Genopedia - Genomics Machine Learning Pipeline

Genopedia is a genomics-focused machine learning pipeline for DNA/RNA sequence analysis, variant detection, and color-coded visualization.

✅ Core Features

Genomics Pipeline

• Nucleotide color coding: A=🔴, T=🟡, G=🟢, C=🔵, U=🟤
• Data loaders: FASTA, FASTQ, VCF
• Sequence analysis: GC content, motif finding, functional region detection
• Variant detection: SNPs, insertions/deletions, pathogenicity scoring
• Visualization: HTML/SVG color-coded sequences

ML Models

• DNA sequence classifier (basic k-mer model implemented)
• Variant pathogenicity prediction
• Gene function annotation
• Extensible architecture for deep learning models

📦 Project Structure

genopedia/
├── src/
│   ├── genomics/          # Core genomics pipeline
│   ├── models/            # ML models
│   ├── api/               # FastAPI backend
│   └── utils/             # Utilities
├── notebooks/             # Jupyter notebooks
├── tests/                 # Unit tests
├── examples/              # Demo scripts
├── docs/                  # Documentation
└── requirements.txt

🚀 Quick Start

cd ~/Desktop/genopedia
pip install -r requirements.txt

# Run a demo
python examples/demo_genomics.py

# Run tests
python -m pytest tests/

🔬 Testing

Tests cover:

• Data loading/generation
• Sequence analysis
• Variant detection
• Visualization utilities

python -m pytest tests/test_genomics.py -v

📊 Visualization

Generates HTML/SVG color-coded nucleotide sequences:

from src.genomics import GenomicsVisualizer
visualizer = GenomicsVisualizer()
dna_sequence = "ATGCCGTAG"
html_output = visualizer.generate_color_html(dna_sequence)

🌐 API (Planned)

FastAPI backend for:

• Sequence analysis endpoints
• Variant detection
• ML model inference
• WebSocket for real-time visualization

🔗 Cloud Dataset Access

No large files stored locally - access datasets via:

• GRCh38: https://www.ncbi.nlm.nih.gov/grc/human
• 1000 Genomes: s3://1000genomes/
• ClinVar: ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/
• Ensembl: ftp://ftp.ensembl.org/pub/
• dbSNP: ftp://ftp.ncbi.nlm.nih.gov/snp/

🧬 Genomics Context

Based on:

• ChatGPT conversation
• Qwen conversation
• Kimi conversation

🔮 Future Enhancements

1. Deep learning-based variant pathogenicity prediction
2. Gene expression analysis
3. CRISPR target identification
4. Web dashboard with interactive visualization
5. Integration with real PCR machines

📜 License

MIT License - see LICENSE ```

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© 2026 Genopedia Project | GitHub