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 (3.11)

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>

Citation (from within R, enter citation("MMUPHin")):

Installation

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

if (!requireNamespace("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")

 

HTML R Script MMUPHin
PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews BatchEffect, Metagenomics, Microbiome, Software
Version 1.1.0
In Bioconductor since BioC 3.10 (R-3.6) (< 6 months)
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_1.1.0.tar.gz
Windows Binary MMUPHin_1.1.0.zip
Mac OS X 10.11 (El Capitan)
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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