MMUPHin

This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see MMUPHin.

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

Bioconductor version: 3.19

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.

Author: Siyuan Ma

Maintainer: Siyuan MA <syma.research at gmail.com>

Citation (from within R, enter citation("MMUPHin")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("MMUPHin")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("MMUPHin")

MMUPHin HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews BatchEffect, Metagenomics, Microbiome, Software

Version 1.18.1

In Bioconductor since BioC 3.10 (R-3.6) (5 years)

License MIT + file LICENSE

Depends R (>= 3.6)

Imports Maaslin2, metafor, fpc, igraph, ggplot2, dplyr, tidyr, stringr, cowplot, utils, stats, grDevices

System Requirements glpk (>= 4.57)

URL

Suggests testthat, BiocStyle, knitr, rmarkdown, magrittr, vegan, phyloseq, curatedMetagenomicData, genefilter

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Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package MMUPHin_1.18.1.tar.gz

Windows Binary (x86_64) MMUPHin_1.18.1.zip

macOS Binary (x86_64) MMUPHin_1.18.1.tgz

macOS Binary (arm64) MMUPHin_1.18.1.tgz

Source Repository git clone https://git.bioconductor.org/packages/MMUPHin

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MMUPHin

Bioc Package Browser https://code.bioconductor.org/browse/MMUPHin/

Package Short Url https://bioconductor.org/packages/MMUPHin/

Package Downloads Report Download Stats

Old Source Packages for BioC 3.19 Source Archive