umap-microbiome-benchmarking

Installation

These notebooks' dependencies are listed in the requirements.yml file.

Additionally, using the notebooks will require Jupyter.

ENV_NAME=umap-benchmarking
conda create -n ${ENV_NAME}
conda activate ${ENV_NAME}
conda env update --file requirements.yml
jupyter notebook

Figures

cd notebooks
mkdir results
jupyter notebook

Then these notebooks contain the analyses:

• real-data-keyboard-benchmark.ipynb
• real-data-soil-benchmark.ipynb
• technical-effects-hmpv13v35.ipynb