Maaslin2

DOI: 10.18129/B9.bioc.Maaslin2    

This is the development version of Maaslin2; for the stable release version, see Maaslin2.

Maaslin2

Bioconductor version: Development (3.11)

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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

 

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PDF   Reference Manual
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Text   LICENSE

Details

biocViews Metagenomics, Microbiome, Normalization, Software
Version 1.1.0
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_1.1.0.tar.gz
Windows Binary Maaslin2_1.1.0.zip
Mac OS X 10.11 (El Capitan) Maaslin2_1.1.0.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

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