Maaslin2
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see Maaslin2.
"Multivariable Association Discovery in Population-scale Meta-omics Studies"
Bioconductor version: 3.19
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("Maaslin2")):
Installation
To install this package, start R (version "4.4") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Metagenomics, Microbiome, Normalization, Software |
| Version | 1.18.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (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 | MMUPHin, Macarron, benchdamic, ggpicrust2 |
| Suggests Me | dar |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | Maaslin2_1.18.0.tar.gz |
| Windows Binary (x86_64) | Maaslin2_1.18.0.zip |
| macOS Binary (x86_64) | Maaslin2_1.18.0.tgz |
| macOS Binary (arm64) | Maaslin2_1.18.0.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 |