Agglomerate data using taxonomic information
Dirichlet-Multinomial Mixture Model: Machine Learning for Microbiome Data
Calculate the Jensen-Shannon Divergence
Estimate overlap
Calculate weighted or unweighted (Fast) Unifrac distance
Estimate divergence
Estimate (alpha) diversity measures
Estimate dominance measures
Estimate Evenness measures
Estimate richness measures
Get abundance values by "SampleID" or "FeatureID"
Calculate correlations between features of two experiments.
Calculation prevalence information for features across samples
decontam functions
Import Metaphlan results to 'TreeSummarizedExperiment'
Import Mothur results as a 'TreeSummarizedExperiment'
Import QIIME2 results to 'TreeSummarizedExperiment'
Create a phyloseq object from a TreeSummarizedExperiment object
Loading a biom file
Coerce 'DADA2' results to 'TreeSummarizedExperiment'
Coerce a 'phyloseq' object to a 'TreeSummarizedExperiment'
Converting a 'SummarizedExperiment' object into a long data.frame
Merge a subset of the rows or columns of a 'SummarizedExperiment'
Merge SE objects into single SE object.
mia datasets
'mia' Package.
Get dominant taxa
Getter / setter for relative abundance data
Canonical Correspondence Analysis
Calculation of Double Principal Correspondance analysis
Perform non-metric MDS on sample-level data
Split/Unsplit a 'SingleCellExperiment' by taxonomic ranks
Split 'TreeSummarizedExperiment' column-wise or row-wise based on grouping variable
Subsample Counts
Subset functions
Summarizing microbiome data
Functions for accessing taxonomic data stored in 'rowData'.
Transform Counts