Package: MMUPHin 2.0.0

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_2.0.0.tar.gz
MMUPHin_2.0.0.zip(r-4.7)MMUPHin_2.0.0.zip(r-4.6)MMUPHin_2.0.0.zip(r-4.5)
MMUPHin_2.0.0.tgz(r-4.6-any)MMUPHin_2.0.0.tgz(r-4.5-any)
MMUPHin_2.0.0.tar.gz(r-4.7-any)MMUPHin_2.0.0.tar.gz(r-4.6-any)
MMUPHin_2.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
MMUPHin/json (API)
NEWS

# Install 'MMUPHin' in R:
install.packages('MMUPHin', repos = c('https://bioc-release.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.

metagenomicsmicrobiomebatcheffect

4.75 score 71 scripts 680 downloads 2 mentions 4 exports 80 dependencies

Last updated from:0aadc8811c (on RELEASE_3_23). Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksERROR283
linux-devel-x86_64NOTE475
source / vignettesOK381
linux-release-x86_64NOTE397
macos-release-arm64NOTE314
macos-oldrel-arm64NOTE351
windows-develNOTE1532
windows-releaseNOTE1573
windows-oldrelNOTE1452
wasm-releaseOK208

Exports:adjust_batchcontinuous_discoverdiscrete_discovermaaslin_meta

Dependencies:BiocGenericsbootclasscliclustercodetoolscollapsecowplotcpp11data.tableDEoptimRdigestdiptestdplyrfarverflexmixfpcgenericsggnewscaleggplot2gluegtableigraphisobandkernlablabelinglatticelifecyclelme4lmerTestloggingmaaslin3magrittrMASSmathjaxrMatrixmclustmetadatmetaforminqamiraimodeltoolsmultcompmvtnormnanonextnlmenloptrnnetnumDerivoptparsepatchworkpbapplypillarpkgconfigprabcluspurrrR6rbibutilsRColorBrewerRcppRcppEigenRdpackreformulasrlangrobustbaseS7sandwichscalesstringistringrsurvivalTH.datatibbletidyrtidyselectutf8vctrsviridisLitewithrzoo

Performing meta-analyses of microbiome studies with MMUPHin

Siyuan Ma

Rendered fromMMUPHin.Rmdusingknitr::rmarkdownon May 29 2026.

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