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Maaslin2

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


Bioconductor version: Release (3.18)

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 "4.3") 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

Details

biocViews Metagenomics, Microbiome, Normalization, Software
Version 1.16.0
In Bioconductor since BioC 3.10 (R-3.6) (4.5 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
See More
Suggests knitr, testthat (>= 2.1.0), rmarkdown, markdown
Linking To
Enhances
Depends On Me
Imports Me benchdamic, Macarron, MMUPHin
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package Maaslin2_1.16.0.tar.gz
Windows Binary Maaslin2_1.16.0.zip
macOS Binary (x86_64) Maaslin2_1.16.0.tgz
macOS Binary (arm64) Maaslin2_1.16.0.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