A B C D E F G H I L M P R S T U Z
| mia-package | 'mia' Package. |
| addCluster | Clustering wrapper |
| addCluster-method | Clustering wrapper |
| addContaminantQC | decontam functions |
| addContaminantQC-method | decontam functions |
| addDivergence | Estimate divergence |
| addDivergence-method | Estimate divergence |
| addHierarchyTree | Calculate hierarchy tree |
| addHierarchyTree-method | Calculate hierarchy tree |
| addNotContaminantQC | decontam functions |
| addNotContaminantQC-method | decontam functions |
| addPerSampleDominantFeatures | Get dominant taxa |
| addPerSampleDominantFeatures-method | Get dominant taxa |
| addPerSampleDominantTaxa | Get dominant taxa |
| addPerSampleDominantTaxa-method | Get dominant taxa |
| addTaxonomyTree | These functions will be deprecated. Please use other functions instead. |
| addTaxonomyTree-method | These functions will be deprecated. Please use other functions instead. |
| agglomerate-methods | Agglomerate data using taxonomic information |
| agglomerateByPrevalence | Agglomerate data using taxonomic information |
| agglomerateByPrevalence-method | Agglomerate data using taxonomic information |
| agglomerateByRank | Agglomerate data using taxonomic information |
| agglomerateByRank-method | Agglomerate data using taxonomic information |
| bestDMNFit | Dirichlet-Multinomial Mixture Model: Machine Learning for Microbiome Data |
| bestDMNFit-method | Dirichlet-Multinomial Mixture Model: Machine Learning for Microbiome Data |
| calculateCCA | Canonical Correspondence Analysis and Redundancy Analysis |
| calculateCCA-method | Canonical Correspondence Analysis and Redundancy Analysis |
| calculateDMN | Dirichlet-Multinomial Mixture Model: Machine Learning for Microbiome Data |
| calculateDMN-method | Dirichlet-Multinomial Mixture Model: Machine Learning for Microbiome Data |
| calculateDMNgroup | Dirichlet-Multinomial Mixture Model: Machine Learning for Microbiome Data |
| calculateDMNgroup-method | Dirichlet-Multinomial Mixture Model: Machine Learning for Microbiome Data |
| calculateDPCoA | Calculation of Double Principal Correspondance analysis |
| calculateDPCoA-method | Calculation of Double Principal Correspondance analysis |
| calculateJSD | Calculate the Jensen-Shannon Divergence |
| calculateJSD-method | Calculate the Jensen-Shannon Divergence |
| calculateNMDS | Perform non-metric MDS on sample-level data |
| calculateNMDS-method | Perform non-metric MDS on sample-level data |
| calculateOverlap | Estimate overlap |
| calculateOverlap-method | Estimate overlap |
| calculateRDA | Canonical Correspondence Analysis and Redundancy Analysis |
| calculateRDA-method | Canonical Correspondence Analysis and Redundancy Analysis |
| calculateUnifrac | Calculate weighted or unweighted (Fast) Unifrac distance |
| calculateUnifrac-method | Calculate weighted or unweighted (Fast) Unifrac distance |
| checkTaxonomy | Functions for accessing taxonomic data stored in 'rowData'. |
| checkTaxonomy-method | Functions for accessing taxonomic data stored in 'rowData'. |
| cluster | These functions will be deprecated. Please use other functions instead. |
| cluster-method | These functions will be deprecated. Please use other functions instead. |
| countDominantFeatures | Summarizing microbiome data |
| countDominantFeatures-method | Summarizing microbiome data |
| countDominantTaxa | Summarizing microbiome data |
| countDominantTaxa-method | Summarizing microbiome data |
| deprecate | These functions will be deprecated. Please use other functions instead. |
| dmn_se | dmn_se |
| enterotype | enterotype |
| esophagus | esophagus |
| estimateDivergence | These functions will be deprecated. Please use other functions instead. |
| estimateDivergence-method | These functions will be deprecated. Please use other functions instead. |
| estimateDiversity | Estimate (alpha) diversity measures |
| estimateDiversity-method | Estimate (alpha) diversity measures |
| estimateDominance | Estimate dominance measures |
| estimateDominance-method | Estimate dominance measures |
| estimateEvenness | Estimate Evenness measures |
| estimateEvenness-method | Estimate Evenness measures |
| estimateFaith | Estimate (alpha) diversity measures |
