PhyloSOLID/requirements.txt at main · baebae0502/PhyloSOLID · GitHub

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# Core scientific computing
numpy>=1.21.0
pandas>=1.3.0
scipy>=1.7.0
matplotlib>=3.4.0
seaborn>=0.11.0

# Machine learning
scikit-learn>=1.0.0
joblib>=1.0.0

# Graph analysis and networks
networkx>=2.6.0
python-igraph>=0.9.0
leidenalg>=0.8.0
python-louvain>=0.15
anytree>=2.8.0

# Single-cell analysis
scanpy>=1.9.0
anndata>=0.8.0

# Bioinformatics
scphylo>=0.1.0
pysam>=0.19.0
pybedtools>=0.9.0
pyfaidx>=0.7.0

# Phylogenetics related
cogent3>=2022.0.0

# Parallel processing and utilities
tqdm>=4.62.0
multiprocess>=0.70.12.2

# Statistics
statsmodels>=0.13.0

# Deep learning (optional)
torch>=1.9.0

# Sequence processing
biopython>=1.79

# Data processing tools
json5>=0.9.0
pyyaml>=5.4.0

# Logging and debugging
loguru>=0.5.0

# Interactive visualization
plotly>=5.3.0

# File operations
h5py>=3.4.0
hdf5plugin>=3.0.0

# Compatibility
pickle5>=0.0.11
cloudpickle>=2.0.0

# Testing
pytest>=6.2.0

# Additional utilities
gitpython>=3.1.0
requests>=2.26.0