LICENSE
README.md
setup.py
scdiffeq/__init__.py
scdiffeq/__version__.py
scdiffeq.egg-info/PKG-INFO
scdiffeq.egg-info/SOURCES.txt
scdiffeq.egg-info/dependency_links.txt
scdiffeq.egg-info/requires.txt
scdiffeq.egg-info/top_level.txt
scdiffeq/_backend_utilities/__init__.py
scdiffeq/_backend_utilities/_configure_logging.py
scdiffeq/callbacks/__init__.py
scdiffeq/callbacks/_stochastic_weight_averaging.py
scdiffeq/core/__init__.py
scdiffeq/core/_scdiffeq.py
scdiffeq/core/_mix_ins/__init__.py
scdiffeq/core/_mix_ins/_knn_mix_in.py
scdiffeq/core/_mix_ins/_logging_mix_in.py
scdiffeq/core/_mix_ins/_model_config_mix_in.py
scdiffeq/core/_mix_ins/_state_characterization_mix_in.py
scdiffeq/core/_mix_ins/_training_routine_mix_ins.py
scdiffeq/core/_mix_ins/_utility_io_mix_in.py
scdiffeq/core/callbacks/__init__.py
scdiffeq/core/callbacks/_basic_progress_bar.py
scdiffeq/core/callbacks/_gradient_potential_callback.py
scdiffeq/core/callbacks/_intermittent_saves.py
scdiffeq/core/callbacks/_memory_monitor.py
scdiffeq/core/callbacks/_model_logging.py
scdiffeq/core/callbacks/_testing.py
scdiffeq/core/configs/__init__.py
scdiffeq/core/configs/_configure_time_key.py
scdiffeq/core/configs/_data_configuration.py
scdiffeq/core/configs/_lightning_callbacks_configuration.py
scdiffeq/core/configs/_lightning_model_configuration.py
scdiffeq/core/configs/_lightning_trainer_configuration.py
scdiffeq/core/configs/_progress_bar_config.py
scdiffeq/core/lightning_models/__init__.py
scdiffeq/core/lightning_models/_lightning_ode.py
scdiffeq/core/lightning_models/_lightning_ode_fixed_potential.py
scdiffeq/core/lightning_models/_lightning_ode_prior_potential.py
scdiffeq/core/lightning_models/_lightning_ode_vae.py
scdiffeq/core/lightning_models/_lightning_ode_vae_fixed_potential.py
scdiffeq/core/lightning_models/_lightning_ode_vae_prior_potential.py
scdiffeq/core/lightning_models/_lightning_sde.py
scdiffeq/core/lightning_models/_lightning_sde_fate_bias_aware.py
scdiffeq/core/lightning_models/_lightning_sde_fixed_potential.py
scdiffeq/core/lightning_models/_lightning_sde_fixed_potential_regularized_velocity_ratio.py
scdiffeq/core/lightning_models/_lightning_sde_prior_potential.py
scdiffeq/core/lightning_models/_lightning_sde_regularized_velocity_ratio.py
scdiffeq/core/lightning_models/_lightning_sde_vae.py
scdiffeq/core/lightning_models/_lightning_sde_vae_fate_bias_aware.py
scdiffeq/core/lightning_models/_lightning_sde_vae_fixed_potential.py
scdiffeq/core/lightning_models/_lightning_sde_vae_prior_potential.py
scdiffeq/core/lightning_models/_lightning_sde_vae_prior_potential_fate_bias_aware.py
scdiffeq/core/lightning_models/base/__init__.py
scdiffeq/core/lightning_models/base/_base_lightning_diffeq.py
scdiffeq/core/lightning_models/base/_batch_processor.py
scdiffeq/core/lightning_models/base/_sinkhorn_divergence.py
scdiffeq/core/lightning_models/mix_ins/__init__.py
scdiffeq/core/lightning_models/mix_ins/_base_forward_mix_in.py
scdiffeq/core/lightning_models/mix_ins/_drift_prior_mix_in.py
scdiffeq/core/lightning_models/mix_ins/_fate_bias_drift_prior_mix_in.py
scdiffeq/core/lightning_models/mix_ins/_fate_bias_drift_prior_vae_mix_in.py
