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README.md

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Summary

Code and notes associated with the study:

Youngblut, Nicholas D., Jacobo de la Cuesta‐Zuluaga, and Ruth E. Ley. "Incorporating genome‐based phylogeny and functional similarity into diversity assessments helps to resolve a global collection of human gut metagenomes." Environmental microbiology 24.9 (2022): 3966-3984. http://dx.doi.org/10.1111/1462-2920.15910

Data retrieval

./CurMetDat-metagenomes/ contains code and files to retrieve metagenomes from the curatedMetagenomicData R package from the Waldron lab.

Data analyses

  • ./ipynb/01_data_explore/
    • Initial exploration, pre-processing, and formatting of the data
  • ./ipynb/02_comm_diversity/
    • Main assessments of community diversity
  • ./ipynb/03_ML/
    • All machine learning analyses
  • ./ipynb/04_tutorial/
    • Tutorials on calculating diversity measures