MicrobiomeStat: Statistical Methods for Microbiome Compositional Data

A suite of methods for powerful and robust microbiome data analysis addressing zero-inflation, phylogenetic structure and compositional effects. Includes the LinDA method for differential abundance analysis (Zhou et al. (2022)<doi:10.1186/s13059-022-02655-5>), the BMDD (Bimodal Dirichlet Distribution) method for accurate modeling and imputation of zero-inflated microbiome sequencing data (Zhou et al. (2025)<doi:10.1371/journal.pcbi.1013124>) and compositional sparse CCA methods for microbiome multi-omics data integration (Deng et al. (2024) <doi:10.3389/fgene.2024.1489694>).

Version:	1.4
Depends:	R (≥ 3.5.0)
Imports:	ggplot2, matrixStats, parallel, stats, utils, Matrix, statmod, MASS, ggrepel, lmerTest, foreach, modeest, dplyr, Rcpp, mlr3, mlr3mbo, bbotk, paradox
LinkingTo:	Rcpp, RcppArmadillo
Suggests:	DiceKriging, randomForest
Published:	2026-03-03
DOI:	10.32614/CRAN.package.MicrobiomeStat
Author:	Xianyang Zhang [aut], Jun Chen [aut, cre], Huijuan Zhou [ctb], Linsui Deng [ctb]
Maintainer:	Jun Chen <chen.jun2 at mayo.edu>
License:	GPL-3
NeedsCompilation:	yes
SystemRequirements:	NLopt library (optional, for high-performance BMDD mode)
In views:	CompositionalData
CRAN checks:	MicrobiomeStat results

Documentation:

Reference manual:

MicrobiomeStat.html , MicrobiomeStat.pdf

Downloads:

Package source:	MicrobiomeStat_1.4.tar.gz
Windows binaries:	r-devel: MicrobiomeStat_1.4.zip, r-release: MicrobiomeStat_1.4.zip, r-oldrel: MicrobiomeStat_1.4.zip
macOS binaries:	r-release (arm64): MicrobiomeStat_1.4.tgz, r-oldrel (arm64): MicrobiomeStat_1.4.tgz, r-release (x86_64): MicrobiomeStat_1.4.tgz, r-oldrel (x86_64): MicrobiomeStat_1.4.tgz
Old sources:	MicrobiomeStat archive

Reverse dependencies:

Reverse suggests:

ggpicrust2

Linking:

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