Metadata-Version: 2.4
Name: targetsage
Version: 0.0.2
Summary: Python reimplementation of RNAither adapted for high-throughput CRISPR screening analysis
Author-email: Rahul Brahma <rahul.brahma@uni-greifswald.de>, Yasas Wijesekara <yasas.wijesekara@uni-greifswald.de>
License: MIT License
        
        Copyright (c) 2025 TargetSage
        
        Permission is hereby granted, free of charge, to any person obtaining a copy
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Project-URL: Homepage, https://github.com/rahul-brahma/TargetSage
Project-URL: Documentation, https://targetsage.readthedocs.io
Project-URL: Repository, https://github.com/rahul-brahma/TargetSage.git
Project-URL: Issues, https://github.com/rahul-brahma/TargetSage/issues
Keywords: CRISPR,screening,RNAi,bioinformatics,genomics
Classifier: Development Status :: 3 - Alpha
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 :: 3.11
Classifier: Programming Language :: Python :: 3.12
Requires-Python: >=3.11
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy>=2.3.0
Requires-Dist: pandas>=2.3.0
Requires-Dist: matplotlib>=3.0
Requires-Dist: scipy>=1.4
Requires-Dist: scikit-learn
Requires-Dist: matplotlib-venn
Requires-Dist: statsmodels
Requires-Dist: ipykernel>=6.29.5
Requires-Dist: openpyxl>=3.1.5
Requires-Dist: seaborn>=0.13.2
Provides-Extra: docs
Requires-Dist: sphinx>=8.2.3; extra == "docs"
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Requires-Dist: sphinx-autodoc-typehints>=3.2.0; extra == "docs"
Provides-Extra: dev
Requires-Dist: sphinx>=8.2.3; extra == "dev"
Requires-Dist: sphinx-rtd-theme>=3.0.2; extra == "dev"
Requires-Dist: sphinx-autodoc-typehints>=3.2.0; extra == "dev"
Dynamic: license-file

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<img width="502" height="457" alt="target_seek_v1" src="https://github.com/user-attachments/assets/02dbde89-f566-499f-8e3b-423139f56342" />

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# TargetSage

  [![Python Version](https://img.shields.io/badge/python-3.11+-blue.svg)](https://www.python.org/)
  [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
  [![Documentation Status](https://readthedocs.org/projects/targetsage/badge/?version=latest)](https://targetsage.readthedocs.io/)
  [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
  [![PyPI version](https://badge.fury.io/py/targetsage.svg)](https://pypi.org/project/targetsage/)

</div>

## 📖 Overview

TargetSage is a powerful Python package for analyzing high-throughput CRISPR screening data. It provides a comprehensive suite of tools for quality control, normalization, statistical analysis, and visualization of CRISPR screening results.

## ✨ Features

- **Data Processing**: Efficient handling of large-scale CRISPR screening data
- **Quality Control**: Comprehensive QC metrics and visualization
- **Normalization**: Multiple normalization methods for CRISPR data
- **Statistical Analysis**: Advanced statistical tests for hit identification
- **Visualization**: Publication-quality plots and interactive visualizations
- **Modular Design**: Easy to extend and customize for specific needs

## 🚀 Installation

### Using pip

```bash
pip install targetsage
```

### From source

```bash
# Clone the repository
git clone https://github.com/rahul-brahma/TargetSage.git
cd TargetSage

# Install in development mode
pip install -e .
```

## 📚 Documentation

For detailed documentation, including API reference and examples, please visit our [documentation](https://targetsage.readthedocs.io/).

## 🎯 Quick Start

We are currently working on a quick start guide consisting of example analysis pipelines and a step-by-step guide to get started with TargetSage. In the meantime, please refer to the [documentation](https://targetsage.readthedocs.io/).

### Basic Usage

```python
import targetsage as ts

# load data
```

### Example Analysis Pipeline

```python
import targetsage as ts
from targetsage import stats, visualization

# Load and preprocess data

```

## 📊 Example Plots

### Quality Control Metrics

### Volcano Plot

### Heatmap

## 📄 License

This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details.

## 📧 Contact

For questions or support, please contact:

- Rahul Brahma: rahul.brahma[at]uni-greifswald[dot]de
- Yasas Wijesekara: yasas.wijesekara[at]uni-greifswald[dot]de

## 📚 References

1. Rieber N, Knapp B, Eils R, Kaderali L. RNAither, an automated pipeline for the statistical analysis of high-throughput RNAi screens. Bioinformatics. 2009 Mar 1;25(5):678-9. doi: 10.1093/bioinformatics/btp014. Epub 2009 Jan 25. PMID: 19168909.

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  Made with ❤️ by the TargetSage Team
</div>
