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MMUPHin

This is the development version of MMUPHin; for the stable release version, see MMUPHin.

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

Bioconductor version: Development (3.18)

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 "4.3") and enter: 

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews BatchEffect, Metagenomics, Microbiome, Software
Version 1.15.0
In Bioconductor since BioC 3.10 (R-3.6) (4 years)
License MIT + file LICENSE
Depends R (>= 3.6)
Imports Maaslin2, metafor, fpc, igraph, ggplot2, dplyr, tidyr, stringr, cowplot, utils, stats, grDevices
Linking To
Suggests testthat, BiocStyle, knitr, rmarkdown, magrittr, vegan, phyloseq, curatedMetagenomicData, genefilter
System Requirements glpk (>= 4.57)
Enhances
URL
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Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package MMUPHin_1.15.0.tar.gz
Windows Binary MMUPHin_1.15.0.zip (64-bit only)
macOS Binary (x86_64) MMUPHin_1.15.0.tgz
macOS Binary (arm64) MMUPHin_1.15.0.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