maaslin3
"Refining and extending generalized multivariate linear models for meta-omic association discovery"
Bioconductor version: 3.23 · Package version: 1.4.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
MaAsLin 3 refines and extends generalized multivariate linear models for meta-omicron association discovery. It finds abundance and prevalence associations between microbiome meta-omics features and complex metadata in population-scale epidemiological studies. The software includes multiple analysis methods (including support for multiple covariates, repeated measures, and ordered predictors), filtering, normalization, and transform options to customize analysis for your specific study.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("maaslin3")Details
| Maintainer | William Nickols <willnickols@g.harvard.edu> |
| Author | William Nickols [aut, cre] (ORCID: <https://orcid.org/0000-0001-8214-9746>), Jacob Nearing [aut] |
| License | MIT + file LICENSE |
| URL | http://huttenhower.sph.harvard.edu/maaslin3 |
| Bug Reports | https://github.com/biobakery/maaslin3/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Metagenomics, Microbiome, MultipleComparison, Normalization, Software |
| Package Short Url | https://bioconductor.org/packages/maaslin3/ |
Citation
From within R, enter citation("maaslin3"):
William Nickols, Jacob Nearing. maaslin3: "Refining and extending generalized multivariate linear models for meta-omic association discovery". doi:10.18129/B9.bioc.maaslin3, R package version 1.4.0, https://bioconductor.org/packages/maaslin3.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | maaslin3_1.4.0.tar.gz |
| Windows binary (x86_64) | maaslin3_1.4.0.zip |
| macOS binary (arm64) | maaslin3_1.4.0.tgz |
| macOS binary (x86_64) | maaslin3_1.4.0.tgz |
Dependencies
Depends: R (>= 4.4)
Imports: data.table, collapse, lmerTest, lme4, optparse, logging, mirai, multcomp, ggplot2, RColorBrewer, patchwork, scales, rlang, ggnewscale, survival, methods, BiocGenerics, reformulas
Suggests: knitr, testthat (>= 2.1.0), rmarkdown, markdown, kableExtra, dplyr, SummarizedExperiment, TreeSummarizedExperiment