Maaslin2

DOI: 10.18129/B9.bioc.Maaslin2    

Maaslin2

Bioconductor version: Release (3.12)

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 "4.0") 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 1.4.0
In Bioconductor since BioC 3.10 (R-3.6) (1 year)
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, MuMIn, grDevices, stats, utils, glmmTMB, MASS, cplm, pscl
LinkingTo
Suggests knitr, testthat (>= 2.1.0)
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_1.4.0.tar.gz
Windows Binary Maaslin2_1.4.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra) Maaslin2_1.4.0.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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: