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

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Documentation for package ‘GUniFrac’ version 1.8

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

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