Index _ | A | B | C | D | E | F | G | I | L | M | N | O | P | R | S | T | U | V _ __init__() (pyrovelocity._trainer.EnumTrainingPlan method) (pyrovelocity._velocity.PyroVelocity method) (pyrovelocity._velocity_model.LogNormalModel method) (pyrovelocity._velocity_model.VelocityModel method) (pyrovelocity._velocity_model.VelocityModelAuto method) (pyrovelocity._velocity_module.VelocityModule method) A align_diffrate() (in module pyrovelocity.cytotrace) align_trajectory_diff() (in module pyrovelocity.plot) alpha() (pyrovelocity._velocity_model.LogNormalModel method) anndata_counts_to_df() (in module pyrovelocity.utils) any() (in module pyrovelocity.cytotrace) assign_colors() (in module pyrovelocity.data) attributes() (in module pyrovelocity.utils) AuxCellVelocityModel (class in pyrovelocity._velocity_model) B batch_cytotrace() (in module pyrovelocity.cytotrace) beta() (pyrovelocity._velocity_model.LogNormalModel method) C cell_code() (pyrovelocity._velocity_model.LogNormalModel method) cell_codebook() (pyrovelocity._velocity_model.LogNormalModel method) cell_time() (pyrovelocity._velocity_model.LogNormalModel method) census_normalize() (in module pyrovelocity.cytotrace) compare_cytotrace() (in module pyrovelocity.cytotrace) compare_cytotrace_ncores() (in module pyrovelocity.cytotrace) compute_gcs() (in module pyrovelocity.cytotrace) compute_mean_vector_field() (in module pyrovelocity.plot) compute_similarity1() (in module pyrovelocity.cytotrace) compute_similarity2() (in module pyrovelocity.cytotrace) compute_statistics_from_posterior_samples() (pyrovelocity._velocity.PyroVelocity method) compute_volcano_data() (in module pyrovelocity.plot) convert_to_markov() (in module pyrovelocity.cytotrace) copy_raw_counts() (in module pyrovelocity.data) create_plate() (pyrovelocity._velocity_model.LogNormalModel method) create_plates() (pyrovelocity._velocity_model.LogNormalModel method) cumulative_boxplot() (in module pyrovelocity.cytotrace) cytotrace() (in module pyrovelocity.cytotrace) cytotrace_ncore() (in module pyrovelocity.cytotrace) D debug() (in module pyrovelocity.utils) denoised_umap() (in module pyrovelocity.plot) diffused() (in module pyrovelocity.cytotrace) dt_switching() (pyrovelocity._velocity_model.LogNormalModel method) E ensure_numpy_array() (in module pyrovelocity.utils) enum_parallel_predict() (pyrovelocity._velocity.PyroVelocity method) EnumTrainingPlan (class in pyrovelocity._trainer) F filter_startswith_dict() (in module pyrovelocity.utils) find_nonzero() (in module pyrovelocity.cytotrace) FNNLSa() (in module pyrovelocity.cytotrace) forward() (pyrovelocity._velocity_model.VelocityModelAuto method) G gamma() (pyrovelocity._velocity_model.LogNormalModel method) gene_offset() (pyrovelocity._velocity_model.LogNormalModel method) generate_cell() (pyrovelocity._velocity_model.AuxCellVelocityModel method) generate_posterior_samples() (pyrovelocity._velocity.PyroVelocity method) generate_sample_data() (in module pyrovelocity.utils) get_clone_trajectory() (in module pyrovelocity.plot) get_high_us_genes() (in module pyrovelocity.data) get_likelihood() (pyrovelocity._velocity_model.LogNormalModel method) get_mlflow_logs() (pyrovelocity._velocity.PyroVelocity method) get_posterior_sample_angle_uncertainty() (in module pyrovelocity.plot) get_pylogger() (in module pyrovelocity.utils) get_rna() (pyrovelocity._velocity_model.VelocityModelAuto method) get_thresh_histogram_title_from_path() (in module pyrovelocity.data) get_velocity_samples() (in module pyrovelocity.utils) guide (pyrovelocity._velocity_module.VelocityModule property) I init_with_all_cells() (in module pyrovelocity.utils) inv() (in module pyrovelocity.utils) L latent_time() (pyrovelocity._velocity_model.LogNormalModel method) likelihood (pyrovelocity._velocity_model.LogNormalModel attribute) load_data() (in module pyrovelocity.data) load_larry() (in module pyrovelocity.data) load_model() (pyrovelocity._velocity.PyroVelocity class method) load_pbmc68k() (in module pyrovelocity.data) load_unipotent_larry() (in