD", "runJSD,SummarizedExperiment-method", "runOverlap", "runOverlap,SummarizedExperiment-method", "runUnifrac", "subsampleCounts", "subsampleCounts,SummarizedExperiment-method", "subsetByPrevalentFeatures", "subsetByPrevalentFeatures,ANY-method", "subsetByPrevalentTaxa", "subsetByPrevalentTaxa,ANY-method", "subsetByRareFeatures", "subsetByRareFeatures,ANY-method", "subsetByRareTaxa", "subsetByRareTaxa,ANY-method", "subsetFeatures", "subsetFeatures,SummarizedExperiment-method", "subsetSamples", "subsetSamples,SummarizedExperiment-method", "subsetTaxa", "subsetTaxa,SummarizedExperiment-method", "taxonomyTree", "taxonomyTree,SummarizedExperiment-method", "testExperimentCrossAssociation", "testExperimentCrossAssociation,ANY-method", "testExperimentCrossCorrelation", "testExperimentCrossCorrelation,ANY-method", "transformCounts", "transformFeatures", "transformFeatures,SummarizedExperiment-method", "transformSamples", "transformSamples,SummarizedExperiment-method", "ZTransform", "ZTransform,SummarizedExperiment-method" ] }, { "page": "dmn_se", "title": "Twins' microbiome data from 278 individuals", "topics": [ "dmn_se", "twins" ] }, { "page": "enterotype", "title": "Human gut microbiome dataset from 22 subjects based on shotgun DNA sequencing", "topics": [ "enterotype" ] }, { "page": "esophagus", "title": "Human esophageal community from 3 individuals", "topics": [ "esophagus" ] }, { "page": "getAbundant", "title": "Determine abundant and rare taxa. Rare taxa can be further classified to conditionally rare and permanently rare.", "topics": [ "addAbundanceClass", "addAbundanceClass,SingleCellExperiment-method", "addAbundanceClass,SummarizedExperiment-method", "getAbundanceClass", "getAbundanceClass,ANY-method", "getAbundanceClass,SingleCellExperiment-method", "getAbundanceClass,SummarizedExperiment-method", "getAbundant", "getAbundant,ANY-method", "getAbundant,SingleCellExperiment-method", "getAbundant,SummarizedExperiment-method", "getConditionallyLowAbundant", "getConditionallyLowAbundant,ANY-method", "getConditionallyLowAbundant,SingleCellExperiment-method", "getConditionallyLowAbundant,SummarizedExperiment-method", "getLowAbundant", "getLowAbundant,ANY-method", "getLowAbundant,SingleCellExperiment-method", "getLowAbundant,SummarizedExperiment-method", "getPermanentlyLowAbundant", "getPermanentlyLowAbundant,ANY-method", "getPermanentlyLowAbundant,SingleCellExperiment-method", "getPermanentlyLowAbundant,SummarizedExperiment-method" ] }, { "page": "runCCA", "title": "Canonical Correspondence Analysis and Redundancy Analysis", "topics": [ "addCCA", "addCCA,SingleCellExperiment-method", "addRDA", "addRDA,SingleCellExperiment-method", "calculateCCA", "calculateRDA", "getCCA", "getCCA,ANY-method", "getCCA,SummarizedExperiment-method", "getRDA", "getRDA,ANY-method", "getRDA,SummarizedExperiment-method", "runCCA", "runRDA" ] }, { "page": "addCluster", "title": "Clustering wrapper", "topics": [ "addCluster", "addCluster,SingleCellExperiment-method", "addCluster,SummarizedExperiment-method", "getCluster", "getCluster,ANY-method", "getCluster,SingleCellExperiment-method", "getCluster,SummarizedExperiment-method" ] }, { "page": "getCrossAssociation", "title": "Calculate correlations between features of two experiments.", "topics": [ "getCrossAssociation", "getCrossAssociation,MultiAssayExperiment-method", "getCrossAssociation,SummarizedExperiment-method" ] }, { "page": "getDominant", "title": "Get dominant