LICENSE
README.md
pyproject.toml
setup.cfg
setup.py
dynamo/__init__.py
dynamo/configuration.py
dynamo/data_io.py
dynamo/docrep.py
dynamo/dynamo_logger.py
dynamo/est.py
dynamo/ext.py
dynamo/get_version.py
dynamo/multi.py
dynamo/mv.py
dynamo/pd.py
dynamo/pl.py
dynamo/pp.py
dynamo/sample_data.py
dynamo/shiny.py
dynamo/sim.py
dynamo/tl.py
dynamo/utils.py
dynamo/vf.py
dynamo/estimation/__init__.py
dynamo/estimation/deprecated.py
dynamo/estimation/fit_jacobian.py
dynamo/estimation/csc/__init__.py
dynamo/estimation/csc/utils_velocity.py
dynamo/estimation/csc/velocity.py
dynamo/estimation/tsc/ODEs.py
dynamo/estimation/tsc/__init__.py
dynamo/estimation/tsc/estimation_kinetic.py
dynamo/estimation/tsc/twostep.py
dynamo/estimation/tsc/utils_moments.py
dynamo/external/__init__.py
dynamo/external/gseapy.py
dynamo/external/hodge.py
dynamo/external/scifate.py
dynamo/external/scribe.py
dynamo/external/utils.py
dynamo/external/celldancer/__init__.py
dynamo/external/celldancer/cdplt.py
dynamo/external/celldancer/compute_cell_velocity.py
dynamo/external/celldancer/diffusion.py
dynamo/external/celldancer/embedding_kinetic_para.py
dynamo/external/celldancer/pseudo_time.py
dynamo/external/celldancer/sampling.py
dynamo/external/celldancer/simulation.py
dynamo/external/celldancer/utilities.py
dynamo/external/celldancer/velocity_estimation.py
dynamo/external/celldancer/plotting/__init__.py
dynamo/external/celldancer/plotting/cell.py
dynamo/external/celldancer/plotting/colormap.py
dynamo/external/celldancer/plotting/gene.py
dynamo/external/celldancer/plotting/graph.py
dynamo/external/deepvelo/__init__.py
dynamo/external/deepvelo/parse_config.py
dynamo/external/deepvelo/train.py
dynamo/external/deepvelo/base/__init__.py
dynamo/external/deepvelo/base/base_data_loader.py
dynamo/external/deepvelo/base/base_model.py
dynamo/external/deepvelo/base/base_trainer.py
dynamo/external/deepvelo/data_loader/__init__.py
dynamo/external/deepvelo/data_loader/data_loaders.py
dynamo/external/deepvelo/logger/__init__.py
dynamo/external/deepvelo/logger/logger.py
dynamo/external/deepvelo/logger/visualization.py
dynamo/external/deepvelo/model/__init__.py
dynamo/external/deepvelo/model/layers.py
dynamo/external/deepvelo/model/loss.py
dynamo/external/deepvelo/model/metric.py
dynamo/external/deepvelo/model/model.py
dynamo/external/deepvelo/pipeline/__init__.py
dynamo/external/deepvelo/pipeline/eval.py
dynamo/external/deepvelo/plot/__init__.py
dynamo/external/deepvelo/plot/plot.py
dynamo/external/deepvelo/plot/scatter.py
dynamo/external/deepvelo/tool/__init__.py
dynamo/external/deepvelo/tool/driver_gene.py
dynamo/external/deepvelo/tool/kinetic_rates.py
dynamo/external/deepvelo/tool/stats.py
dynamo/external/deepvelo/tool/velocity.py
dynamo/external/deepvelo/trainer/__init__.py
dynamo/external/deepvelo/trainer/trainer.py
dynamo/external/deepvelo/utils/__init__.py
dynamo/external/deepvelo/utils/confidence.py
dynamo/external/deepvelo/utils/map_velocity_expression.py
