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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: | 1.3 |
| Depends: | R (≥ 3.5.0) |
| Imports: | ggplot2, matrixStats, parallel, stats, utils, Matrix, statmod, MASS, ggrepel, lmerTest, foreach, modeest, dplyr, mlrMBO, Rcpp, ParamHelpers, smoof, lhs, mlr, BBmisc |
| LinkingTo: | Rcpp, RcppArmadillo |
| Suggests: | DiceKriging, randomForest |
| Published: | 2026-01-09 |
| 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 |
| Reference manual: | MicrobiomeStat.html , MicrobiomeStat.pdf |
| Package source: | MicrobiomeStat_1.3.tar.gz |
| Windows binaries: | r-devel: MicrobiomeStat_1.3.zip, r-release: MicrobiomeStat_1.3.zip, r-oldrel: MicrobiomeStat_1.3.zip |
| macOS binaries: | r-release (arm64): MicrobiomeStat_1.3.tgz, r-oldrel (arm64): MicrobiomeStat_1.3.tgz, r-release (x86_64): MicrobiomeStat_1.3.tgz, r-oldrel (x86_64): MicrobiomeStat_1.3.tgz |
| Old sources: | MicrobiomeStat archive |
| Reverse suggests: | ggpicrust2 |
Please use the canonical form https://CRAN.R-project.org/package=MicrobiomeStat to link to this page.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.