Agglomerate data using taxonomic information
Dirichlet-Multinomial Mixture Model: Machine Learning for Microbiome Data
Calculate weighted or unweighted (Fast) Unifrac distance
Get abundance values by "SampleID" or "FeatureID"
Calculate correlations between features of two experiments.
Calculation prevalence information for features across samples
Import Metaphlan results to 'TreeSummarizedExperiment'
Import Mothur results as a 'TreeSummarizedExperiment'
Import QIIME2 results to 'TreeSummarizedExperiment'
Create a phyloseq object from a TreeSummarizedExperiment object
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'
Getter / setter for relative abundance data
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
Functions for accessing taxonomic data stored in 'rowData'.