Package: GUniFrac 1.9

Jun Chen

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.

Authors:Jun Chen [aut, cre], Xianyang Zhang [aut], Lu Yang [aut], Lujun Zhang [aut]

GUniFrac_1.9.tar.gz
GUniFrac_1.9.tar.gz(r-4.7-arm64)GUniFrac_1.9.tar.gz(r-4.7-x86_64)GUniFrac_1.9.tar.gz(r-4.6-arm64)GUniFrac_1.9.tar.gz(r-4.6-x86_64)
GUniFrac_1.9.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
GUniFrac/json (API)

# Install 'GUniFrac' in R:

install.packages('GUniFrac', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

stool.otu.tab - Stool Microbiome OTU Count Table
throat.meta - Throat Microbiome Meta Data
throat.otu.tab - Throat Microbiome OTU Count Table
throat.tree - UPGMA Tree of Throat Microbiome OTUs
vaginal.otu.tab - Vaginal Microbiome OTU Count Table

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

cpp

6.21 score 8 packages 399 scripts 1.7k downloads 91 mentions 14 exports 48 dependencies

Last updated from:50f6df3575. Checks:6 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	209
linux-devel-x86_64	OK	206
source / vignettes	OK	242
linux-release-arm64	OK	198
linux-release-x86_64	OK	189
wasm-release	OK	881

Exports:adonis3 dICC dICC.SE.asympt dICC.SE.bt dmanova GMPR GUniFrac PermanovaG PermanovaG2 Rarefy SimulateMSeq SimulateMSeqC ZicoSeq ZicoSeq.plot

Dependencies:ape cli clue cluster codetools cpp11 digest dirmult farver fBasics foreach ggplot2 ggrepel glue gss gtable inline isoband iterators labeling lattice lifecycle MASS Matrix matrixStats mgcv modeest nlme permute R6 RColorBrewer Rcpp rlang rmutil rpart S7 scales spatial stable stabledist statip statmod timeDate timeSeries vctrs vegan viridisLite withr

Performing differential abundance analysis using ZicoSeq

Rendered fromZicoSeq.Rmdusingknitr::rmarkdown

Last update: 2025-08-25
Started: 2022-04-05

Help page	Topics
Permutational Multivariate Analysis of Variance Using Distance Matrices (Freedman-Lane permutation)	adonis3
Distance-based Intra-Class Correlation Coefficient	dICC
Asymptotic Standard Error of Distance-based Intra-Class Correlation Coefficient	dICC.SE.asympt
Bootstrap Standard Error of Distance-based Intra-Class Correlation Coefficient	dICC.SE.bt
Distance-based Multivariate Analysis of Variance (Analytical P-value Calculation)	dmanova
Geometric Mean of Pairwise Ratios (GMPR) Normalization for Zero-inflated Count Data	GMPR
Generalized UniFrac distances for comparing microbial communities.	GUniFrac
Permutational Multivariate Analysis of Variance Using Multiple Distance Matrices	PermanovaG
Permutational Multivariate Analysis of Variance Using Multiple Distance Matrices(Freedman-Lane Permutation)	PermanovaG2
Rarefy a Count Table to Equal Sequencing Depth	Rarefy
A Semiparametric Model-based Microbiome Sequencing Data Simulator for Cross-sectional and Case-control Studies	SimulateMSeq
A Semiparametric Model-based Microbiome Sequencing Data Simulator for Longitudinal, Matched-pair, and Replicate Sampling Designs	SimulateMSeqC
Stool Microbiome OTU Count Table	stool.otu.tab
Throat Microbiome Meta Data	throat.meta
Throat Microbiome OTU Count Table	throat.otu.tab
UPGMA Tree of Throat Microbiome OTUs	throat.tree
Vaginal Microbiome OTU Count Table	vaginal.otu.tab
A linear Model-based Permutation Test for Differential Abundance Analysis of Microbiome Data and Other Omics Data	ZicoSeq
A Plot Function for Visualizing the ZicoSeq Results	ZicoSeq.plot

Package: GUniFrac 1.9

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

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)