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.


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install.packages("GUniFrac")

1.3 by Jun Chen, a month ago


Browse source code at https://github.com/cran/GUniFrac


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