scdiffeq/core/lightning_models/mix_ins/_fate_bias_mix_in.py
scdiffeq/core/lightning_models/mix_ins/_fate_bias_vae_mix_in.py
scdiffeq/core/lightning_models/mix_ins/_potential_mix_in.py
scdiffeq/core/lightning_models/mix_ins/_pre_train_mix_in.py
scdiffeq/core/lightning_models/mix_ins/_regularized_velocity_ratio_mix_in.py
scdiffeq/core/lightning_models/mix_ins/_sde_mix_in.py
scdiffeq/core/lightning_models/mix_ins/_vae_mix_in.py
scdiffeq/core/utils/__init__.py
scdiffeq/core/utils/_anndata_inspector.py
scdiffeq/core/utils/_display_tracked_loss.py
scdiffeq/core/utils/_fast_graph.py
scdiffeq/core/utils/_filter_df.py
scdiffeq/core/utils/_flexible_component_loader.py
scdiffeq/core/utils/_function_fetch.py
scdiffeq/core/utils/_function_kwargs.py
scdiffeq/core/utils/_idx_to_int_str.py
scdiffeq/core/utils/_knn_graph_query.py
scdiffeq/core/utils/_logger_bridge.py
scdiffeq/core/utils/_logging_learnable_hparams.py
scdiffeq/core/utils/_logs.py
scdiffeq/core/utils/_normalize_time_to_range.py
scdiffeq/core/utils/_sum_normalize.py
scdiffeq/datasets/__init__.py
scdiffeq/datasets/_figshare_downloader.py
scdiffeq/datasets/_human_hematopoiesis.py
scdiffeq/datasets/_larry_in_vitro.py
scdiffeq/datasets/_pancreatic_endocrinogenesis.py
scdiffeq/io/__init__.py
scdiffeq/io/_logs.py
scdiffeq/io/_data/__init__.py
scdiffeq/io/_data/_pickle_io.py
scdiffeq/io/_data/_read_h5ad.py
scdiffeq/io/_model/__init__.py
scdiffeq/io/_model/_checkpoint.py
scdiffeq/io/_model/_grouped_metrics.py
scdiffeq/io/_model/_hparams.py
scdiffeq/io/_model/_model_loader.py
scdiffeq/io/_model/_project.py
scdiffeq/io/_model/_version.py
scdiffeq/plotting/__init__.py
scdiffeq/plotting/_smoothed_gene_expression.py
scdiffeq/plotting/_temporal_expression.py
scdiffeq/plotting/_velocity_stream.py
scdiffeq/plotting/potential_landscape/__init__.py
scdiffeq/plotting/potential_landscape/_mesh_grid.py
scdiffeq/plotting/potential_landscape/_neighbor_smoothing.py
scdiffeq/plotting/potential_landscape/_potential_landscape.py
scdiffeq/plotting/potential_landscape/_scatter_3d.py
scdiffeq/plotting/potential_landscape/_surface_3d.py
scdiffeq/tools/__init__.py
scdiffeq/tools/_annotate_cell_fate.py
scdiffeq/tools/_annotate_cell_state.py
scdiffeq/tools/_annotate_gene_features.py
scdiffeq/tools/_bin_pseudotime.py
scdiffeq/tools/_cell_potential.py
scdiffeq/tools/_drift_diffusion_state_characterization.py
scdiffeq/tools/_fate_perturbation_experiment.py
scdiffeq/tools/_fate_perturbation_screen.py
scdiffeq/tools/_final_state_per_simulation.py
scdiffeq/tools/_grid_velocity.py
scdiffeq/tools/_invert_scaled_gex.py
scdiffeq/tools/_knn.py
scdiffeq/tools/_knn_smoothing.py
scdiffeq/tools/_perturb.py
scdiffeq/tools/_perturb_scan_z_range.py
scdiffeq/tools/_simulation.py
scdiffeq/tools/_velocity_embedding.py
scdiffeq/tools/_velocity_graph.py
scdiffeq/tools/utils/__init__.py
scdiffeq/tools/utils/_compute_cosines.py
scdiffeq/tools/utils/_get_iterative_indices.py
scdiffeq/tools/utils/_get_neighbor_indices.py
scdiffeq/tools/utils/_norm.py
scdiffeq/tools/utils/_scverse_neighbors.py
scdiffeq/tools/utils/_transition_matrix.py