/Tutorial-Microbiome

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

Primary LanguageJupyter Notebook

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.