| estimateFaith-method | Estimate (alpha) diversity measures |
| estimateRichness | Estimate richness measures |
| estimateRichness-method | Estimate richness measures |
| full_join | These functions will be deprecated. Please use other functions instead. |
| full_join-method | These functions will be deprecated. Please use other functions instead. |
| getBestDMNFit | Dirichlet-Multinomial Mixture Model: Machine Learning for Microbiome Data |
| getBestDMNFit-method | Dirichlet-Multinomial Mixture Model: Machine Learning for Microbiome Data |
| getDMN | Dirichlet-Multinomial Mixture Model: Machine Learning for Microbiome Data |
| getDMN-method | Dirichlet-Multinomial Mixture Model: Machine Learning for Microbiome Data |
| getExperimentCrossAssociation | Calculate correlations between features of two experiments. |
| getExperimentCrossAssociation-method | Calculate correlations between features of two experiments. |
| getExperimentCrossCorrelation | Calculate correlations between features of two experiments. |
| getExperimentCrossCorrelation-method | Calculate correlations between features of two experiments. |
| getHierarchyTree | Calculate hierarchy tree |
| getHierarchyTree-method | Calculate hierarchy tree |
| getPrevalence | Calculation prevalence information for features across samples |
| getPrevalence-method | Calculation prevalence information for features across samples |
| getPrevalentAbundance | Calculation prevalence information for features across samples |
| getPrevalentAbundance-method | Calculation prevalence information for features across samples |
| getPrevalentFeatures | Calculation prevalence information for features across samples |
| getPrevalentFeatures-method | Calculation prevalence information for features across samples |
| getPrevalentTaxa | Calculation prevalence information for features across samples |
| getPrevalentTaxa-method | Calculation prevalence information for features across samples |
| getRareFeatures | Calculation prevalence information for features across samples |
| getRareFeatures-method | Calculation prevalence information for features across samples |
| getRarePrevalentTaxa | Calculation prevalence information for features across samples |
| getRareTaxa | Calculation prevalence information for features across samples |
| getRareTaxa-method | Calculation prevalence information for features across samples |
| getTaxonomyLabels | Functions for accessing taxonomic data stored in 'rowData'. |
| getTaxonomyLabels-method | Functions for accessing taxonomic data stored in 'rowData'. |
| getTaxonomyRanks | Functions for accessing taxonomic data stored in 'rowData'. |
| getTopFeatures | Summarizing microbiome data |
| getTopFeatures-method | Summarizing microbiome data |
| getTopTaxa | Summarizing microbiome data |
| getTopTaxa-method | Summarizing microbiome data |
| getUniqueFeatures | Summarizing microbiome data |
| getUniqueFeatures-method | Summarizing microbiome data |
| getUniqueTaxa | Summarizing microbiome data |
| getUniqueTaxa-method | Summarizing microbiome data |
| GlobalPatterns | GlobalPatterns |
| hierarchy-tree | Calculate hierarchy tree |
| HintikkaXOData | HintikkaXOData |
| IdTaxaToDataFrame | Functions for accessing taxonomic data stored in 'rowData'. |
| importBIOM | Loading a biom file |
| importHUMAnN | Import HUMAnN results to 'TreeSummarizedExperiment' |
| importMetaPhlAn | Import Metaphlan results to 'TreeSummarizedExperiment' |
| importMothur | Import Mothur results as a 'TreeSummarizedExperiment' |
| importQIIME2 | Import QIIME2 results to 'TreeSummarizedExperiment' |
| importQZA | Import QIIME2 results to 'TreeSummarizedExperiment' |
| inner_join | These functions will be deprecated. Please use other functions instead. |
| inner_join-method | These functions will be deprecated. Please use other functions instead. |
| isContaminant | decontam functions |
| isContaminant-method | decontam functions |
| isNotContaminant-method | decontam functions |
| left_join | These functions will be deprecated. Please use other functions instead. |
| left_join-method | These functions will be deprecated. Please use other functions instead. |
| loadFromBiom | These functions will be deprecated. Please use other functions instead. |
