Metadata-Version: 2.4
Name: sc-big-caller
Version: 0.2.0
Summary: Bayesian model for somatic SNV re-detection in single-cell DNA sequencing using bulk sequencing data
Author-email: Daniel Schütte <daniel.schuette@iccb-cologne.org>
Maintainer-email: Daniel Schütte <daniel.schuette@iccb-cologne.org>, Thomas Kono <thomas.kono@iccb-cologne.org>
License-Expression: GPL-3.0
Project-URL: Homepage, https://github.com/ICCB-Cologne/sc-big
Requires-Python: >=3.12
Description-Content-Type: text/markdown
License-File: LICENSE.md
Requires-Dist: numpy>=2.0.0
Requires-Dist: matplotlib>=3.7.0
Requires-Dist: scipy>=1.10.0
Requires-Dist: torch>=2.0.0
Requires-Dist: pyro-ppl>=1.8.0
Requires-Dist: pysam>=0.22.0
Provides-Extra: dev
Requires-Dist: pytest>=7.0.0; extra == "dev"
Requires-Dist: pytest_xdist>=3.8.0; extra == "dev"
Requires-Dist: flake8>=6.0.0; extra == "dev"
Dynamic: license-file

# Bayesian scDNA SNV Caller

![SC-BIG logo](docs/sc_big_logo.png)

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

## Installation

```bash
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.

```bash
# 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`:

```bash
pytest tests/ -v
```

## Documentation

See <biorxiv-paper-link> 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.
