Bridge Omics to Mechanism

This package contains two self-contained teaching notebooks and their local data files.

Run

1. Extract the complete ZIP archive. Do not open a notebook while it is still inside the archive.
2. Keep the data folder beside student.ipynb and solutions.ipynb.
3. Open a terminal in the extracted Bridge_omics_to_mechanism folder.
4. Install the environment and start Jupyter:

python -m pip install -r requirements.txt
python -m jupyter lab

Open student.ipynb for the exercise or solutions.ipynb for the worked analysis. After the packages are installed, the notebooks require no network access.

Package layout

Bridge_omics_to_mechanism/
├── README.md
├── requirements.txt
├── student.ipynb
├── solutions.ipynb
└── data/
    ├── u2os_cell_cycle_blind.h5ad
    ├── u2os_fucci_reveal.csv.gz
    ├── human_cd34_bone_marrow_blind.h5ad
    └── human_cd34_reference_reveal.csv.gz

The reveal tables are held-out reference information. The notebooks locate all four files relative to the extracted package and do not require paths from the original repository.