Maaslin2

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see Maaslin2.

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

Bioconductor version: 3.17

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Metagenomics, Microbiome, Normalization, Software

Version 1.14.1

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

Suggests knitr, testthat (>= 2.1.0), rmarkdown, markdown

Linking To

Enhances

Depends On Me

Imports Me benchdamic, Macarron, MMUPHin

Suggests Me

Links To Me

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