Data cleaning and munging for the biorepository etc.
├── configs
├── data
│ ├── external <- Data from third party sources
│ ├── interim <- Intermediate data that has been transformed.
│ ├── processed <- The final, canonical data sets for modeling.
│ └── raw <- The original, immutable data dump.
├── docs <- A default Sphinx project; see sphinx-doc.org for details
├── github <- Contains a script for creating and pushing to github
├── LICENSE
├── Makefile <- Makefile with commands to provision a Conda environment and register
│ the environment's kernel with Jupyter
├── models <- Trained and serialized models, model predictions, or model summaries
├── notebooks <- Jupyter notebooks. Naming convention is a date and title
│ (`2016-07-28__initial_exploration.ipynb`)
├── README.md <- The top-level README for developers using this project.
├── references <- Data dictionaries, manuals, and all other explanatory materials.
├── reports <- Generated analysis as HTML, PDF, LaTeX, etc.
│ └── figures <- Generated graphics and figures to be used in reporting
├── requirements.txt <- The requirements file for reproducing the analysis environment.
├── setup.py <- Allows installing this project's python code for Notebook importation
├── Snakefile <- Snakemake file for reproducing a full pipeline
├── src <- Source code for use in this project.
│ ├── python
│ │ ├── data <- Code to download or generate data
│ │ ├── features <- Code to turn raw data into features for modeling
│ │ ├── models <- Code to train models and then use trained models to make
│ │ ├── rules <- Scripts meant to be plugged in as Snakemake Rules
│ │ └── visualization <- Code to create exploratory and results oriented visualizations
│ └── R
│ └── rules <- Scripts meant to be plugged in as Snakemake Rules
└── tox.ini