README and Documentation

A good README.md is like a well-written Methods section — it should help others reproduce your work.

Dr. X's README.md:

# CellClusterFlow 🧬

Single-cell RNA-seq analysis pipeline with automated QC, normalization, and clustering.

## Installation
```bash
git clone https://github.com/DrX/CellClusterFlow.git
cd CellClusterFlow
pip install -r requirements.txt
```

## Quick Start
```python
from cellclusterflow import Pipeline

pipeline = Pipeline()
adata = pipeline.load_data("data/pbmc3k.h5ad")
adata = pipeline.run_qc(adata)
adata = pipeline.normalize(adata)
adata = pipeline.cluster(adata)
pipeline.plot_umap(adata)
```

## Citation

If you use CellClusterFlow, please cite:

Dr. X et al. (2025). CellClusterFlow: Reproducible scRNA-seq analysis.

## License

MIT License — see LICENSE file

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