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README.md

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@@ -8,6 +8,8 @@ A reproducible computational pipeline for processing and analyzing single-cell R
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This pipeline transforms raw single-cell RNA-seq data with genetic perturbations into high-quality, balanced datasets suitable for training ML/AI models to predict perturbation effects. It supports multiple dataset types and provides comprehensive quality control, normalization, and integration capabilities.
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[Pipeline report for the demo data.](https://actn3bioinformatics.github.io/VCC-project/)
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### Key Features
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- **🔄 Automated Workflow**: Snakemake-based pipeline with dependency management
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- [**Pipeline Guide**](docs/PIPELINE_GUIDE.md) - Complete pipeline documentation
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- [**Troubleshooting**](docs/TROUBLESHOOTING.md) - Common issues and solutions
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- [**Demo Notebook**](notebooks/demo_exploration.ipynb) - Interactive demo data exploration
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- [**Demo Report**](docs/demo_exploration.html) - HTML version of the report for the demo data
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- [**Demo Report**](https://actn3bioinformatics.github.io/VCC-project/) - HTML version of the report for the demo data
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- [**Contributing Guide**](CONTRIBUTING.md) - How to contribute
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## 📓 Jupyter Notebooks

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