module pyrovelocity.data) log() (in module pyrovelocity.utils) LogNormalModel (class in pyrovelocity._velocity_model) M mae() (in module pyrovelocity.utils) mae_evaluate() (in module pyrovelocity.utils) mae_per_gene() (in module pyrovelocity.plot) model (pyrovelocity._velocity_module.VelocityModule property) module pyrovelocity._trainer pyrovelocity._velocity pyrovelocity._velocity_model pyrovelocity._velocity_module pyrovelocity.api pyrovelocity.cytotrace pyrovelocity.data pyrovelocity.plot pyrovelocity.utils mRNA() (in module pyrovelocity.utils) mse_loss_sum() (in module pyrovelocity.utils) N num_cells (pyrovelocity._velocity_model.LogNormalModel attribute) num_genes (pyrovelocity._velocity_model.LogNormalModel attribute) O ode_mRNA() (in module pyrovelocity.utils) P p_velocity() (pyrovelocity._velocity_model.LogNormalModel method) plate_size (pyrovelocity._velocity_model.LogNormalModel attribute) plot_arrow_examples() (in module pyrovelocity.plot) plot_dynamic_pyro() (in module pyrovelocity.plot) plot_evaluate_dynamic_orig() (in module pyrovelocity.plot) plot_gene_ranking() (in module pyrovelocity.plot) plot_high_us_genes() (in module pyrovelocity.data) plot_mean_vector_field() (in module pyrovelocity.plot) plot_multiadata() (in module pyrovelocity.cytotrace) plot_multigenes_dynamical() (in module pyrovelocity.plot) plot_posterior_time() (in module pyrovelocity.plot) plot_state_uncertainty() (in module pyrovelocity.plot) plot_vector_field_uncertain() (in module pyrovelocity.plot) pretty_print_dict() (in module pyrovelocity.utils) print_anndata() (in module pyrovelocity.utils) print_attributes() (in module pyrovelocity.utils) project_grid_points() (in module pyrovelocity.plot) PyroVelocity (class in pyrovelocity._velocity) pyrovelocity._trainer module pyrovelocity._velocity module pyrovelocity._velocity_model module pyrovelocity._velocity_module module pyrovelocity.api module pyrovelocity.cytotrace module pyrovelocity.data module pyrovelocity.plot module pyrovelocity.utils module R rainbowplot() (in module pyrovelocity.plot) regressed() (in module pyrovelocity.cytotrace) remove_zero_mvg() (in module pyrovelocity.cytotrace) rescale_time() (in module pyrovelocity.utils) S s_inf() (pyrovelocity._velocity_model.LogNormalModel method) s_scale() (pyrovelocity._velocity_model.LogNormalModel method) save_model() (pyrovelocity._velocity.PyroVelocity method) save_pyrovelocity_data() (pyrovelocity._velocity.PyroVelocity method) set_colorbar() (in module pyrovelocity.plot) set_loss_plot_axes() (in module pyrovelocity.api) setup_anndata() (pyrovelocity._velocity.PyroVelocity class method) site_is_discrete() (in module pyrovelocity.utils) step() (pyrovelocity._trainer.VelocityAdam method) T t_scale() (pyrovelocity._velocity_model.LogNormalModel method) tau_inv() (in module pyrovelocity.utils) trace() (in module pyrovelocity.utils) train() (pyrovelocity._trainer.VelocityTrainingMixin method) (pyrovelocity._velocity.PyroVelocity method) train_faster() (pyrovelocity._trainer.VelocityTrainingMixin method) train_faster_with_batch() (pyrovelocity._trainer.VelocityTrainingMixin method) train_model() (in module pyrovelocity.api) training_epoch_end() (pyrovelocity._trainer.EnumTrainingPlan method) training_step() (pyrovelocity._trainer.EnumTrainingPlan method) U u_inf() (pyrovelocity._velocity_model.LogNormalModel method) u_scale() (pyrovelocity._velocity_model.LogNormalModel method) us_rainbowplot() (in module pyrovelocity.plot) V validation_epoch_end() (pyrovelocity._trainer.EnumTrainingPlan method) validation_step() (pyrovelocity._trainer.EnumTrainingPlan method) vector_field_uncertainty() (in module pyrovelocity.plot) velocity_dus_dt() (in module pyrovelocity.utils) VelocityAdam (class in pyrovelocity._trainer) VelocityClippedAdam() (in module pyrovelocity._trainer) VelocityModel (class in pyrovelocity._velocity_model) VelocityModelAuto (class in pyrovelocity._velocity_model) VelocityModule (class in pyrovelocity._velocity_module) VelocityTrainingMixin (class in pyrovelocity._trainer)