PlasmidNet Documentation
PlasmidNet is an interactive dashboard for exploring 182,362 bacterial plasmids from PLSDB 2025 and NCBI Nucleotide. It provides comprehensive analytics for antimicrobial resistance, plasmid mobility, geographic distribution, and sequence analysis.
Live Dashboard: plasmidnet-7302570f4818.herokuapp.com
Source Code: github.com/lcerdeira/plasmidnet
Quick Start
pip install -r requirements.txt
python build_db.py # downloads PLSDB data from Figshare, builds SQLite DB
python app.py # open http://localhost:8050
Contents
- Dashboard Features
- REST API
- Sequence Analysis
- Plasmid Comparison
- Statistical Analytics
- 1. Matched Comparison
- 2. Rarefaction Analysis
- 3. XGBoost + SHAP
- 4. Temporal Trends
- 5. Simpson’s Paradox Detector
- 6. AMR Co-occurrence Network
- 7. Integron & Gene Cassette Analysis
- 8. Co-mobilization Analysis
- 9. Retro-mobilization & HGT Routes
- 10. blaKPC Transposon Context
- 11. Integron ML & Transposon-AMR Correlations
- Database
- Deployment