gos-example

This repo contains a set of Jupyter notebooks introducing key features of the gos genomics visualization library for Python.

The notebooks can be run via Google Colab,

• getting-started.ipynb

• data-loading.ipynb

• clinvar.ipynb

• navigation.ipynb

or locally with Jupyter,

jupyter notebook notebooks/

Note The clinvar.ipynb notebook contains the option to load large datasets locally rather than via a remote HiGlass server. The Snakemake workflow contained in this repo will generate those files if desired, but running these scripts are optional.

conda env create -f environment.yaml
conda activate gos-example
# preprocess data
snakemake -c all data/agg/clinvar.bed.beddb data/agg/density.multires.mv5
# run the notebook
jupyter notebook 

Alternatively, using uv:

# brew install llvm (make sure you have `llvm-ar` and specify explicitly)
# preprocess data
AR=/opt/homebrew/opt/llvm/bin/llvm-ar uv run snakemake.py -c all data/agg/clinvar.bed.beddb data/agg/density.multires.mv5
# run the notebook
uvx juv run notebooks/clinvar.ipynb
# or uvx juv run notebooks/getting-started.ipynb, etc