taxa", "topics": [ "addDominant", "addDominant,SummarizedExperiment-method", "getDominant", "getDominant,SummarizedExperiment-method" ] }, { "page": "runDPCoA", "title": "Calculation of Double Principal Correspondence analysis", "topics": [ "addDPCoA", "calculateDPCoA", "getDPCoA", "getDPCoA,ANY,ANY-method", "getDPCoA,TreeSummarizedExperiment,missing-method", "runDPCoA" ] }, { "page": "hierarchy-tree", "title": "Calculate hierarchy tree", "topics": [ "addHierarchyTree", "addHierarchyTree,SummarizedExperiment-method", "getHierarchyTree", "getHierarchyTree,SummarizedExperiment-method", "hierarchy-tree" ] }, { "page": "addLDA", "title": "Latent Dirichlet Allocation", "topics": [ "addLDA", "addLDA,SummarizedExperiment-method", "getLDA", "getLDA,SummarizedExperiment-method" ] }, { "page": "addMDS", "title": "Perform multi-dimensional scaling (MDS)", "topics": [ "addMDS", "addMDS,SingleCellExperiment-method", "getMDS", "getMDS,SingleCellExperiment-method", "getMDS,TreeSummarizedExperiment-method" ] }, { "page": "runNMDS", "title": "Perform non-metric MDS on sample-level data", "topics": [ "addNMDS", "calculateNMDS", "getNMDS", "getNMDS,ANY-method", "getNMDS,SingleCellExperiment-method", "getNMDS,SummarizedExperiment-method", "runNMDS" ] }, { "page": "addNMF", "title": "Non-negative Matrix Factorization", "topics": [ "addNMF", "addNMF,SummarizedExperiment-method", "getNMF", "getNMF,SummarizedExperiment-method" ] }, { "page": "getPERMANOVA", "title": "Calculate PERMANOVA (Permutational Multivariate Analysis of Variance)", "topics": [ "addPERMANOVA", "addPERMANOVA,SummarizedExperiment-method", "getPERMANOVA", "getPERMANOVA,ANY-method", "getPERMANOVA,SingleCellExperiment-method", "getPERMANOVA,SummarizedExperiment-method" ] }, { "page": "getPrevalence", "title": "Calculation prevalence information for features across samples", "topics": [ "addPrevalence", "addPrevalence,SummarizedExperiment-method", "addPrevalentAbundance", "addPrevalentAbundance,SummarizedExperiment-method", "getPrevalence", "getPrevalence,ANY-method", "getPrevalence,SummarizedExperiment-method", "getPrevalent", "getPrevalent,ANY-method", "getPrevalent,SummarizedExperiment-method", "getPrevalentAbundance", "getPrevalentAbundance,ANY-method", "getPrevalentAbundance,SummarizedExperiment-method", "getRare", "getRare,ANY-method", "getRare,SummarizedExperiment-method", "subsetByPrevalent", "subsetByPrevalent,SummarizedExperiment-method", "subsetByPrevalent,TreeSummarizedExperiment-method", "subsetByRare", "subsetByRare,SummarizedExperiment-method", "subsetByRare,TreeSummarizedExperiment-method" ] }, { "page": "utilization_functions", "title": "Utilization functions for 'TreeSummarizedExperiment' objects", "topics": [ "getReducedDimAttribute", "getReducedDimAttribute,SingleCellExperiment-method", "utilization_functions" ] }, { "page": "getRPCA", "title": "Run (joint) robust principal component analysis (RPCA)", "topics": [ "addJointRPCA", "addJointRPCA,MultiAssayExperiment-method", "addJointRPCA,SingleCellExperiment-method", "addRPCA", "addRPCA,SummarizedExperiment-method", "getJointRPCA", "getJointRPCA,MultiAssayExperiment-method", "getJointRPCA,SingleCellExperiment-method", "getRPCA", "getRPCA,SingleCellExperiment-method", "getRPCA,SummarizedExperiment-method" ] }, { "page": "GlobalPatterns", "title": "Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample.", "topics": [ "GlobalPatterns" ] }, { "page": "HintikkaXOData", "title": "Multiomics dataset