Package: maaslin3 1.5.3

William Nickols

maaslin3: "Refining and extending generalized multivariate linear models for meta-omic association discovery"

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.

Authors:William Nickols [aut, cre], Jacob Nearing [aut]

maaslin3_1.5.3.tar.gz
maaslin3_1.5.3.zip(r-4.7)maaslin3_1.5.3.zip(r-4.6)maaslin3_1.5.3.zip(r-4.5)
maaslin3_1.5.3.tgz(r-4.6-any)maaslin3_1.5.3.tgz(r-4.5-any)
maaslin3_1.5.3.tar.gz(r-4.7-any)maaslin3_1.5.3.tar.gz(r-4.6-any)
maaslin3_1.5.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
maaslin3/json (API)

# Install 'maaslin3' in R:
install.packages('maaslin3', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/biobakery/maaslin3/issues

On BioConductor:maaslin3-1.5.1(bioc 3.24)maaslin3-1.4.0(bioc 3.23)

metagenomicssoftwaremicrobiomenormalizationmultiplecomparisonr-tools

10.17 score 83 stars 4 packages 167 scripts 20 exports 48 dependencies

Last updated from:d0bf185869. Checks:8 NOTE, 2 OK. Indexed: yes.

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bioc-checksNOTE273
linux-devel-x86_64NOTE444
source / vignettesOK642
linux-release-x86_64NOTE441
macos-release-arm64NOTE314
macos-oldrel-arm64NOTE305
windows-develNOTE417
windows-releaseNOTE453
windows-oldrelNOTE470
wasm-releaseOK319

Exports:maaslin_check_argumentsmaaslin_check_formulamaaslin_compute_formulamaaslin_contrast_testmaaslin_filtermaaslin_fitmaaslin_log_argumentsmaaslin_log_resetmaaslin_normalizemaaslin_plot_resultsmaaslin_plot_results_from_outputmaaslin_process_metadatamaaslin_read_datamaaslin_reorder_datamaaslin_transformmaaslin_write_resultsmaaslin_write_results_lefse_formatmaaslin3preprocess_dna_mtxpreprocess_taxa_mtx

Dependencies:BiocGenericsbootclicodetoolscollapsecpp11data.tablefarvergenericsggnewscaleggplot2gluegtableisobandlabelinglatticelifecyclelme4lmerTestMASSMatrixminqamiraimultcompmvtnormnanonextnlmenloptrnumDerivoptparsepatchworkR6rbibutilsRColorBrewerRcppRcppEigenRdpackreformulasrlangS7sandwichscalessurvivalTH.datavctrsviridisLitewithrzoo

MaAsLin 3 User Manual
Introduction | Support | Contents | Requirements | Installation | Install using GitHub and devtools | Running MaAsLin 3 | Input data | Output files | Diagnostics | Run a demo | In R | Replotting | Contrast testing | Command line | Options | Required parameters | Model formula | Feature specific covariates | Analysis options | Compositionality corrections | Absolute abundance | Compositionality corrections continued | Median comparisons | Plotting parameters | Technical/miscellaneous parameters | Tool comparison | Troubleshooting
Rendered frommaaslin3_manual.Rmdusingknitr::rmarkdown

Last update: 2026-05-11
Started: 2024-07-05

MaAsLin 3 Tutorial
Introduction | Support | Contents | 1. Installing R | Installing R for the first time | (Optional) the RStudio IDE | Important: the correct R version | 2. Installing MaAsLin 3 | 3. Microbiome association detection with MaAsLin 3 | 3.1 MaAsLin 3 input | 3.2 Running MaAsLin 3 | Running MaAsLin 3 on HMP2 data | Median comparisons | 3.3 MaAsLin 3 output | Significant associations | Full output file structure | Diagnostics | Replotting | 4. Advanced Topics | 4.1 Absolute abundance | Spike-in | Total abundance scaling | Computationally estimated absolute abundance | 4.2 Random effects (clustered samples) | Alternatives to random effects | 4.3 Interactions (differences in differences) | 4.4 Level contrasts | 4.5 Group-wise differences | 4.6 Contrast tests | 5. Command line #### | Tool comparison
Rendered frommaaslin3_tutorial.Rmdusingknitr::rmarkdown

Last update: 2026-03-07
Started: 2024-07-05