requirements.txt

# GeneLab_benchmark Python dependencies
# Install: pip install -r requirements.txt

# -- Core (evaluation + baselines) -----------------------------------------------
numpy>=1.21
pandas>=1.4
scipy>=1.7
scikit-learn>=1.0
requests>=2.28
xgboost>=2.0
shap>=0.42
matplotlib>=3.5

# -- v4: Pathway score generation + additional classifiers -----------------------
gseapy>=1.0
lightgbm>=4.0

# -- Optional: Geneformer / Foundation Models (HPC only) -------------------------
# Uncomment to enable Tier 2 (Geneformer, scGPT, UCE, scFoundation) evaluation.
# Requires GPU; tested on NVIDIA A40/A100 (CUDA 12.x).
# torch>=2.0
# transformers>=4.28
# datasets>=2.12
# huggingface_hub>=0.14
# safetensors>=0.3

# -- Optional: TabNet (v4 classifier) -------------------------------------------
# pytorch-tabnet>=4.0