Bayesian scDNA SNV Caller

SC-BIG is a Bayesian model for somatic SNV calling in single-cell DNA sequencing that uses bulk sequencing data as a prior.

Installation

The sc-big-caller package provides an SC-BIG implementation and can be downloaded from the Python packaging index PyPI as follows:

python3 -m pip install sc-big-caller

Alternatively, you can clone this repository and install the most recent version of SC-BIG in development mode:

git clone https://github.com/ICCB-Cologne/sc-big.git
cd sc-big
python3 -m pip install -e .

Usage

Command-line Interface

After installation, the sc-big command is available. It can be used to create synthetic data, perform inference, and plot results.

# Simulate 50 single cells with custom parameters, exporting to JSON.
sc-big simulate -n 50 --ccf 0.3 --purity 0.7 -o simulation.json -v

# See all available options.
sc-big simulate --help
sc-big infer --help
sc-big infer-prosolo --help
sc-big compare --help

Tests

Run the test suite using pytest:

pytest tests/ -v

Documentation

See our preprint for background information on the model and its implementation.

License

The SC-BIG logo was created using the large language model ChatGPT. All code in this repository is licensed under the GPL-v3 as indicated in the source files. Please direct requests to daniel.schuette@iccb-cologne.org. If you use SC-BIG in your work, please cite the preprint mentioned above.