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CONTRIBUTING.rst
LICENSE
MANIFEST.in
README.rst
pyproject.toml
requirements.txt
setup.py
tox.ini
cellrank/__init__.py
cellrank/_key.py
cellrank/estimators.py
cellrank/kernels.py
cellrank/models.py
cellrank.egg-info/PKG-INFO
cellrank.egg-info/SOURCES.txt
cellrank.egg-info/dependency_links.txt
cellrank.egg-info/not-zip-safe
cellrank.egg-info/requires.txt
cellrank.egg-info/top_level.txt
cellrank/datasets/__init__.py
cellrank/datasets/_datasets.py
cellrank/external/__init__.py
cellrank/external/_error_mixin.py
cellrank/external/estimators/__init__.py
cellrank/external/estimators/_import_error_estim.py
cellrank/external/kernels/__init__.py
cellrank/external/kernels/_import_error_kernel.py
cellrank/external/kernels/_statot_kernel.py
cellrank/external/kernels/_utils.py
cellrank/external/kernels/_wot_kernel.py
cellrank/external/models/__init__.py
cellrank/external/models/_import_error_model.py
cellrank/logging/__init__.py
cellrank/logging/_logging.py
cellrank/pl/__init__.py
cellrank/pl/_circular_projection.py
cellrank/pl/_cluster_fates.py
cellrank/pl/_cluster_lineage.py
cellrank/pl/_gene_trend.py
cellrank/pl/_graph.py
cellrank/pl/_heatmap.py
cellrank/pl/_init_term_states.py
cellrank/pl/_lineages.py
cellrank/pl/_log_odds.py
cellrank/pl/_utils.py
cellrank/settings/__init__.py
cellrank/settings/_settings.py
cellrank/tl/__init__.py
cellrank/tl/_colors.py
cellrank/tl/_enum.py
cellrank/tl/_init_term_states.py
cellrank/tl/_lineage.py
cellrank/tl/_lineages.py
cellrank/tl/_linear_solver.py
cellrank/tl/_read.py
cellrank/tl/_transition_matrix.py
cellrank/tl/_utils.py
cellrank/tl/_mixins/__init__.py
cellrank/tl/_mixins/_anndata.py
cellrank/tl/_mixins/_io.py
cellrank/tl/_mixins/_kernel.py
cellrank/tl/estimators/__init__.py
cellrank/tl/estimators/_base_estimator.py
cellrank/tl/estimators/_utils.py
cellrank/tl/estimators/mixins/__init__.py
cellrank/tl/estimators/mixins/_absorption_probabilities.py
cellrank/tl/estimators/mixins/_lineage_drivers.py
cellrank/tl/estimators/mixins/_utils.py
cellrank/tl/estimators/mixins/decomposition/__init__.py
cellrank/tl/estimators/mixins/decomposition/_eigen.py
cellrank/tl/estimators/mixins/decomposition/_schur.py
cellrank/tl/estimators/terminal_states/__init__.py
cellrank/tl/estimators/terminal_states/_cflare.py
cellrank/tl/estimators/terminal_states/_gpcca.py
cellrank/tl/estimators/terminal_states/_term_states_estimator.py
cellrank/tl/kernels/__init__.py
cellrank/tl/kernels/_base_kernel.py
cellrank/tl/kernels/_connectivity_kernel.py
cellrank/tl/kernels/_cytotrace_kernel.py
cellrank/tl/kernels/_exp_time_kernel.py
cellrank/tl/kernels/_precomputed_kernel.py
cellrank/tl/kernels/_pseudotime_kernel.py
cellrank/tl/kernels/_pseudotime_schemes.py
cellrank/tl/kernels/_random_walk.py
cellrank/tl/kernels/_tmat_flow.py
cellrank/tl/kernels/_utils.py
cellrank/tl/kernels/_velocity_kernel.py
cellrank/tl/kernels/_velocity_schemes.py
cellrank/ul/__init__.py
cellrank/ul/_docs.py
cellrank/ul/_parallelize.py
cellrank/ul/_utils.py
cellrank/ul/models/__init__.py
cellrank/ul/models/_base_model.py
cellrank/ul/models/_gamr_model.py
cellrank/ul/models/_pygam_model.py
cellrank/ul/models/_sklearn_model.py
cellrank/ul/models/_utils.py
docs/requirements.txt
examples/README.rst
examples/estimators/README.rst
examples/estimators/compute_abs_probs.py
examples/estimators/compute_coarse_T.py
examples/estimators/compute_lineage_drivers.py
examples/estimators/compute_macrostates.py
examples/estimators/compute_terminal_states_gpcca.py
examples/kernels/README.rst
examples/kernels/compute_kernel_tricks.py
examples/kernels/plot_projection.py
examples/kernels/plot_random_walks.py
examples/other/README.rst
examples/other/compute_lineage_tricks.py
examples/other/plot_model.py
examples/plotting/README.rst
examples/plotting/plot_circular_embedding.py
examples/plotting/plot_cluster_fates.py
examples/plotting/plot_cluster_lineage.py
examples/plotting/plot_directed_paga.py
examples/plotting/plot_gene_trends.py
examples/plotting/plot_graph.py
examples/plotting/plot_heatmap.py
examples/plotting/plot_initial_states.py
examples/plotting/plot_lineage_drivers.py
examples/plotting/plot_lineages.py
examples/plotting/plot_terminal_states.py
tests/_helpers.py
tests/conftest.py
tests/test_cflare.py
tests/test_colors.py
tests/test_datasets.py
tests/test_external.py
tests/test_gpcca.py
tests/test_kernels.py
tests/test_lineage.py
tests/test_linear_solver.py
tests/test_logging.py
tests/test_model.py
tests/test_pipeline.py
tests/test_plotting.py
tests/test_random_walk.py
tests/test_read.py
tests/test_tools.py
tests/test_utils.py