Paradoxical G-quadruplex distribution in coronavirus genomes reveals functional constraints and antiviral therapeutic opportunities

 # G-quadruplex Distribution in Coronavirus Genomes: Analysis Code and Data

  ## Overview

  This dataset contains all code, data, and supplementary materials for the manuscript "Paradoxical G-quadruplex distribution in coronavirus genomes reveals
  functional constraints and antiviral therapeutic opportunities" published in *Virus Research* (2025).

  ## Key Findings

  - **Genome-wide G4 depletion**: Fold-change = 0.56 (95% CI: 0.24-2.30)
  - **Regional enrichment in critical proteins**:
    - Spike protein: IRR = 17.9 (95% CI: 11.7-27.6)
    - Nucleocapsid protein: IRR = 14.4 (95% CI: 8.3-25.1)
  - **Therapeutic targets**: 38 thermodynamically stable G4 candidates (ΔG < -5 kcal/mol)
  - **Primary target**: GGCTGGCAATGGCGG (ΔG = -7.35 kcal/mol, 54.8% conservation)

  ## Dataset Contents

  ### Genomes (31 files)
  - **SARS-CoV-2 variants** (n=19): Alpha, Beta, Gamma, Delta, Omicron sublineages (BA.1, BA.2, BA.5, BQ.1.1, XBB.1.5, XBB.1.16, JN.1), Epsilon, Eta, Kappa,
  Lambda, Mu, D614G, B.1, Wuhan reference
  - **Other coronaviruses** (n=12): SARS-CoV, MERS-CoV, bat coronaviruses (RmYN02, RaTG13, BANAL-52), pangolin coronaviruses, HCoV-OC43, HCoV-HKU1, HCoV-229E,
  HCoV-NL63

  ### Code (95 Python scripts)
  - G4 detection and regional mapping
  - Statistical robustness analysis (Bootstrap, Poisson GLM, GEE models)
  - Thermodynamic stability assessment (ΔG calculations)
  - Bayesian network analysis (pgmpy)
  - Machine learning predictions (XGBoost)
  - Cross-virus comparative analysis

  ### Results
  - Supplementary Tables S1-S7, S6A
  - Complete analysis outputs (CSV format)
  - Reproducible analysis pipeline

  ## Usage

  ```bash
  # Install dependencies
  pip install -r requirements.txt

  # Run complete analysis
  ./run_all.sh

  # Or use Make
  make all