Metadata-Version: 2.4
Name: sortscore
Version: 0.1.0b2
Summary: A modular Python package for Sort-seq variant analysis
Author-email: Caitlyn Chitwood <c.chitwood@wustl.edu>
License: MIT
Project-URL: Homepage, https://github.com/dbaldridge-lab/sortscore
Keywords: bioinformatics,sequencing,variant-analysis,sort-seq
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: pandas>=2.0.0
Requires-Dist: numpy>=1.24.0
Requires-Dist: scipy>=1.10.0
Requires-Dist: matplotlib>=3.6.0
Requires-Dist: seaborn>=0.12.0
Requires-Dist: biopython>=1.81
Requires-Dist: mavehgvs>=0.7.0
Dynamic: license-file

# sortscore

`sortscore` is a Python package for Sort-seq variant analysis, including scoring, normalization, and visualization.

## Quick Start

```bash
git clone https://github.com/dbaldridge-lab/sortscore
cd sortscore
python -m venv .venv
source .venv/bin/activate
pip install -e .
```
Run a standard variant scoring analysis:

```bash
sortscore -n EXPERIMENT_NAME -e path/to/experiment_setup.csv -c path/to/config.json
```
If you did not install the CLI entry point, run:

```bash
python -m sortscore -n EXPERIMENT_NAME -e path/to/experiment_setup.csv -c path/to/config.json
```

## Documentation
- [Installation](https://github.com/dbaldridge-lab/sortscore/blob/main/docs/installation.md)
- [Usage](https://github.com/dbaldridge-lab/sortscore/blob/main/docs/usage.md)
- [CLI Arguments](https://github.com/dbaldridge-lab/sortscore/blob/main/docs/cli_arguments.md)
- [Visualization](https://github.com/dbaldridge-lab/sortscore/blob/main/docs/visualization.md)
- [Batch Processing](https://github.com/dbaldridge-lab/sortscore/blob/main/docs/batch_processing.md)
- [Troubleshooting](https://github.com/dbaldridge-lab/sortscore/blob/main/TROUBLESHOOTING.md)
- [Contributing](https://github.com/dbaldridge-lab/sortscore/blob/main/CONTRIBUTING.md)

## Demo

- [Single Experiment Scoring Notebook Demo](https://github.com/dbaldridge-lab/sortscore/blob/main/demo_data/single_experiment_demo.ipynb)
- [Batch Normalization Notebook Demo](https://github.com/dbaldridge-lab/sortscore/blob/main/demo_data/tiled_demo.ipynb)
- [Example Config](https://github.com/dbaldridge-lab/sortscore/blob/main/demo_data/GLI2_oPool5b/config.json)
- [Example Experiment Setup](https://github.com/dbaldridge-lab/sortscore/blob/main/demo_data/GLI2_oPool5b/experiment_setup.csv)