dynamo/external/deepvelo/utils/optimization.py
dynamo/external/deepvelo/utils/plot.py
dynamo/external/deepvelo/utils/preprocess.py
dynamo/external/deepvelo/utils/scatter.py
dynamo/external/deepvelo/utils/temporal.py
dynamo/external/deepvelo/utils/util.py
dynamo/external/dynode/__init__.py
dynamo/external/dynode/dynamics/__init__.py
dynamo/external/dynode/dynamics/abstract_vf.py
dynamo/external/dynode/dynamics/ef_vf.py
dynamo/external/dynode/dynamics/fm_loss.py
dynamo/external/dynode/dynamics/mlp_vf.py
dynamo/external/dynode/dynamics/scheduler.py
dynamo/external/dynode/embedding/__init__.py
dynamo/external/dynode/embedding/abstract_ae.py
dynamo/external/dynode/embedding/autoencoder.py
dynamo/external/dynode/embedding/vae.py
dynamo/external/dynode/utils/__init__.py
dynamo/external/dynode/utils/classification.py
dynamo/external/dynode/utils/ffn.py
dynamo/external/gtfparse/__init__.py
dynamo/external/gtfparse/attribute_parsing.py
dynamo/external/gtfparse/create_missing_features.py
dynamo/external/gtfparse/parsing_error.py
dynamo/external/gtfparse/read_gtf.py
dynamo/external/latentvelo/__init__.py
dynamo/external/latentvelo/anvi_dataloader.py
dynamo/external/latentvelo/anvi_dataloader_nogcn.py
dynamo/external/latentvelo/atac_dataloader.py
dynamo/external/latentvelo/collate.py
dynamo/external/latentvelo/dataloader.py
dynamo/external/latentvelo/dataloader_nogcn.py
dynamo/external/latentvelo/dataloader_utils.py
dynamo/external/latentvelo/ev.py
dynamo/external/latentvelo/output_results.py
dynamo/external/latentvelo/path_regularization.py
dynamo/external/latentvelo/pl.py
dynamo/external/latentvelo/tl.py
dynamo/external/latentvelo/train.py
dynamo/external/latentvelo/trainer.py
dynamo/external/latentvelo/trainer_anvi.py
dynamo/external/latentvelo/trainer_anvi_nogcn.py
dynamo/external/latentvelo/trainer_atac.py
dynamo/external/latentvelo/trainer_nogcn.py
dynamo/external/latentvelo/utils.py
dynamo/external/latentvelo/velocity_genes.py
dynamo/external/latentvelo/evaluation/__init__.py
dynamo/external/latentvelo/evaluation/metrics.py
dynamo/external/latentvelo/evaluation/run_metric.py
dynamo/external/latentvelo/models/__init__.py
dynamo/external/latentvelo/models/annot_vae_model.py
dynamo/external/latentvelo/models/atac_reg_model.py
dynamo/external/latentvelo/models/gclayer.py
dynamo/external/latentvelo/models/modules.py
dynamo/external/latentvelo/models/refine_model.py
dynamo/external/latentvelo/models/vae_model.py
dynamo/external/latentvelo/models/velocity_field.py
dynamo/external/latentvelo/plotting/__init__.py
dynamo/external/latentvelo/plotting/metrics.py
dynamo/external/latentvelo/plotting/scatter_stream.py
dynamo/external/latentvelo/tools/__init__.py
dynamo/external/latentvelo/tools/batch_correction.py
dynamo/external/latentvelo/tools/cell_trajectories.py
dynamo/external/latentvelo/tools/check_velocity.py
dynamo/external/latentvelo/tools/trad_velocity.py
dynamo/external/pyensembl/__init__.py
dynamo/external/pyensembl/common.py
