├── .coveragerc ├── .flake8_code ├── .flake8_notebooks ├── .github └── workflows │ ├── main.yml │ └── publish-package.yml ├── .gitignore ├── .idea ├── preferred-vcs.xml └── vcs.xml ├── .isort.cfg ├── BranchedGP ├── BranchingTree.py ├── FitBranchingModel.py ├── MBGP │ ├── BranchingTree.py │ ├── FitBranchingModel.py │ ├── VBHelperFunctions.py │ ├── __init__.py │ ├── assigngp.py │ ├── assigngp_denseSparse.py │ ├── data_generation.py │ ├── experiment_utils.py │ ├── gene_expression_api.py │ ├── label_utils.py │ ├── plotting_helpers.py │ ├── sampling_helpers.py │ └── training_helpers.py ├── VBHelperFunctions.py ├── __init__.py ├── assigngp_dense.py ├── assigngp_denseSparse.py ├── branch_kernParamGPflow.py └── pZ_construction_singleBP.py ├── LICENSE ├── Makefile ├── README.md ├── images └── VAMP5_BGPAssignmentProbability.png ├── jupytext.toml ├── monocle └── runMonocle.R ├── notebooks ├── Hematopoiesis.ipynb ├── Hematopoiesis.py ├── MBGP │ ├── experiment3-sample-data.tsv │ ├── experiments-figure-1-simple-fits.ipynb │ ├── experiments-figure-2-correct-cell-histogram.ipynb │ ├── experiments-figure-3-bgp-label-inconsistency.ipynb │ ├── new_experiments-figure-2-correct-cell-histogram.ipynb │ ├── new_experiments-figure-3-bgp-label-inconsistency.ipynb │ ├── rediscover_early_branching.ipynb │ ├── rediscover_early_branching2.ipynb │ ├── synthetic-data-4-gene-fit.png │ ├── synthetic_Y_without_crossing.ipynb │ └── synthetic_noise_free.ipynb ├── SamplingFromTheModel.ipynb ├── SamplingFromTheModel.py ├── SyntheticData.ipynb ├── SyntheticData.py ├── runsynteticData.py ├── singlecelldata │ ├── hematoData.csv │ └── hematoMonocle.csv └── syntheticdata │ ├── synthetic20.csv │ └── syntheticDataRun.p ├── pyproject.toml ├── setup.py ├── setup_tensorflow_on_apple_silicon.sh ├── test_requirements.txt └── testing ├── MBGP ├── __init__.py ├── manual_gene_expression_test.py ├── manual_spline_beam_test.py ├── test_assigngp.py ├── test_data.py ├── test_equivalence_multi_to_single.py ├── test_helpers.py ├── test_lengthscale_bounds.py ├── test_model_selection.py ├── test_synthetic_data.py └── test_training_helpers.py ├── test_KL.py ├── test_assignment.py ├── test_kernel.py ├── test_notebooks.py ├── test_objective.py ├── test_pZ_construct.py ├── test_sampling_and_plotting.py ├── test_sparse_to_full_model.py └── test_tree.py /.coveragerc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ManchesterBioinference/BranchedGP/HEAD/.coveragerc -------------------------------------------------------------------------------- /.flake8_code: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ManchesterBioinference/BranchedGP/HEAD/.flake8_code -------------------------------------------------------------------------------- /.flake8_notebooks: -------------------------------------------------------------------------------- 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