├── .devcontainer ├── Dockerfile └── devcontainer.json ├── .gitattributes ├── .gitignore ├── LICENSE ├── README.md ├── condalist.txt ├── environment.yml ├── examples ├── Breast Cancer Dataset Analysis.ipynb ├── Merfish Analysis.ipynb └── Slideseq Analysis.ipynb ├── images ├── multi_hotspot.png ├── nested_plot.png └── tracks.png ├── nest ├── __init__.py ├── benchmarks │ ├── __init__.py │ ├── agglomerative.py │ ├── comparison.py │ ├── parameters_synthetic.py │ ├── parameters_synthetic_segmentation.py │ ├── subsampling.py │ └── synthetic_analysis.py ├── cci │ ├── __init__.py │ ├── cci.py │ ├── cellchat.py │ └── spatial.py ├── data │ ├── __init__.py │ ├── data.py │ └── database.py ├── goa.py ├── hmrf │ ├── __init__.py │ └── hmrf.py ├── hotspot │ ├── __init__.py │ ├── coexpression.py │ ├── geometry.py │ ├── hotspot.py │ ├── hotspots_3d.py │ └── interaction_hotspot.py ├── methods.py ├── plot │ ├── __init__.py │ ├── hotspots.py │ ├── pl3d.py │ ├── plot.py │ └── tracksplot.py ├── synthetic │ └── data.py └── utility │ ├── __init__.py │ └── utility.py ├── pyproject.toml └── setup.cfg /.devcontainer/Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bwalker1/NeST/HEAD/.devcontainer/Dockerfile -------------------------------------------------------------------------------- /.devcontainer/devcontainer.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bwalker1/NeST/HEAD/.devcontainer/devcontainer.json -------------------------------------------------------------------------------- /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bwalker1/NeST/HEAD/.gitattributes -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 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