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 permutation tests for differential abundance analysis of zero-inflated compositional data.

Version: 1.3
Depends: R (≥ 3.5.0), vegan
Imports: Rcpp (≥ 0.12.13), matrixStats, Matrix, ape, parallel, stats, utils, statmod, rmutil, dirmult, MASS
LinkingTo: Rcpp
Suggests: ade4
Published: 2021-08-18
Author: Jun Chen
Maintainer: Jun Chen <chen.jun2 at mayo.edu>
License: GPL-3
NeedsCompilation: yes
In views: Phylogenetics
CRAN checks: GUniFrac results

Documentation:

Reference manual: GUniFrac.pdf

Downloads:

Package source: GUniFrac_1.3.tar.gz
Windows binaries: r-devel: GUniFrac_1.3.zip, r-devel-UCRT: GUniFrac_1.3.zip, r-release: GUniFrac_1.3.zip, r-oldrel: GUniFrac_1.3.zip
macOS binaries: r-release (arm64): GUniFrac_1.3.tgz, r-release (x86_64): GUniFrac_1.3.tgz, r-oldrel: GUniFrac_1.3.tgz
Old sources: GUniFrac archive

Reverse dependencies:

Reverse imports: animalcules, MiRKAT
Reverse suggests: microeco

Linking:

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