Metadata-Version: 2.3
Name: credtools
Version: 0.0.28
Summary: multi-ancestry fine-mapping pipeline.
License: MIT
Author: Jianhua Wang
Author-email: jianhua.mert@gmail.com
Requires-Python: >=3.9,<3.13
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Provides-Extra: web
Requires-Dist: cojopy (==0.1.2)
Requires-Dist: dash (>=2.10.0) ; extra == "web"
Requires-Dist: dash-bootstrap-components (>=1.4.0) ; extra == "web"
Requires-Dist: dash-mantine-components (>=0.12.0) ; extra == "web"
Requires-Dist: matplotlib (>=3.9.2)
Requires-Dist: numba (>=0.60.0,<0.61.0)
Requires-Dist: numpy (>=1.21.2)
Requires-Dist: pandas (>=1.3.3)
Requires-Dist: plotly (>=5.14.0) ; extra == "web"
Requires-Dist: rich (>=12.4.0)
Requires-Dist: rpy2 (>=3.5.16,<4.0.0)
Requires-Dist: scikit-learn (>=1.5.2)
Requires-Dist: scipy (>=1.7.3)
Requires-Dist: tqdm (>=4.66.5,<5.0.0)
Requires-Dist: typer (>=0.7.0)
Project-URL: Homepage, https://github.com/Jianhua-Wang/credtools
Description-Content-Type: text/markdown

# credtools


[![pypi](https://img.shields.io/pypi/v/credtools.svg)](https://pypi.org/project/credtools/)
[![python](https://img.shields.io/pypi/pyversions/credtools.svg)](https://pypi.org/project/credtools/)
[![Build Status](https://github.com/Jianhua-Wang/credtools/actions/workflows/dev.yml/badge.svg)](https://github.com/Jianhua-Wang/credtools/actions/workflows/dev.yml)
[![codecov](https://codecov.io/gh/Jianhua-Wang/credtools/branch/main/graphs/badge.svg)](https://codecov.io/github/Jianhua-Wang/credtools)
[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)



Multi-ancestry fine-mapping pipeline with interactive web visualization.


* Documentation: <https://Jianhua-Wang.github.io/credtools>
* GitHub: <https://github.com/Jianhua-Wang/credtools>
* PyPI: <https://pypi.org/project/credtools/>
* Free software: MIT


## Features

- **Multi-ancestry fine-mapping**: Support for multiple fine-mapping tools (SuSiE, FINEMAP, etc.)
- **Meta-analysis capabilities**: Combine results across populations and cohorts
- **Quality control**: Built-in QC metrics and visualizations
- **Interactive web interface**: Explore results through a modern web dashboard
- **Command-line interface**: Easy-to-use CLI for all operations

## Installation

### Basic Installation
```bash
pip install credtools
```

### With Web Visualization
To use the interactive web interface, install with web dependencies:
```bash
pip install credtools[web]
```

## Quick Start

### Command Line Usage

```bash
# Run complete fine-mapping pipeline
credtools pipeline input_loci.txt output_dir/

# Launch web visualization interface
credtools web /path/to/results --port 8080

# View specific loci files
credtools web /path/to/data \
  --allmeta-loci data/allmeta_loci.txt \
  --popumeta-loci data/popumeta_loci.txt \
  --nometa-loci data/nometa_loci.txt
```

### Web Interface

The web interface provides:
- **Home page**: Overview of all loci with interactive filtering
- **Locus pages**: Detailed views with LocusZoom-style plots
- **Quality control**: Comprehensive QC metrics and visualizations
- **Multi-tool comparison**: Compare results across different fine-mapping methods

Access the web interface at `http://localhost:8080` after running `credtools web`.

## Documentation

For detailed documentation, see <https://Jianhua-Wang.github.io/credtools>

## Web Visualization

The web module (`credtools.web`) provides interactive visualization of fine-mapping results. See [credtools/web/README.md](credtools/web/README.md) for detailed usage instructions.

