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>
citation("MMUPHin")):
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")| MMUPHin | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | BatchEffect, Metagenomics, Microbiome, Software |
| Version | 1.12.1 |
| 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_1.12.1.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 |
| Old Source Packages for BioC 3.16 | Source Archive |