Man pages for microbiome/mia
Microbiome analysis
| addCluster | Clustering wrapper |
| addDivergence | Estimate divergence |
| agglomerate-methods | Agglomerate data using taxonomic information |
| calculateDMN | Dirichlet-Multinomial Mixture Model: Machine Learning for... |
| calculateJSD | Calculate the Jensen-Shannon Divergence |
| calculateOverlap | Estimate overlap |
| calculateUnifrac | Calculate weighted or unweighted (Fast) Unifrac distance |
| deprecate | These functions will be deprecated. Please use other... |
| dmn_se | dmn_se |
| enterotype | enterotype |
| esophagus | esophagus |
| estimateDiversity | Estimate (alpha) diversity measures |
| estimateDominance | Estimate dominance measures |
| estimateEvenness | Estimate Evenness measures |
| estimateRichness | Estimate richness measures |
| getExperimentCrossAssociation | Calculate correlations between features of two experiments. |
| getPrevalence | Calculation prevalence information for features across... |
| GlobalPatterns | GlobalPatterns |
| hierarchy-tree | Calculate hierarchy tree |
| HintikkaXOData | HintikkaXOData |
| 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' |
| isContaminant | decontam functions |
| makePhyloseqFromTreeSE | Create a phyloseq object from a TreeSummarizedExperiment... |
| makeTreeSEFromBiom | Loading a biom file |
| makeTreeSEFromDADA2 | Coerce 'DADA2' results to 'TreeSummarizedExperiment' |
| makeTreeSEFromPhyloseq | Coerce a 'phyloseq' object to a 'TreeSummarizedExperiment' |
| meltAssay | Converting a 'SummarizedExperiment' object into a long... |
| merge-methods | Merge a subset of the rows or columns of a... |
| mergeSEs | Merge SE objects into single SE object. |
| mia-datasets | mia datasets |
| mia-package | 'mia' Package. |
| peerj13075 | peerj13075 |
| perSampleDominantTaxa | Get dominant taxa |
| relabundance | Getter / setter for relative abundance data |
| runCCA | Canonical Correspondence Analysis and Redundancy Analysis |
| runDPCoA | Calculation of Double Principal Correspondance analysis |
| runNMDS | Perform non-metric MDS on sample-level data |
| splitByRanks | Split/Unsplit a 'SingleCellExperiment' by taxonomic ranks |
| splitOn | Split 'TreeSummarizedExperiment' column-wise or row-wise... |
| subsampleCounts | Subsample Counts |
| subsetSamples | Subset functions |
| summaries | Summarizing microbiome data |
| taxonomy-methods | Functions for accessing taxonomic data stored in 'rowData'. |
| Tengeler2020 | Tengeler2020 |
| transformAssay | Transform assay |