dynamo/external/pyensembl/database.py
dynamo/external/pyensembl/download_cache.py
dynamo/external/pyensembl/ensembl_release.py
dynamo/external/pyensembl/ensembl_url_templates.py
dynamo/external/pyensembl/ensembl_versions.py
dynamo/external/pyensembl/exon.py
dynamo/external/pyensembl/fasta.py
dynamo/external/pyensembl/gene.py
dynamo/external/pyensembl/genome.py
dynamo/external/pyensembl/locus.py
dynamo/external/pyensembl/locus_with_genome.py
dynamo/external/pyensembl/normalization.py
dynamo/external/pyensembl/reference_name.py
dynamo/external/pyensembl/search.py
dynamo/external/pyensembl/sequence_data.py
dynamo/external/pyensembl/serializable.py
dynamo/external/pyensembl/shell.py
dynamo/external/pyensembl/species.py
dynamo/external/pyensembl/transcript.py
dynamo/external/pyensembl/version.py
dynamo/external/sude_py/__init__.py
dynamo/external/sude_py/clle.py
dynamo/external/sude_py/init_pca.py
dynamo/external/sude_py/learning_l.py
dynamo/external/sude_py/learning_s.py
dynamo/external/sude_py/mds.py
dynamo/external/sude_py/opt_scale.py
dynamo/external/sude_py/pca.py
dynamo/external/sude_py/plotcluster2.py
dynamo/external/sude_py/pps.py
dynamo/external/sude_py/sude.py
dynamo/movie/__init__.py
dynamo/movie/fate.py
dynamo/movie/utils.py
dynamo/multivelo/ATACseqTools.py
dynamo/multivelo/ChromatinVelocity.py
dynamo/multivelo/MultiConfiguration.py
dynamo/multivelo/MultiIO.py
dynamo/multivelo/MultiPreprocessor.py
dynamo/multivelo/MultiQC.py
dynamo/multivelo/MultiVelo.py
dynamo/multivelo/__init__.py
dynamo/multivelo/dynamical_chrom_func.py
dynamo/multivelo/globals.py
dynamo/multivelo/old_MultiVelocity.py
dynamo/multivelo/old_MultiomicVectorField.py
dynamo/multivelo/pyWNN.py
dynamo/multivelo/settings.py
dynamo/multivelo/sparse_matrix_utils.py
dynamo/multivelo/neural_nets/dir0.pt
dynamo/multivelo/neural_nets/dir1.pt
dynamo/multivelo/neural_nets/dir2_m1.pt
dynamo/multivelo/neural_nets/dir2_m2.pt
dynamo/plot/__init__.py
dynamo/plot/_jacobian.py
dynamo/plot/_trends.py
dynamo/plot/animation_lines.py
dynamo/plot/cell_cycle.py
dynamo/plot/clustering.py
dynamo/plot/connectivity.py
dynamo/plot/dimension_reduction.py
dynamo/plot/dynamics.py
dynamo/plot/ezplots.py
dynamo/plot/fate.py
dynamo/plot/fate_utilities_deprecated.py
dynamo/plot/heatmaps.py
dynamo/plot/least_action_path.py
dynamo/plot/markers.py
dynamo/plot/networks.py
dynamo/plot/preprocess.py
dynamo/plot/pseudotime.py
dynamo/plot/scPotential.py
dynamo/plot/scVectorField.py
dynamo/plot/scatters.py
dynamo/plot/sctransform.py
dynamo/plot/space.py
dynamo/plot/state_graph.py
dynamo/plot/streamtube.py
dynamo/plot/theme.py
dynamo/plot/time_series.py
dynamo/plot/topography.py
dynamo/plot/utils.py
dynamo/plot/utils_dynamics.py
dynamo/plot/utils_graph.py
dynamo/plot/vector_calculus.py
dynamo/plot/violin_box.py
dynamo/prediction/__init__.py
dynamo/prediction/_tf_eval.py
dynamo/prediction/fate.py
dynamo/prediction/least_action_path.py
dynamo/prediction/perturbation.py
