├── .gitignore ├── .readthedocs.yaml ├── LICENSE ├── README.md ├── data ├── MDT_data_prepare.py └── data_preprocessing │ ├── cao_organogenesis │ ├── README.md │ ├── environment.yaml │ ├── process2anndata.py │ └── scripts │ │ ├── alevin_fry_data_dl.sh │ │ ├── cao_et_al_get_quant.R │ │ └── cao_et_al_update_anno.R │ └── hindbrain_dev │ ├── README.md │ ├── Snakefile │ ├── config.json │ ├── environment.yaml │ ├── kallisto_readme │ └── README.md │ └── scripts │ ├── loom_metadata.py │ ├── loom_subset.py │ ├── loompy_combine.py │ ├── manifest.json │ ├── metadata.py │ ├── mouse_build.py │ ├── mouse_download.sh │ └── mouse_generate_fragments.py ├── deepvelo ├── __init__.py ├── base │ ├── __init__.py │ ├── base_data_loader.py │ ├── base_model.py │ └── base_trainer.py ├── data_loader │ └── data_loaders.py ├── logger │ ├── __init__.py │ ├── logger.py │ ├── logger_config.json │ └── visualization.py ├── model │ ├── layers.py │ ├── loss.py │ ├── metric.py │ └── model.py ├── parse_config.py ├── pipeline │ ├── __init__.py │ └── eval.py ├── plot │ ├── __init__.py │ ├── plot.py │ └── scatter.py ├── tool │ ├── __init__.py │ ├── driver_gene.py │ ├── kinetic_rates.py │ ├── stats.py │ └── velocity.py ├── train.py ├── trainer │ ├── __init__.py │ └── trainer.py └── utils │ ├── __init__.py │ ├── confidence.py │ ├── map_velocity_expression.py │ ├── optimization.py │ ├── plot.py │ ├── preprocess.py │ ├── scatter.py │ ├── temporal.py │ └── util.py ├── docs ├── Makefile ├── conf.py ├── index.rst └── make.bat ├── examples ├── README.md ├── computation_time_plot.ipynb ├── figure2.ipynb ├── figure3(d-h).ipynb ├── figure3.ipynb ├── figure4_hindbrain.ipynb ├── incorporate_cellrank.ipynb ├── la_manno_hippocampus.ipynb ├── minimal_example.ipynb ├── mouse_gastrulation.py ├── multifacet_check.py ├── organogenesis_chondrocyte.ipynb ├── r_analysis │ ├── README.md │ ├── env.yaml │ ├── helpers │ │ └── scIB_knit_table.R │ └── scripts │ │ ├── 00_extra_package_installs.R │ │ ├── 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