throat.tree

<p>
The OTU tree is constructed using UPGMA on the K80 distance matrice of
the OTUs. It is a rooted tree of class "phylo".</p>

datasets

A suite of methods for powerful and robust microbiome data analysis including data normalization, data simulation, community-level association testing and differential abundance analysis. It implements generalized UniFrac distances,  Geometric Mean of Pairwise Ratios (GMPR) normalization, semiparametric data simulator, distance-based statistical methods, and feature-based statistical methods. The distance-based statistical methods include three extensions of PERMANOVA: (1) PERMANOVA using the Freedman-Lane permutation scheme, (2) PERMANOVA omnibus test using multiple matrices, and  (3) analytical approach to approximating PERMANOVA p-value. Feature-based statistical methods include linear model-based methods for differential abundance analysis of zero-inflated high-dimensional compositional data.

Jun Chen

throat.tree: UPGMA Tree of Throat Microbiome OTUs

Description

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Details

Examples