Generalized UniFrac Distances, Distance-Based Multivariate Methods and Feature-Based Univariate Methods for Microbiome Data Analysis

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 permutation tests for differential abundance analysis of zero-inflated compositional data.


Reference manual

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1.3 by Jun Chen, a month ago

Browse source code at

Authors: Jun Chen

Documentation:   PDF Manual  

Task views: Phylogenetics, Especially Comparative Methods

GPL-3 license

Imports Rcpp, matrixStats, Matrix, ape, parallel, stats, utils, statmod, rmutil, dirmult, MASS

Depends on vegan

Suggests ade4

Linking to Rcpp

Imported by MiRKAT.

Suggested by microeco.

See at CRAN