├── .github ├── scripts │ └── release.py └── workflows │ ├── publish.yml │ └── release.yml ├── .gitignore ├── LICENSE ├── MANIFEST.in ├── _static └── training_progress.png ├── dist ├── celldancer-1.1.4-py3-none-any.whl ├── celldancer-1.1.4.tar.gz ├── celldancer-1.1.7-py3-none-any.whl └── celldancer-1.1.7.tar.gz ├── notebooks ├── case_study_gastrulation.ipynb ├── case_study_hgforebrian.ipynb ├── case_study_neuro.ipynb ├── case_study_pancreas.ipynb ├── case_study_pancreas_dynamo.ipynb ├── case_study_rpe1.ipynb └── celldancer_prototype_model.ipynb ├── readme.rst ├── readme_pypi.rst ├── requirements.txt ├── setup.py └── src └── celldancer ├── .Rapp.history ├── __init__.py ├── cdplt.py ├── compute_cell_velocity.py ├── diffusion.py ├── embedding_kinetic_para.py ├── model ├── branch.pt └── circle.pt ├── plotting ├── .Rapp.history ├── __init__.py ├── cell.py ├── colormap.py ├── gene.py └── graph.py ├── pseudo_time.py ├── sampling.py ├── simulation.py ├── utilities.py └── velocity_estimation.py 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