# Mian

## Mian

- [Mian Overview](https://tbj128.gitbook.io/mian/readme.md): OTU table visualization, data analysis, and machine learning
- [Tutorial](https://tbj128.gitbook.io/mian/tutorial.md): Here we will analyze a lung microbiome OTU dataset from a Sze et al. COPD study using some of Mian's basic features.
- [Getting Started](https://tbj128.gitbook.io/mian/getting-started.md)
- [Projects](https://tbj128.gitbook.io/mian/projects.md)
- [Tool Parameters and Filters](https://tbj128.gitbook.io/mian/tool-parameters-and-filters.md)
- [Boxplots](https://tbj128.gitbook.io/mian/boxplots.md): Generates a series of boxplots based on a grouping parameter.
- [Barplot (Composition)](https://tbj128.gitbook.io/mian/barplot-composition.md)
- [Donut (Composition)](https://tbj128.gitbook.io/mian/donut-composition.md)
- [Scatterplot (Correlation)](https://tbj128.gitbook.io/mian/scatterplot-correlation.md)
- [Heatmap (Correlation)](https://tbj128.gitbook.io/mian/heatmap-correlation.md)
- [Heatmap (Composition)](https://tbj128.gitbook.io/mian/heatmap-composition.md)
- [Correlation Network](https://tbj128.gitbook.io/mian/correlation-network.md)
- [Rarefaction Curves](https://tbj128.gitbook.io/mian/rarefaction-curves.md)
- [Taxonomic Tree View](https://tbj128.gitbook.io/mian/taxonomic-tree-view.md)
- [Table](https://tbj128.gitbook.io/mian/table.md)
- [Alpha Diversity](https://tbj128.gitbook.io/mian/alpha-diversity.md)
- [Beta Diversity](https://tbj128.gitbook.io/mian/beta-diversity.md)
- [NMDS](https://tbj128.gitbook.io/mian/nmds.md)
- [PCoA](https://tbj128.gitbook.io/mian/pcoa.md)
- [Boruta (Feature Selection)](https://tbj128.gitbook.io/mian/boruta-feature-selection.md)
- [Elastic Net Classification](https://tbj128.gitbook.io/mian/elastic-net-classification.md): This tool fits a linear classifier with elastic-net regularization. This tool will then subsequently select the highest weight OTUs or taxonomic groups using recursive feature elimination.
- [Elastic Net Regression](https://tbj128.gitbook.io/mian/elastic-net-regression.md): This tool fits a linear regressor with elastic-net regularization. This tool will then subsequently select the highest weighted OTUs or taxonomic groups using recursive feature elimination.
- [Fisher Exact Test](https://tbj128.gitbook.io/mian/fisher-exact-test.md)
- [Differential Selection](https://tbj128.gitbook.io/mian/differential-selection.md): Univariate feature selection (categorical variables)
- [Correlations Selection](https://tbj128.gitbook.io/mian/correlations-selection.md): Univariate feature selection (numeric values)
- [Linear Regressor](https://tbj128.gitbook.io/mian/linear-regressor.md)
- [Linear Classifier](https://tbj128.gitbook.io/mian/linear-classifier.md)
- [Random Forest Classifier](https://tbj128.gitbook.io/mian/random-forest-classifier.md)
- [Deep Learning](https://tbj128.gitbook.io/mian/deep-learning.md)