maaslin3
This is the development version of maaslin3; for the stable release version, see maaslin3.
"Refining and extending generalized multivariate linear models for meta-omic association discovery"
Bioconductor version: Development (3.22)
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.
Author: William Nickols [aut, cre]
, Jacob Nearing [aut]
Maintainer: William Nickols <willnickols at g.harvard.edu>
citation("maaslin3")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("maaslin3")
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("maaslin3")| Manual | HTML | R Script |
| Tutorial | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Metagenomics, Microbiome, MultipleComparison, Normalization, Software |
| Version | 1.1.2 |
| In Bioconductor since | BioC 3.21 (R-4.5) (0.5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.4) |
| Imports | dplyr, plyr, pbapply, lmerTest, parallel, lme4, optparse, logging, multcomp, ggplot2, RColorBrewer, patchwork, scales, rlang, tibble, ggnewscale, survival, methods, BiocGenerics, SummarizedExperiment, TreeSummarizedExperiment |
| System Requirements | |
| URL | http://huttenhower.sph.harvard.edu/maaslin3 |
| Bug Reports | https://github.com/biobakery/maaslin3/issues |
See More
| Suggests | knitr, testthat (>= 2.1.0), rmarkdown, markdown, kableExtra |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | maaslin3_1.1.2.tar.gz |
| Windows Binary (x86_64) | maaslin3_1.1.0.zip |
| macOS Binary (x86_64) | maaslin3_1.1.2.tgz |
| macOS Binary (arm64) | maaslin3_1.1.2.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/maaslin3 |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/maaslin3 |
| Bioc Package Browser | https://code.bioconductor.org/browse/maaslin3/ |
| Package Short Url | https://bioconductor.org/packages/maaslin3/ |
| Package Downloads Report | Download Stats |