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 or merge data using taxonomic information |
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 |
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 |
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