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


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Documentation for package ‘maaslin3’ version 1.1.0

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maaslin3 MaAsLin 3: A multivariable statistical framework for finding abundance and prevalence associations between metadata and high-dimensional microbial multi-omics data.
maaslin_check_arguments Check parameter arguments to ensure a successful MaAsLin 3 run.
maaslin_check_formula Check a MaAsLin 3 formula to ensure a proper MaAsLin 3 run.
maaslin_compute_formula Compute a formula for a MaAsLin 3 run based on the specified effects.
maaslin_contrast_test Perform a contrast from a fit MaAsLin 3 model.
maaslin_filter Filter abundance data before MaAsLin 3 model fitting.
maaslin_fit Fit MaAsLin 3 models.
maaslin_log_arguments Log MaAsLin 3 parameters.
maaslin_normalize Normalize abundance data for MaAsLin 3 model fitting.
maaslin_plot_results Plot the results from a MaAsLin 3 run.
maaslin_plot_results_from_output Plot the results from a MaAsLin 3 run.
maaslin_process_metadata Process metadata before MaAsLin 3 model fitting.
maaslin_read_data Read in the abundance data and metadata.
maaslin_reorder_data Reorder the abundance data and metadata.
maaslin_transform Transform abundance data for MaAsLin 3 modeling.
maaslin_write_results Write the results from a MaAsLin 3 run.
maaslin_write_results_lefse_format Write the results from a MaAsLin 3 run in LEfSe format.
preprocess_dna_mtx Pre-process the DNA covariates for metatranscriptomics
preprocess_taxa_mtx Pre-process the taxa covariates for metatranscriptomics