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

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

Conditional hypergeometric story | Conditional hypergeometric PMF for 2 populations | Conditional hypergeometric extension to arbitrarily many populations | Computational optimizations | PMF, CDF, quantile function, random number generator | Maximum likelihood estimation | Method of moments estimators | Examples | Applications | Thank-yous