from 40 rat samples", "topics": [ "HintikkaXOData" ] }, { "page": "ibdmdb", "title": "IBDMDB 2-omic demo dataset (MGX + MTX)", "topics": [ "ibdmdb" ] }, { "page": "importHUMAnN", "title": "Import HUMAnN results to 'TreeSummarizedExperiment'", "topics": [ "importHUMAnN" ] }, { "page": "importMetaPhlAn", "title": "Import Metaphlan results to 'TreeSummarizedExperiment'", "topics": [ "importMetaPhlAn" ] }, { "page": "importMothur", "title": "Import Mothur results as a 'TreeSummarizedExperiment'", "topics": [ "importMothur" ] }, { "page": "importQIIME2", "title": "Import QIIME2 results to 'TreeSummarizedExperiment'", "topics": [ "importQIIME2", "importQZA" ] }, { "page": "importTaxpasta", "title": "Import taxpasta-specific BIOM results to 'TreeSummarizedExperiment'", "topics": [ "importTaxpasta" ] }, { "page": "meltSE", "title": "Converting a 'SummarizedExperiment' object into a long data.frame", "topics": [ "meltSE", "meltSE,SingleCellExperiment-method", "meltSE,SummarizedExperiment-method" ] }, { "page": "mergeSEs", "title": "Merge SE objects into single SE object.", "topics": [ "mergeSEs", "mergeSEs,list-method", "mergeSEs,SimpleList-method", "mergeSEs,SummarizedExperiment-method" ] }, { "page": "mia-datasets", "title": "mia datasets", "topics": [ "mia-datasets" ] }, { "page": "peerj13075", "title": "Skin microbial profiles 58 genetically unrelated individuals", "topics": [ "peerj13075" ] }, { "page": "rarefyAssay", "title": "Subsample Counts", "topics": [ "rarefyAssay", "rarefyAssay,SummarizedExperiment-method" ] }, { "page": "splitOn", "title": "Split 'TreeSummarizedExperiment' column-wise or row-wise based on grouping variable", "topics": [ "splitOn", "splitOn,SingleCellExperiment-method", "splitOn,SummarizedExperiment-method", "splitOn,TreeSummarizedExperiment-method", "unsplitOn", "unsplitOn,list-method", "unsplitOn,SimpleList-method", "unsplitOn,SingleCellExperiment-method" ] }, { "page": "summary", "title": "Summarizing microbiome data", "topics": [ "getTop", "getTop,SummarizedExperiment-method", "getUnique", "getUnique,SummarizedExperiment-method", "summarizeDominance", "summarizeDominance,SummarizedExperiment-method", "summary", "summary,SummarizedExperiment-method" ] }, { "page": "taxonomy-methods", "title": "Functions for accessing taxonomic data stored in 'rowData'.", "topics": [ "checkTaxonomy", "checkTaxonomy,SummarizedExperiment-method", "getTaxonomyLabels", "getTaxonomyLabels,SummarizedExperiment-method", "getTaxonomyRanks", "IdTaxaToDataFrame", "mapTaxonomy", "mapTaxonomy,SummarizedExperiment-method", "setTaxonomyRanks", "taxonomy-methods", "taxonomyRankEmpty", "taxonomyRankEmpty,SummarizedExperiment-method", "taxonomyRanks", "taxonomyRanks,SummarizedExperiment-method" ] }, { "page": "Tengeler2020", "title": "Gut microbiota profiles of 27 individuals with ADHD and healthy controls", "topics": [ "Tengeler2020" ] }, { "page": "Tito2024QMP", "title": "Fecal microbiota samples from 589 patients across different colorectal cancer stages", "topics": [ "Tito2024QMP" ] }, { "page": "transformAssay", "title": "Transform assay", "topics": [ "transformAssay", "transformAssay,SingleCellExperiment-method", "transformAssay,SummarizedExperiment-method" ] } ], "_readme": "https://github.com/bioc/mia/raw/HEAD/README.md", "_rundeps": [ "abind", "ape", "assorthead", "base64enc", "beachmat", "beeswarm", "BH", "Biobase", "BiocBaseUtils", "BiocGenerics", 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