GUniFrac: 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 methods for differential abundance analysis of zero-inflated high-dimensional compositional data.

Version:	1.9
Depends:	R (≥ 3.5.0)
Imports:	Rcpp (≥ 0.12.13), vegan, ggplot2, matrixStats, Matrix, ape, parallel, stats, utils, statmod, rmutil, dirmult, MASS, ggrepel, foreach, modeest, inline, methods
LinkingTo:	Rcpp
Suggests:	ade4, knitr, markdown, ggpubr
Published:	2025-08-25
DOI:	10.32614/CRAN.package.GUniFrac
Author:	Jun Chen [aut, cre], Xianyang Zhang [aut], Lu Yang [aut], Lujun Zhang [aut]
Maintainer:	Jun Chen <chen.jun2 at mayo.edu>
License:	GPL-3
NeedsCompilation:	yes
In views:	Phylogenetics
CRAN checks:	GUniFrac results

Documentation:

Reference manual:	GUniFrac.html , GUniFrac.pdf
Vignettes:	Performing differential abundance analysis using ZicoSeq (source, R code)

Downloads:

Package source:	GUniFrac_1.9.tar.gz
Windows binaries:	r-devel: GUniFrac_1.9.zip, r-release: GUniFrac_1.9.zip, r-oldrel: GUniFrac_1.9.zip
macOS binaries:	r-release (arm64): GUniFrac_1.9.tgz, r-oldrel (arm64): GUniFrac_1.9.tgz, r-release (x86_64): GUniFrac_1.9.tgz, r-oldrel (x86_64): GUniFrac_1.9.tgz
Old sources:	GUniFrac archive

Reverse dependencies:

Reverse imports:	animalcules, chemodiv, LDM, mecoturn, MiRKAT, phymapnet
Reverse suggests:	microeco

Linking:

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