Maaslin2

DOI: 10.18129/B9.bioc.Maaslin2    

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see Maaslin2.

Maaslin2

Bioconductor version: 3.10

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 "3.6") and enter:

if (!requireNamespace("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	1.0.0
In Bioconductor since	BioC 3.10 (R-3.6) (< 6 months)
License	MIT + file LICENSE
Depends	R (>= 3.6)
Imports	robustbase, biglm, pcaPP, edgeR, metagenomeSeq, lpsymphony, pscl, pbapply, car, dplyr, vegan, chemometrics, ggplot2, pheatmap, cplm, logging, data.table, lmerTest, hash, optparse, MASS, MuMIn, grDevices, stats, utils
LinkingTo
Suggests	knitr, testthat (>= 2.1.0)
SystemRequirements
Enhances
URL	http://huttenhower.sph.harvard.edu/maaslin2
BugReports	https://bitbucket.org/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_1.0.0.tar.gz
Windows Binary	Maaslin2_1.0.0.zip (64-bit only)
Mac OS X 10.11 (El Capitan)	Maaslin2_1.0.0.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