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CHANGELOG.md
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README.md
RESTRUCTURING_PLAN.md
pixi.toml
pyproject.toml
requirements.txt
run_complete_analysis.py
run_pipe_regev_test_TODELETE.sh
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docs/.gitignore
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docs/architecture.md
docs/atac-peaks.md
docs/celloracle.md
docs/checkpoints.md
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docs/hotspot.md
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examples/celloracle_workflow.py
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genecircuitry/__init__.py
genecircuitry/atac_peaks_processing.py
genecircuitry/celloracle_processing.py
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genecircuitry/enrichment_analysis.py
genecircuitry/grn_deep_analysis.py
genecircuitry/hotspot_processing.py
genecircuitry/logging_utils.py
genecircuitry/preprocessing.py
genecircuitry.egg-info/PKG-INFO
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genecircuitry.egg-info/top_level.txt
genecircuitry/pipeline/__init__.py
genecircuitry/pipeline/controller.py
genecircuitry/plotting/__init__.py
genecircuitry/plotting/grn_plots.py
genecircuitry/plotting/hotspot_plots.py
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