Lecturer: Csaba Kerepesi
- Assignment 1: Train epigenetic clock for microarray-based methylation dataset
- Assignment 2: Train epigenetic clock for RRBS-based methylation dataset (with missing data)
Presentation: epigenetic_clock_assignment.pdf
- Create a virtual env which uses Python 3.8 (replace
VENV_DIR
e.g. to~/.envs/bio
):pyenv install 3.8 pyenv shell 3.8 python -m venv VENV_DIR
- Activate the virtual env:
source VENV_DIR/bin/activate
- Enter into project root
- Start developing with editable (or develop) mode:
python -m pip install --editable ".[dev]"
- Optional, install pre-commit hooks
pre-commit install
- Install python environment as Jupyter kernel
python -m ipykernel install --user --name=bio
- Start jupyter lab:
jupyter lab
- Run the jupyter notebooks using
bio
kernel:
assignment1_microarray.ipynb
assignment2_rrbs.ipynb
pip uninstall epigenetic_clock_assignment
pip freeze | xargs pip uninstall -y
pip cache purge