Welcome to the new bioconductor.org!

MMUPHin

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


Bioconductor version: Release (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")

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 1.16.0
In Bioconductor since BioC 3.10 (R-3.6) (4.5 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
See More
Suggests testthat, BiocStyle, knitr, rmarkdown, magrittr, vegan, phyloseq, curatedMetagenomicData, genefilter
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package MMUPHin_1.16.0.tar.gz
Windows Binary MMUPHin_1.16.0.zip
macOS Binary (x86_64) MMUPHin_1.16.0.tgz
macOS Binary (arm64) MMUPHin_1.16.0.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