Epigenetic clock assignments for "Bioinformatics aspects of aging and rejuvenation" lecture

Info

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

Development

Creating and activating virtual env

1. 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

2. Activate the virtual env:

   source VENV_DIR/bin/activate

Initialize the project for development

1. Enter into project root
2. Start developing with editable (or develop) mode:

   python -m pip install --editable ".[dev]"

3. Optional, install pre-commit hooks

   pre-commit install

4. Install python environment as Jupyter kernel

   python -m ipykernel install --user --name=bio

Running

1. Start jupyter lab:

   jupyter lab

2. Run the jupyter notebooks using bio kernel:

• assignment1_microarray.ipynb
• assignment2_rrbs.ipynb

Other goodies

Tips for development

Uninstall all packages (and purge pip cache)

pip uninstall epigenetic_clock_assignment
pip freeze | xargs pip uninstall -y
pip cache purge