MuTopia Tutorials

Welcome to the MuTopia tutorials. These interactive notebooks guide you through the key features of MuTopia, from building G-Tensors to training and applying mutational topographic models.

Tutorial data

All six tutorials share a single data bundle hosted on Zenodo. Download and unpack it once before starting any tutorial:

# Tutorial data bundle (≈ 2 GB): reference genome, pre-built G-Tensor,
# pre-trained model, and supporting files.
wget -O tutorial_data.tar.gz https://zenodo.org/records/18803136/files/tutorial_data.tar.gz
tar -xzf tutorial_data.tar.gz

This produces a tutorial_data/ directory that every tutorial references.

The same Zenodo record also hosts standalone pre-trained models for several tumor types (<tumor_type>.nc, <tumor_type>.nc.regions.bed and <tumor_type>.model.pkl). These live at the record root and can be downloaded individually — see Tutorial 5 for details.

Tutorials

• Tutorial 1: Building G-Tensors
• Tutorial 2: Analyzing G-Tensors
• Tutorial 3: Tuning and training models
• Tutorial 4: Analyzing Topographic Models
• Tutorial 5: Annotating VCFs with a Pre-Trained Model
• Tutorial 6: Genome-browser plotting with a trained model