MMUPHin

DOI: 10.18129/B9.bioc.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 (3.16)

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 "4.2") 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")

 

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PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews BatchEffect, Metagenomics, Microbiome, Software
Version 1.11.4
In Bioconductor since BioC 3.10 (R-3.6) (3 years)
License MIT + file LICENSE
Depends R (>= 3.6)
Imports Maaslin2, metafor, fpc, igraph, ggplot2, dplyr, tidyr, stringr, cowplot, utils, stats, grDevices
LinkingTo
Suggests testthat, BiocStyle, knitr, rmarkdown, magrittr, vegan, phyloseq, curatedMetagenomicData, genefilter
SystemRequirements glpk (>= 4.57)
Enhances
URL
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_1.11.4.tar.gz
Windows Binary MMUPHin_1.11.4.zip
macOS Binary (x86_64) MMUPHin_1.11.1.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/MMUPHin
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MMUPHin
Package Short Url https://bioconductor.org/packages/MMUPHin/
Package Downloads Report Download Stats

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