Maaslin2

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see Maaslin2.

Maaslin2


Bioconductor version: 3.10

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 "3.6") 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 1.0.0
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, lpsymphony, pscl, pbapply, car, dplyr, vegan, chemometrics, ggplot2, pheatmap, cplm, logging, data.table, lmerTest, hash, optparse, MASS, MuMIn, grDevices, stats, utils
System Requirements
URL http://huttenhower.sph.harvard.edu/maaslin2
Bug Reports https://bitbucket.org/biobakery/maaslin2/issues
See More
Suggests knitr, testthat (>= 2.1.0)
Linking To
Enhances
Depends On Me
Imports Me 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_1.0.0.tar.gz
Windows Binary Maaslin2_1.0.0.zip (64-bit only)
Mac OS X 10.11 (El Capitan) Maaslin2_1.0.0.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
Old Source Packages for BioC 3.10 Source Archive