| loadFromHumann | These functions will be deprecated. Please use other functions instead. |
| loadFromMetaphlan | These functions will be deprecated. Please use other functions instead. |
| loadFromMothur | These functions will be deprecated. Please use other functions instead. |
| loadFromQIIME2 | These functions will be deprecated. Please use other functions instead. |
| makePhyloseqFromTreeSE | Create a phyloseq object from a TreeSummarizedExperiment object |
| makePhyloseqFromTreeSE-method | Create a phyloseq object from a TreeSummarizedExperiment object |
| makePhyloseqFromTreeSummarizedExperiment | Create a phyloseq object from a TreeSummarizedExperiment object |
| makePhyloseqFromTreeSummarizedExperiment-method | Create a phyloseq object from a TreeSummarizedExperiment object |
| makeTreeSEFromBiom | Loading a biom file |
| makeTreeSEFromDADA2 | Coerce 'DADA2' results to 'TreeSummarizedExperiment' |
| makeTreeSEFromPhyloseq | Coerce a 'phyloseq' object to a 'TreeSummarizedExperiment' |
| makeTreeSummarizedExperimentFromBiom | Loading a biom file |
| makeTreeSummarizedExperimentFromDADA2 | Coerce 'DADA2' results to 'TreeSummarizedExperiment' |
| makeTreeSummarizedExperimentFromPhyloseq | Coerce a 'phyloseq' object to a 'TreeSummarizedExperiment' |
| makeTreeSummarizedExperimentFromPhyloseq-method | Coerce a 'phyloseq' object to a 'TreeSummarizedExperiment' |
| mapTaxonomy | Functions for accessing taxonomic data stored in 'rowData'. |
| mapTaxonomy-method | Functions for accessing taxonomic data stored in 'rowData'. |
| meltAssay | Converting a 'SummarizedExperiment' object into a long data.frame |
| meltAssay-method | Converting a 'SummarizedExperiment' object into a long data.frame |
| merge-methods | Merge a subset of the rows or columns of a 'SummarizedExperiment' |
| mergeCols | Merge a subset of the rows or columns of a 'SummarizedExperiment' |
| mergeCols-method | Merge a subset of the rows or columns of a 'SummarizedExperiment' |
| mergeFeatures | Merge a subset of the rows or columns of a 'SummarizedExperiment' |
| mergeFeatures-method | Merge a subset of the rows or columns of a 'SummarizedExperiment' |
| mergeFeaturesByPrevalence | These functions will be deprecated. Please use other functions instead. |
| mergeFeaturesByPrevalence-method | These functions will be deprecated. Please use other functions instead. |
| mergeFeaturesByRank | Agglomerate data using taxonomic information |
| mergeFeaturesByRank-method | Agglomerate data using taxonomic information |
| mergeRows | Merge a subset of the rows or columns of a 'SummarizedExperiment' |
| mergeRows-method | Merge a subset of the rows or columns of a 'SummarizedExperiment' |
| mergeSamples | Merge a subset of the rows or columns of a 'SummarizedExperiment' |
| mergeSamples-method | Merge a subset of the rows or columns of a 'SummarizedExperiment' |
| mergeSEs | Merge SE objects into single SE object. |
| mergeSEs-method | Merge SE objects into single SE object. |
| mergeSmaples | Merge a subset of the rows or columns of a 'SummarizedExperiment' |
| mia | 'mia' Package. |
| mia-datasets | mia datasets |
| peerj13075 | peerj13075 |
| performDMNgroupCV | Dirichlet-Multinomial Mixture Model: Machine Learning for Microbiome Data |
| performDMNgroupCV-method | Dirichlet-Multinomial Mixture Model: Machine Learning for Microbiome Data |
| perSampleDominantFeatures | Get dominant taxa |
| perSampleDominantFeatures-method | Get dominant taxa |
| perSampleDominantTaxa | Get dominant taxa |
| perSampleDominantTaxa-method | Get dominant taxa |
| plotNMDS | These functions will be deprecated. Please use other functions instead. |
| rarifyCounts | Subsample Counts |
| readQZA | These functions will be deprecated. Please use other functions instead. |
| relabundance | Getter / setter for relative abundance data |
| relabundance-method | Getter / setter for relative abundance data |
| relabundance<- | Getter / setter for relative abundance data |
| relabundance<--method | Getter / setter for relative abundance data |
| relAbundanceCounts | Transform assay |
| relAbundanceCounts-method | Transform assay |
| right_join | These functions will be deprecated. Please use other functions instead. |
| right_join-method | These functions will be deprecated. Please use other functions instead. |
