numpy>=1.24
pandas>=2.0
matplotlib>=3.7
seaborn>=0.12
scipy>=1.10
scikit-learn>=1.3
customtkinter>=5.2
tqdm>=4.65
pytest>=7.0
biopython>=1.81
networkx>=3.0
plotly>=5.0

# === Tier 1: Core Bioinformatics ===
goatools>=1.3
gseapy>=1.0
cutadapt>=4.0

# === Tier 2: Advanced Analysis ===
scanpy>=1.9
anndata>=0.9
scikit-bio>=0.5
biotite>=0.37

# === Tier 3: Specialized ===
ete3>=3.1
cobra>=3.0
shap>=0.42
statsmodels>=0.14
umap-learn>=0.5

# === Tier 4: API/Web ===
fastapi>=0.100
uvicorn>=0.23
python-jose[cryptography]>=3.3
slowapi>=0.1.9
# === Tier 5: Jupyter ===
ipython>=8.0
ipywidgets>=8.0

# === Tier 6: Optional (may need C build tools) ===
# pysam>=0.21       # BAM/CRAM support (complex install on Windows)
# openmm>=8.0       # Molecular dynamics (complex install)
# pymzml>=2.5       # Metabolomics
# esm               # Protein structure prediction (requires torch)
# torch             # Deep learning backend for ESMFold