dynamo/prediction/state_graph.py
dynamo/prediction/trajectory.py
dynamo/prediction/trajectory_analysis.py
dynamo/prediction/tscRNA_seq.py
dynamo/prediction/utils.py
dynamo/preprocessing/CnmfPreprocessor.py
dynamo/preprocessing/Preprocessor.py
dynamo/preprocessing/QC.py
dynamo/preprocessing/__init__.py
dynamo/preprocessing/cell_cycle.py
dynamo/preprocessing/deprecated.py
dynamo/preprocessing/dynast.py
dynamo/preprocessing/gene_selection.py
dynamo/preprocessing/normalization.py
dynamo/preprocessing/pca.py
dynamo/preprocessing/transform.py
dynamo/preprocessing/utils.py
dynamo/preprocessing/external/__init__.py
dynamo/preprocessing/external/integration.py
dynamo/preprocessing/external/pearson_residual_recipe.py
dynamo/preprocessing/external/sctransform.py
dynamo/shiny/__init__.py
dynamo/shiny/lap.py
dynamo/shiny/perturbation.py
dynamo/shiny/utils.py
dynamo/simulation/Gillespie.py
dynamo/simulation/ODE.py
dynamo/simulation/__init__.py
dynamo/simulation/bif_os_inclusive_sim.py
dynamo/simulation/evaluation.py
dynamo/simulation/simulate_anndata.py
dynamo/simulation/utils.py
dynamo/tools/DDRTree.py
dynamo/tools/DDRTree_graph.py
dynamo/tools/Markov.py
dynamo/tools/__init__.py
dynamo/tools/_enum.py
dynamo/tools/_extvelo.py
dynamo/tools/_track.py
dynamo/tools/cell_velocities.py
dynamo/tools/clustering.py
dynamo/tools/connectivity.py
dynamo/tools/deprecated.py
dynamo/tools/dimension_reduction.py
dynamo/tools/dynamics.py
dynamo/tools/graph_calculus.py
dynamo/tools/graph_operators.py
dynamo/tools/growth.py
dynamo/tools/markers.py
dynamo/tools/metric_velocity.py
dynamo/tools/moments.py
dynamo/tools/pseudotime.py
dynamo/tools/pseudotime_velocity.py
dynamo/tools/psl.py
dynamo/tools/recipes.py
dynamo/tools/sampling.py
dynamo/tools/utils.py
dynamo/tools/utils_reduceDimension.py
dynamo/tools/velocyto_scvelo.py
dynamo/vectorfield/Ao.py
dynamo/vectorfield/Bhattacharya.py
dynamo/vectorfield/FixedPoints.py
dynamo/vectorfield/Tang.py
dynamo/vectorfield/VectorField.py
dynamo/vectorfield/Wang.py
dynamo/vectorfield/__init__.py
dynamo/vectorfield/cell_vectors.py
dynamo/vectorfield/clustering.py
dynamo/vectorfield/least_action_path.py
dynamo/vectorfield/networks.py
dynamo/vectorfield/rank_vf.py
dynamo/vectorfield/scPotential.py
dynamo/vectorfield/scVectorField.py
dynamo/vectorfield/stochastic_process.py
dynamo/vectorfield/topography.py
dynamo/vectorfield/util_vector_calculus.py
dynamo/vectorfield/utils.py
dynamo/vectorfield/vector_calculus.py
dynamo/vectorfield/vfGraph_deprecated.py
dynamo_release.egg-info/PKG-INFO
dynamo_release.egg-info/SOURCES.txt
dynamo_release.egg-info/dependency_links.txt
dynamo_release.egg-info/requires.txt
dynamo_release.egg-info/top_level.txt
tests/test_config.py
tests/test_data_io.py
tests/test_logger.py
tests/test_pipeline.py
tests/test_pl.py
tests/test_prediction.py
tests/test_preprocess.py
tests/test_simulation.py
tests/test_space.py
tests/test_sude.py
tests/test_tl.py
tests/test_vf.py
tests/tests.py