aman
acadbd780c
Full reproducible pipeline: .mcool + ChIP-seq bigwigs → latent embeddings → A/B compartment calls → cross-cell comparison. Key results (chr21, 25 kb, latent dim=32): - Test AUC=0.777, AP=0.759 (converged epoch 31/300) - GM12878 A/B silhouette (cosine) = 0.775 - IMR90 zero-shot silhouette = 0.443 - A-compartment bins stable across cell types (mean cosine Δ=0.042) - B-compartment bins shift substantially (mean cosine Δ=0.451) - 101 B→A and 70 A→B compartment switches GM12878→IMR90
31 lines
302 B
Plaintext
31 lines
302 B
Plaintext
# Raw sequencing and contact data (large files; download via run_pipeline.sh)
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data/raw/
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# Python
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__pycache__/
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*.py[cod]
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*.pyo
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.pytest_cache/
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*.egg-info/
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dist/
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build/
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# Environments
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.env
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*.env
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.venv/
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# Editors
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.vscode/
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.idea/
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*.swp
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*~
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# Jupyter
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.ipynb_checkpoints/
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*.ipynb
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# OS
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.DS_Store
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Thumbs.db
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