Package: MMUPHin 2.1.0

Siyuan MA

MMUPHin: Meta-analysis Methods with Uniform Pipeline for Heterogeneity in Microbiome Studies

MMUPHin is an R package for meta-analysis tasks of microbiome cohorts. It has function interfaces for: a) covariate-controlled batch- and cohort effect adjustment, b) meta-analysis differential abundance testing, c) meta-analysis unsupervised discrete structure (clustering) discovery, and d) meta-analysis unsupervised continuous structure discovery.

Authors:Siyuan Ma

MMUPHin_2.1.0.tar.gz
MMUPHin_2.1.0.zip(r-4.7)MMUPHin_2.1.0.zip(r-4.6)MMUPHin_2.1.0.zip(r-4.5)
MMUPHin_2.1.0.tgz(r-4.6-any)MMUPHin_2.1.0.tgz(r-4.5-any)
MMUPHin_2.1.0.tar.gz(r-4.7-any)MMUPHin_2.1.0.tar.gz(r-4.6-any)
MMUPHin_2.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
MMUPHin/json (API)

# Install 'MMUPHin' in R:

install.packages('MMUPHin', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

CRC_abd - Species level feature abundance data of five public CRC studies
CRC_meta - Sample metadata of five public CRC studies
vaginal_abd - Species level feature abundance data of two public vaginal studies
vaginal_meta - Sample metadata of two public vaginal studies

On BioConductor:MMUPHin-2.1.0(bioc 3.24)MMUPHin-2.0.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

metagenomics microbiome batcheffect

4.78 score 76 scripts 2 mentions 4 exports 79 dependencies

Last updated from:11850208e2. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	248
linux-devel-x86_64	NOTE	387
source / vignettes	OK	365
linux-release-x86_64	NOTE	339
macos-release-arm64	NOTE	169
macos-oldrel-arm64	NOTE	245
windows-devel	NOTE	905
windows-release	NOTE	972
windows-oldrel	NOTE	656
wasm-release	OK	247

Exports:adjust_batch continuous_discover discrete_discover maaslin_meta

Dependencies:BiocGenerics boot class cli cluster codetools collapse cowplot cpp11 data.table DEoptimR digest diptest dplyr farver flexmix fpc generics ggnewscale ggplot2 glue gtable igraph isoband kernlab labeling lattice lifecycle lme4 lmerTest maaslin3 magrittr MASS mathjaxr Matrix mclust metadat metafor minqa mirai modeltools multcomp mvtnorm nanonext nlme nloptr nnet numDeriv optparse patchwork pbapply pillar pkgconfig prabclus purrr R6 rbibutils RColorBrewer Rcpp RcppEigen Rdpack reformulas rlang robustbase S7 sandwich scales stringi stringr survival TH.data tibble tidyr tidyselect utf8 vctrs viridisLite withr zoo

Performing meta-analyses of microbiome studies with MMUPHin

Rendered fromMMUPHin.Rmdusingknitr::rmarkdown

Last update: 2026-01-16
Started: 2019-08-29

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Zero-inflated empirical Bayes adjustment of batch effect in compositional feature abundance data	adjust_batch
Unsupervised meta-analytical discovery and validation of continuous structures in microbial abundance data	continuous_discover
Species level feature abundance data of five public CRC studies	CRC_abd
Sample metadata of five public CRC studies	CRC_meta
Unsupervised meta-analytical discovery and validation of discrete clustering structures in microbial abundance data	discrete_discover
maaslin3-based meta-analytical differential abundance testing	maaslin_meta
Species level feature abundance data of two public vaginal studies	vaginal_abd
Sample metadata of two public vaginal studies	vaginal_meta