GUniFrac

swMATH10012CRANGUniFracMaRDI QIDQ21987

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

Jun Chen

Last update: 14 September 2023

Copyright license: GNU General Public License, version 3.0

Software version identifier: 1.7, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.8

Source code repository: https://github.com/cran/GUniFrac

Description

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.