├── .coveragerc ├── .gitignore ├── .travis.yml ├── LICENSE ├── README.md ├── notebooks ├── ExampleWorkflow.ipynb └── trajectory_simulation.ipynb ├── setup.cfg ├── setup.py ├── topslam ├── __init__.py ├── __version__.py ├── examples.py ├── filtering.py ├── landscape.py ├── optimization.py ├── plotting.py ├── pseudo_time │ ├── __init__.py │ ├── distance_correction.py │ ├── distances.py │ ├── knn_correction.py │ └── tree_correction.py ├── simulation │ ├── __init__.py │ ├── graph_extraction.py │ └── simulate_trajectory.py └── tests │ ├── __init__.py │ ├── baseline │ ├── other_comparison.npz │ ├── other_dist_hist.npz │ ├── other_landscape_labs.npz │ ├── topslam_graph_nodes_labels_nobox_noadjust.npz │ ├── topslam_graph_nodes_nolabs_box_adjust.npz │ ├── topslam_time_tree_labels.npz │ ├── topslam_time_tree_no_lab.npz │ └── topslam_waddington_nodes.npz │ ├── test_data_model.npz │ ├── test_data_others.npz │ ├── test_distances.py │ ├── test_plotting.py │ └── test_pseudotime.py └── travis_tests.py 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