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

## Documentation for package ‘maaslin3’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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