Maaslin2

DOI: 10.18129/B9.bioc.Maaslin2    

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see Maaslin2.

"Multivariable Association Discovery in Population-scale Meta-omics Studies"

Bioconductor version: 3.14

MaAsLin2 is comprehensive R package for efficiently determining multivariable association between clinical metadata and microbial meta'omic features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods. MaAsLin2 is the next generation of MaAsLin.

Author: Himel Mallick [aut], Ali Rahnavard [aut], Lauren McIver [aut, cre]

Maintainer: Lauren McIver <lauren.j.mciver at gmail.com>

Installation

To install this package, start R (version "4.1") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("Maaslin2")

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("Maaslin2")

 

HTML	R Script	MaAsLin2
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Metagenomics, Microbiome, Normalization, Software
Version	1.8.0
In Bioconductor since	BioC 3.10 (R-3.6) (2.5 years)
License	MIT + file LICENSE
Depends	R (>= 3.6)
Imports	robustbase, biglm, pcaPP, edgeR, metagenomeSeq, lpsymphony, pbapply, car, dplyr, vegan, chemometrics, ggplot2, pheatmap, logging, data.table, lmerTest, hash, optparse, grDevices, stats, utils, glmmTMB, MASS, cplm, pscl, lme4
LinkingTo
Suggests	knitr, testthat (>= 2.1.0), rmarkdown
SystemRequirements
Enhances
URL	http://huttenhower.sph.harvard.edu/maaslin2
BugReports	https://github.com/biobakery/maaslin2/issues
Depends On Me
Imports Me	MMUPHin
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	Maaslin2_1.8.0.tar.gz
Windows Binary	Maaslin2_1.8.0.zip
macOS 10.13 (High Sierra)	Maaslin2_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/Maaslin2
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/Maaslin2
Package Short Url	https://bioconductor.org/packages/Maaslin2/
Package Downloads Report	Download Stats