MMUPHin

DOI: 10.18129/B9.bioc.MMUPHin  

This package is for version 3.16 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: 3.16

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>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	MMUPHin
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	BatchEffect, Metagenomics, Microbiome, Software
Version	1.12.1
In Bioconductor since	BioC 3.10 (R-3.6) (3.5 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_1.12.1.tar.gz
Windows Binary	MMUPHin_1.12.1.zip
macOS Binary (x86_64)	MMUPHin_1.12.1.tgz
macOS Binary (arm64)	MMUPHin_1.12.1.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