Maaslin2
This is the released version of Maaslin2; for the devel version, see Maaslin2.
"Multivariable Association Discovery in Population-scale Meta-omics Studies"
Bioconductor version: Release (3.23)
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], Thomas Kuntz [aut], Sagun Maharjan [aut, cre]
Maintainer: Sagun Maharjan <sagunmaharjann at gmail.com>
citation("Maaslin2")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Metagenomics, Microbiome, Normalization, Software |
| Version | 1.26.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (7 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 | benchdamic, Macarron |
| Suggests Me | ggpicrust2 |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | Maaslin2_1.26.0.tar.gz |
| Windows Binary (x86_64) | Maaslin2_1.26.0.zip |
| macOS Binary (big-sur-x86_64) | Maaslin2_1.26.0.tgz |
| macOS Binary (sonoma-arm64) | Maaslin2_1.26.0.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 |