peterjsadowski / Tutorial-Microbiome

Tutorial on machine learning methods for microbiome amplicon data analysis. Used for BOT 662 Spring 2023.

Tutorial-Microbiome

Tutorial on machine learning methods for microbiome amplicon data analysis. Used for workshop in BOT 662 Spring 2023.

Included:

1. Jupyter notebook tutorials:
   • Part 1: Exploratory data analysis (EDA) with PCA and UMAP.
   • Part 2: Machine learning (ML) with logistic regression, decision trees, and random forests in scikit-learn.
   • Part 3: Latent Dirichlet Allocation (LDA)
2. Data files used by tutorials.
   • Lyons dataset (32 samples)
     • brom_meta.csv contains sample meta data.
     • OTUs.100.rep.count_table.csv contains raw sample count data.
     • Taxonomy
   • Waimea dataset (1410 samples)
     • OTU table
     • Sample data
     • Taxonomy
3. Guide to writing a machine learning methods sections.