scottsnapperlab / ileal_tx_cd_haberman_2014

Ileal_Tx_CD_Haberman_2014

A re-analysis using the VIPER pipeline from Dana Farber.

Project Organization

├── 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
├── main.snake             <- Snakemake file for reproducing a full pipeline
├── 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
├── 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