Maaslin2

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

Bioconductor version: Release (3.19)

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>

Citation (from within R, enter citation("Maaslin2")):

Installation

To install this package, start R (version "4.4") 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")

Maaslin2	HTML	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Metagenomics, Microbiome, Normalization, Software
Version	1.18.0
In Bioconductor since	BioC 3.10 (R-3.6) (5 years)
License	MIT + file LICENSE
Depends	R (>= 3.6)
Imports	robustbase, biglm, pcaPP, edgeR, metagenomeSeq, pbapply, car, dplyr, vegan, chemometrics, ggplot2, pheatmap, logging, data.table, lmerTest, hash, optparse, grDevices, stats, utils, glmmTMB, MASS, cplm, pscl, lme4, tibble
System Requirements
URL	http://huttenhower.sph.harvard.edu/maaslin2
Bug Reports	https://github.com/biobakery/maaslin2/issues

Suggests	knitr, testthat (>= 2.1.0), rmarkdown, markdown
Linking To
Enhances
Depends On Me
Imports Me	MMUPHin, Macarron, benchdamic, ggpicrust2
Suggests Me	dar
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	Maaslin2_1.18.0.tar.gz
Windows Binary (x86_64)	Maaslin2_1.18.0.zip
macOS Binary (x86_64)	Maaslin2_1.18.0.tgz
macOS Binary (arm64)	Maaslin2_1.18.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/Maaslin2
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/Maaslin2
Bioc Package Browser	https://code.bioconductor.org/browse/Maaslin2/
Package Short Url	https://bioconductor.org/packages/Maaslin2/
Package Downloads Report	Download Stats