LICENSE
MANIFEST.in
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/_anndata_index_lookup.py
scdiffeq/core/__init__.py
scdiffeq/core/_scdiffeq.py
scdiffeq/core/callbacks/__init__.py
scdiffeq/core/callbacks/_gradient_potential_callback.py
scdiffeq/core/callbacks/_intermittent_saves.py
scdiffeq/core/callbacks/_loss_accounting.py
scdiffeq/core/callbacks/_model_logging.py
scdiffeq/core/callbacks/_testing.py
scdiffeq/core/callbacks/_visualize_predictions.py
scdiffeq/core/callbacks/_visualize_tracked_loss.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/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_prior_potential.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/_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/_default_neural_sde.py
scdiffeq/core/utils/_display_tracked_loss.py
scdiffeq/core/utils/_fast_graph.py
scdiffeq/core/utils/_fetch_format.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/_info_message.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/_not_none_type.py
scdiffeq/core/utils/_scdiffeq_logger.py
scdiffeq/core/utils/_sum_normalize.py
scdiffeq/datasets/__init__.py
scdiffeq/datasets/_pancreas.py
scdiffeq/io/__init__.py
scdiffeq/io/_model_loader.py
scdiffeq/io/_pickle_io.py
scdiffeq/io/_read_h5ad.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_cells.py
scdiffeq/tools/_annotate_gene_features.py
scdiffeq/tools/_cell_potential.py
scdiffeq/tools/_compared_temporal_gene_expression.py
scdiffeq/tools/_dimension_reduction.py
scdiffeq/tools/_drift_diffusion_state_characterization.py
scdiffeq/tools/_fate_commitment.py
scdiffeq/tools/_feature_correlation.py
scdiffeq/tools/_final_state_per_simulation.py
scdiffeq/tools/_func_from_version.py
scdiffeq/tools/_grouped_expression.py
scdiffeq/tools/_hyperparams.py
scdiffeq/tools/_knn.py
scdiffeq/tools/_knn_smoothing.py
scdiffeq/tools/_negative_cross_entropy.py
scdiffeq/tools/_norm.py
scdiffeq/tools/_perturbation.py
scdiffeq/tools/_reconstruct_function.py
scdiffeq/tools/_simulator.py
scdiffeq/tools/_smoothed_expression.py
scdiffeq/tools/_sum_norm_df.py
scdiffeq/tools/_temporal_expression.py
scdiffeq/tools/_time_free_sampling.py
scdiffeq/tools/_umap.py
scdiffeq/tools/_versions.py