# Core dependencies
numpy>=1.24,<3
# pandas>=2.2 required for NumPy 2.x; 2.1.x pins numpy<2
pandas>=2.2.0
scipy>=1.10.0

# Visualization
matplotlib

# Machine learning / Deep learning
torch
openspliceai

# NOTE: borzoi-pytorch is optional (for transcription-effect prediction):
# pip install borzoi-pytorch

# Biology-specific tools
seqmat
biopython>=1.80

# NOTE: pangolin must be installed separately:
# pip install git+https://github.com/tkzeng/Pangolin.git