| runCCA | Canonical Correspondence Analysis and Redundancy Analysis |
| runCCA-method | Canonical Correspondence Analysis and Redundancy Analysis |
| runDMN | Dirichlet-Multinomial Mixture Model: Machine Learning for Microbiome Data |
| runDPCoA | Calculation of Double Principal Correspondance analysis |
| runJSD | Calculate the Jensen-Shannon Divergence |
| runNMDS | Perform non-metric MDS on sample-level data |
| runOverlap | Estimate overlap |
| runOverlap-method | Estimate overlap |
| runRDA | Canonical Correspondence Analysis and Redundancy Analysis |
| runRDA-method | Canonical Correspondence Analysis and Redundancy Analysis |
| runUnifrac | Calculate weighted or unweighted (Fast) Unifrac distance |
| setTaxonomyRanks | Functions for accessing taxonomic data stored in 'rowData'. |
| splitByRanks | Split/Unsplit a 'SingleCellExperiment' by taxonomic ranks |
| splitByRanks-method | Split/Unsplit a 'SingleCellExperiment' by taxonomic ranks |
| splitOn | Split 'TreeSummarizedExperiment' column-wise or row-wise based on grouping variable |
| splitOn-method | Split 'TreeSummarizedExperiment' column-wise or row-wise based on grouping variable |
| subsampleCounts | Subsample Counts |
| subsampleCounts-method | Subsample Counts |
| subsetByPrevalentFeatures | Calculation prevalence information for features across samples |
| subsetByPrevalentFeatures-method | Calculation prevalence information for features across samples |
| subsetByPrevalentTaxa | Calculation prevalence information for features across samples |
| subsetByPrevalentTaxa-method | Calculation prevalence information for features across samples |
| subsetByRareFeatures | Calculation prevalence information for features across samples |
| subsetByRareFeatures-method | Calculation prevalence information for features across samples |
| subsetByRareTaxa | Calculation prevalence information for features across samples |
| subsetByRareTaxa-method | Calculation prevalence information for features across samples |
| subsetFeatures | Subset functions |
| subsetFeatures-method | Subset functions |
| subsetSamples | Subset functions |
| subsetSamples-method | Subset functions |
| subsetTaxa | Subset functions |
| subsetTaxa-method | Subset functions |
| summaries | Summarizing microbiome data |
| summary-method | Summarizing microbiome data |
| taxonomy-methods | Functions for accessing taxonomic data stored in 'rowData'. |
| taxonomyRankEmpty | Functions for accessing taxonomic data stored in 'rowData'. |
| taxonomyRankEmpty-method | Functions for accessing taxonomic data stored in 'rowData'. |
| taxonomyRanks | Functions for accessing taxonomic data stored in 'rowData'. |
| taxonomyRanks-method | Functions for accessing taxonomic data stored in 'rowData'. |
| taxonomyTree | These functions will be deprecated. Please use other functions instead. |
| taxonomyTree-method | These functions will be deprecated. Please use other functions instead. |
| TAXONOMY_RANKS | Functions for accessing taxonomic data stored in 'rowData'. |
| Tengeler2020 | Tengeler2020 |
| testExperimentCrossAssociation | Calculate correlations between features of two experiments. |
| testExperimentCrossAssociation-method | Calculate correlations between features of two experiments. |
| testExperimentCrossCorrelation | Calculate correlations between features of two experiments. |
| testExperimentCrossCorrelation-method | Calculate correlations between features of two experiments. |
| transformAssay | Transform assay |
| transformAssay-method | Transform assay |
| transformCounts | Transform assay |
| transformFeatures | Transform assay |
| transformFeatures-method | Transform assay |
| transformSamples | Transform assay |
| transformSamples-method | Transform assay |
| twins | dmn_se |
| unsplitByRanks | Split/Unsplit a 'SingleCellExperiment' by taxonomic ranks |
| unsplitByRanks-method | Split/Unsplit a 'SingleCellExperiment' by taxonomic ranks |
| unsplitOn | Split 'TreeSummarizedExperiment' column-wise or row-wise based on grouping variable |
| unsplitOn-method | Split 'TreeSummarizedExperiment' column-wise or row-wise based on grouping variable |
| ZTransform | Transform assay |
| ZTransform-method | Transform assay |