├── .dockerignore ├── .flake8 ├── .github ├── ISSUE_TEMPLATE │ ├── analyses-&-predictions.md │ ├── bug_report.md │ └── docs-bug-or-enhancement.md └── workflows │ ├── python-docker.yml │ ├── python-package.yml │ ├── python-plain-run-test.yml │ ├── python-publish.yml │ └── stale.yml ├── .gitignore ├── .gitmodules ├── .pre-commit-config.yaml ├── .readthedocs.yml ├── .travis.yml ├── CHANGELOG.md ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── Dockerfile ├── LICENSE ├── README.md ├── docs ├── Makefile ├── _static │ ├── Preprocessor_tutorial_files │ │ ├── output_20_1.png │ │ ├── output_23_1.png │ │ ├── output_26_1.png │ │ ├── output_29_1.png │ │ ├── output_38_0.png │ │ ├── output_40_1.png │ │ ├── output_42_0.png │ │ ├── output_49_1.png │ │ ├── output_54_1.png │ │ └── output_67_1.png │ ├── Shiny_tutorial_files │ │ ├── lap │ │ │ ├── 1_1.png │ │ │ ├── 1_2.png │ │ │ ├── 2_1.jpg │ │ │ ├── 2_2.jpg │ │ │ ├── 2_3.jpg │ │ │ ├── 2_4.png │ │ │ ├── 2_5.jpg │ │ │ ├── 2_6.jpg │ │ │ ├── 3_1.jpg │ │ │ ├── 3_2.png │ │ │ ├── 4_1.jpg │ │ │ ├── 4_2.png │ │ │ ├── 5_1.jpg │ │ │ ├── 5_2.jpg │ │ │ ├── 6.png │ │ │ ├── 7_1.png │ │ │ ├── 7_2.jpg │ │ │ ├── 8_1.jpg │ │ │ ├── 8_2.png │ │ │ ├── 9_1.png │ │ │ ├── 9_2.jpg │ │ │ ├── 9_3.jpg │ │ │ ├── 9_4.jpg │ │ │ ├── 9_5.png │ │ │ ├── 9_6.jpg │ │ │ ├── 9_7.png │ │ │ └── 9_8.png │ │ └── perturbation │ │ │ ├── 1.png │ │ │ ├── 1_1.jpg │ │ │ ├── 2_1.jpg │ │ │ ├── 2_2.jpg │ │ │ ├── 2_3.jpg │ │ │ └── 3_1.jpg │ ├── css │ │ ├── custom.css │ │ └── override.css │ ├── dynamo-horizontal.svg │ ├── img │ │ ├── anndata_manager_schematic.svg │ │ └── setup_anndata_before_after.svg │ ├── logo.png │ └── logo.svg ├── _templates │ ├── autosummary │ │ └── class.rst │ └── class_no_inherited.rst ├── api │ ├── datasets.md │ ├── index.md │ └── user.md ├── changelog.md ├── conf.py ├── developer.md ├── extensions │ ├── edit_colab_url.py │ └── typed_returns.py ├── faq.md ├── index.md ├── installation.md ├── introduction │ ├── dynamo_paper_figures │ │ ├── fig6_a.png │ │ ├── fig6_b.png │ │ ├── fig6_c.png │ │ └── fig7_a.png │ ├── index.md │ ├── index_cellfate.md │ ├── index_geo.md │ ├── index_silico.md │ ├── index_time.md │ ├── lap_tutorial │ │ ├── bas-hsc-kinetic.png │ │ ├── lap_tutorial.rst │ │ ├── output_19_0.png │ │ ├── output_22_2.png │ │ ├── output_24_0.png │ │ ├── output_25_0.png │ │ ├── output_31_0.png │ │ ├── output_55_1.png │ │ ├── output_58_2.png │ │ ├── output_6_0.png │ │ ├── output_9_1.png │ │ ├── reprogram-lap.png │ │ └── transdifferentiation-lap.png │ └── perturbation_tutorial │ │ ├── output_14_1.png │ │ ├── output_16_1.png │ │ ├── output_18_1.png │ │ ├── output_20_1.png │ │ ├── output_22_1.png │ │ └── perturbation_tutorial.rst ├── make.bat ├── references.bib ├── references.md ├── requirements.txt ├── tutorials │ ├── index.md │ ├── index_conventional.md │ ├── index_differential_geometry.md │ ├── index_gallery.md │ ├── index_labeling.md │ ├── index_multivelo.md │ ├── index_preprocessing.md │ ├── index_vector_pre.md │ └── shiny.md └── user_guide │ └── index.md ├── dynamo ├── __init__.py ├── configuration.py ├── data_io.py ├── docrep.py ├── dynamo_logger.py ├── est.py ├── estimation │ ├── __init__.py │ ├── csc │ │ ├── __init__.py │ │ ├── utils_velocity.py │ │ └── velocity.py │ ├── deprecated.py │ ├── fit_jacobian.py │ └── tsc │ │ ├── ODEs.py │ │ ├── __init__.py │ │ ├── estimation_kinetic.py │ │ ├── twostep.py │ │ └── utils_moments.py ├── ext.py ├── external │ ├── __init__.py │ ├── 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 │ ├── deepvelo │ │ ├── __init__.py │ │ ├── base │ │ │ ├── __init__.py │ │ │ ├── base_data_loader.py │ │ │ ├── base_model.py │ │ │ └── base_trainer.py │ │ ├── data_loader │ │ │ ├── __init__.py │ │ │ └── data_loaders.py │ │ ├── logger │ │ │ ├── __init__.py │ │ │ ├── logger.py │ │ │ ├── logger_config.json │ │ │ └── visualization.py │ │ ├── model │ │ │ ├── __init__.py │ │ │ ├── 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 │ ├── dynode │ │ ├── __init__.py │ │ ├── dynamics │ │ │ ├── __init__.py │ │ │ ├── abstract_vf.py │ │ │ ├── ef_vf.py │ │ │ ├── fm_loss.py │ │ │ ├── mlp_vf.py │ │ │ └── scheduler.py │ │ ├── embedding │ │ │ ├── __init__.py │ │ │ ├── abstract_ae.py │ │ │ ├── autoencoder.py │ │ │ └── vae.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── classification.py │ │ │ └── ffn.py │ ├── gseapy.py │ ├── gtfparse │ │ ├── __init__.py │ │ ├── attribute_parsing.py │ │ ├── create_missing_features.py │ │ ├── parsing_error.py │ │ └── read_gtf.py │ ├── hodge.py │ ├── latentvelo │ │ ├── __init__.py │ │ ├── anvi_dataloader.py │ │ ├── anvi_dataloader_nogcn.py │ │ ├── atac_dataloader.py │ │ ├── collate.py │ │ ├── dataloader.py │ │ ├── dataloader_nogcn.py │ │ ├── dataloader_utils.py │ │ ├── ev.py │ │ ├── evaluation │ │ │ ├── __init__.py │ │ │ ├── metrics.py │ │ │ └── run_metric.py │ │ ├── models │ │ │ ├── __init__.py │ │ │ ├── annot_vae_model.py │ │ │ ├── atac_reg_model.py │ │ │ ├── gclayer.py │ │ │ ├── modules.py │ │ │ ├── refine_model.py │ │ │ ├── vae_model.py │ │ │ └── velocity_field.py │ │ ├── output_results.py │ │ ├── path_regularization.py │ │ ├── pl.py │ │ ├── plotting │ │ │ ├── __init__.py │ │ │ ├── metrics.py │ │ │ └── scatter_stream.py │ │ ├── tl.py │ │ ├── tools │ │ │ ├── __init__.py │ │ │ ├── batch_correction.py │ │ │ ├── cell_trajectories.py │ │ │ ├── check_velocity.py │ │ │ └── trad_velocity.py │ │ ├── train.py │ │ ├── trainer.py │ │ ├── trainer_anvi.py │ │ ├── trainer_anvi_nogcn.py │ │ ├── trainer_atac.py │ │ ├── trainer_nogcn.py │ │ ├── utils.py │ │ └── velocity_genes.py │ ├── pyensembl │ │ ├── __init__.py │ │ ├── common.py │ │ ├── database.py │ │ ├── download_cache.py │ │ ├── ensembl_release.py │ │ ├── ensembl_url_templates.py │ │ ├── ensembl_versions.py │ │ ├── exon.py │ │ ├── fasta.py │ │ ├── gene.py │ │ ├── genome.py │ │ ├── locus.py │ │ ├── locus_with_genome.py │ │ ├── logging.conf │ │ ├── normalization.py │ │ ├── reference_name.py │ │ ├── search.py │ │ ├── sequence_data.py │ │ ├── serializable.py │ │ ├── shell.py │ │ ├── species.py │ │ ├── transcript.py │ │ └── version.py │ ├── scifate.py │ ├── scribe.py │ ├── sude_py │ │ ├── __init__.py │ │ ├── clle.py │ │ ├── init_pca.py │ │ ├── learning_l.py │ │ ├── learning_s.py │ │ ├── mds.py │ │ ├── opt_scale.py │ │ ├── pca.py │ │ ├── plotcluster2.py │ │ ├── pps.py │ │ └── sude.py │ └── utils.py ├── get_version.py ├── movie │ ├── __init__.py │ ├── fate.py │ └── utils.py ├── multi.py ├── multivelo │ ├── ATACseqTools.py │ ├── ChromatinVelocity.py │ ├── MultiConfiguration.py │ ├── MultiIO.py │ ├── MultiPreprocessor.py │ ├── MultiQC.py │ ├── MultiVelo.py │ ├── __init__.py │ ├── dynamical_chrom_func.py │ ├── globals.py │ ├── neural_nets │ │ ├── dir0.pt │ │ ├── dir1.pt │ │ ├── dir2_m1.pt │ │ └── dir2_m2.pt │ ├── old_MultiVelocity.py │ ├── old_MultiomicVectorField.py │ ├── pyWNN.py │ ├── settings.py │ └── sparse_matrix_utils.py ├── mv.py ├── pd.py ├── pl.py ├── plot │ ├── __init__.py │ ├── _jacobian.py │ ├── _trends.py │ ├── animation_lines.py │ ├── cell_cycle.py │ ├── clustering.py │ ├── connectivity.py │ ├── dimension_reduction.py │ ├── dynamics.py │ ├── ezplots.py │ ├── fate.py │ ├── fate_utilities_deprecated.py │ ├── heatmaps.py │ ├── least_action_path.py │ ├── markers.py │ ├── networks.py │ ├── preprocess.py │ ├── pseudotime.py │ ├── scPotential.py │ ├── scVectorField.py │ ├── scatters.py │ ├── sctransform.py │ ├── space.py │ ├── state_graph.py │ ├── streamtube.py │ ├── theme.py │ ├── time_series.py │ ├── topography.py │ ├── utils.py │ ├── utils_dynamics.py │ ├── utils_graph.py │ ├── vector_calculus.py │ └── violin_box.py ├── pp.py ├── prediction │ ├── __init__.py │ ├── _tf_eval.py │ ├── fate.py │ ├── least_action_path.py │ ├── perturbation.py │ ├── state_graph.py │ ├── trajectory.py │ ├── trajectory_analysis.py │ ├── tscRNA_seq.py │ └── utils.py ├── preprocessing │ ├── CnmfPreprocessor.py │ ├── Preprocessor.py │ ├── QC.py │ ├── __init__.py │ ├── cell_cycle.py │ ├── deprecated.py │ ├── dynast.py │ ├── external │ │ ├── __init__.py │ │ ├── integration.py │ │ ├── pearson_residual_recipe.py │ │ └── sctransform.py │ ├── gene_selection.py │ ├── normalization.py │ ├── pca.py │ ├── transform.py │ └── utils.py ├── sample_data.py ├── shiny.py ├── shiny │ ├── __init__.py │ ├── lap.py │ ├── perturbation.py │ ├── styles.css │ └── utils.py ├── sim.py ├── simulation │ ├── Gillespie.py │ ├── ODE.py │ ├── __init__.py │ ├── bif_os_inclusive_sim.py │ ├── evaluation.py │ ├── simulate_anndata.py │ └── utils.py ├── tl.py ├── tools │ ├── DDRTree.py │ ├── DDRTree_graph.py │ ├── Markov.py │ ├── __init__.py │ ├── _enum.py │ ├── _extvelo.py │ ├── _track.py │ ├── cell_velocities.py │ ├── clustering.py │ ├── connectivity.py │ ├── deprecated.py │ ├── dimension_reduction.py │ ├── dynamics.py │ ├── graph_calculus.py │ ├── graph_operators.py │ ├── growth.py │ ├── markers.py │ ├── metric_velocity.py │ ├── moments.py │ ├── pseudotime.py │ ├── pseudotime_velocity.py │ ├── psl.py │ ├── recipes.py │ ├── sampling.py │ ├── utils.py │ ├── utils_reduceDimension.py │ └── velocyto_scvelo.py ├── utils.py ├── vectorfield │ ├── Ao.py │ ├── Bhattacharya.py │ ├── FixedPoints.py │ ├── Tang.py │ ├── VectorField.py │ ├── Wang.py │ ├── __init__.py │ ├── cell_vectors.py │ ├── clustering.py │ ├── least_action_path.py │ ├── networks.py │ ├── rank_vf.py │ ├── scPotential.py │ ├── scVectorField.py │ ├── stochastic_process.py │ ├── topography.py │ ├── util_vector_calculus.py │ ├── utils.py │ ├── vector_calculus.py │ └── vfGraph_deprecated.py └── vf.py ├── pyproject.toml ├── pytest.ini ├── requirements.txt ├── setup.cfg ├── setup.py ├── sinfo-requirements.txt └── tests ├── __init__.py ├── conftest.py ├── run_plain_tests.sh ├── test_config.py ├── test_data_io.py ├── test_logger.py ├── test_pipeline.py ├── test_pl.py ├── test_prediction.py ├── test_preprocess.py ├── test_simulation.py ├── test_space.py ├── test_sude.py ├── test_tl.py ├── test_vf.py └── tests.py /.dockerignore: 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References 2 | 3 | ```{bibliography} 4 | :cited: 5 | ``` 6 | -------------------------------------------------------------------------------- /docs/requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aristoteleo/dynamo-release/HEAD/docs/requirements.txt -------------------------------------------------------------------------------- /docs/tutorials/index.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aristoteleo/dynamo-release/HEAD/docs/tutorials/index.md -------------------------------------------------------------------------------- /docs/tutorials/index_conventional.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aristoteleo/dynamo-release/HEAD/docs/tutorials/index_conventional.md -------------------------------------------------------------------------------- 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