├── .gitignore ├── LICENSE.md ├── README.md ├── basiss ├── __init__.py ├── glmm │ ├── __init__.py │ └── glmm.py ├── histology │ ├── __init__.py │ ├── _data_aggregation.py │ ├── _glmm_data_preparation.py │ ├── _glmm_data_processing.py │ ├── _histogenomic.py │ ├── _name_exchange.py │ └── plots.py ├── models │ ├── __init__.py │ ├── _distr.py │ ├── _parameter_manipulation.py │ └── diagnostic_plots.py ├── plots │ ├── __init__.py │ └── _clone_maps.py ├── preprocessing │ ├── __init__.py │ ├── _iss_sample.py │ └── _model_data_preparation.py ├── sc_annot │ ├── __init__.py │ └── _direct_typing.py └── utils │ ├── __init__.py │ ├── _misc.py │ ├── _plots.py │ └── stats.py ├── data ├── PD14780_tree.csv └── PD9694_tree.csv ├── environment.yml ├── images ├── .DS_Store ├── main-readme.png ├── pd14780_readme.png └── pd9694_readme.png └── notebooks ├── BaSISS_spatial_signal_analysis.ipynb ├── Clones_characterisation.ipynb ├── Data_preparation.ipynb ├── PD14780_main_analysis.ipynb ├── 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