Man pages for microbiome/mia
Microbiome analysis
| addAlpha | Estimate alpha diversity indices |
| addCluster | Clustering wrapper |
| addDivergence | Estimate divergence |
| addLDA | Latent Dirichlet Allocation |
| addNMF | Non-negative Matrix Factorization |
| agglomerateByPrevalence | Agglomerate data based on population prevalence |
| agglomerate-methods | Agglomerate data using taxonomic information or other... |
| calculateDMN | Dirichlet-Multinomial Mixture Model: Machine Learning for... |
| convertFromDADA2 | Create a 'TreeSummarizedExperiment' object from 'DADA2'... |
| convertFromPhyloseq | Create a 'TreeSummarizedExperiment' object from a phyloseq... |
| deprecate | These functions will be deprecated. Please use other... |
| dmn_se | Twins' microbiome data from 278 individuals |
| enterotype | Human gut microbiome dataset from 22 subjects based on... |
| esophagus | Human esophageal community from 3 individuals |
| getCrossAssociation | Calculate correlations between features of two experiments. |
| getDissimilarity | Calculate dissimilarities |
| getDominant | Get dominant taxa |
| getMediation | Perform mediation analysis |
| getPERMANOVA | Calculate PERMANOVA (Permutational Multivariate Analysis of... |
| getPrevalence | Calculation prevalence information for features across... |
| GlobalPatterns | Global patterns of 16S rRNA diversity at a depth of millions... |
| hierarchy-tree | Calculate hierarchy tree |
| HintikkaXOData | Multiomics dataset from 40 rat samples |
| importBIOM | Convert a 'TreeSummarizedExperiment' object to/from 'BIOM'... |
| 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' |
| importTaxpasta | Import taxpasta-specific BIOM results to... |
| isContaminant | decontam functions |
| meltSE | Converting a 'SummarizedExperiment' object into a long... |
| mergeSEs | Merge SE objects into single SE object. |
| mia-datasets | mia datasets |
| mia-package | 'mia' Package. |
| peerj13075 | Skin microbial profiles 58 genetically unrelated individuals |
| rarefyAssay | Subsample Counts |
| runCCA | Canonical Correspondence Analysis and Redundancy Analysis |
| runDPCoA | Calculation of Double Principal Correspondance analysis |
| runNMDS | Perform non-metric MDS on sample-level data |
| splitOn | Split 'TreeSummarizedExperiment' column-wise or row-wise... |
| summaries | Summarizing microbiome data |
| taxonomy-methods | Functions for accessing taxonomic data stored in 'rowData'. |
| Tengeler2020 | Gut microbiota profiles of 27 individuals with ADHD and... |
| Tito2024QMP | Fecal microbiota samples from 589 patients across different... |
| transformAssay | Transform assay |
