MMUPHin

DOI: 10.18129/B9.bioc.MMUPHin    

This package is for version 3.11 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: 3.11

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 <siyuanma at g.harvard.edu>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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	1.2.0
In Bioconductor since	BioC 3.10 (R-3.6) (1 year)
License	MIT + file LICENSE
Depends	R (>= 3.6)
Imports	Maaslin2, metafor, fpc, igraph, ggplot2, dplyr, tidyr, cowplot, utils, stats, grDevices
LinkingTo
Suggests	testthat, BiocStyle, knitr, rmarkdown, magrittr, vegan, phyloseq, curatedMetagenomicData, genefilter
SystemRequirements
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_1.2.0.tar.gz
Windows Binary	MMUPHin_1.2.0.zip
macOS 10.13 (High Sierra)	MMUPHin_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MMUPHin
Source Repository (Developer Access)	git clone [email protected]:packages/MMUPHin
Package Short Url	https://bioconductor.org/packages/MMUPHin/
Package Downloads Report	Download Stats