Index

_

_config module _data_loader module _distributions module _error module _inference module

_logger_config module _model module _preffect module _utils module

A

adjusted_categorical_correction_variable() (in module _utils)

arg_constraints (_distributions.NegativeBinomial attribute), [1] (_distributions.ZeroInflatedNegativeBinomial attribute)

B

batch_centroid_loss() (_model.VAE method)

C

calculate_and_sort_by_iqr() (in module _utils) calculate_imputation_error() (_inference.Inference method) categorical_correction_variable() (in module _utils) check_fidelity_of_anndata() (_data_loader.FFPE_dataset method) check_folder_access() (in module _utils) check_for_nans() (in module _utils) check_int_and_uniq() (in module _utils) clamp_tensor_values() (_data_loader.FFPE_dataset method)

Cluster (class in wrappers._cluster) cluster_counts() (wrappers._cluster.Cluster method) cluster_latent_space() (wrappers._cluster.Cluster method) cluster_true_counts() (wrappers._cluster.Cluster method) compute_zinb_params() (wrappers._ZINBEstimator.ZINBEstimator method) concatenate_1d_minibatch() (_inference.Inference method) concatenate_2d_minibatch() (_inference.Inference method) copy_file() (in module _utils) core_only_copy() (in module preffect_factory)

D

decode() (_model.Decoder method) (_model.LibDecoder method) (_model.VAE method)

Decoder (class in _model)

E

encode() (_model.Encoder method) (_model.LibEncoder method) encode_reparameterization() (_model.VAE method)

Encoder (class in _model) ensure_directory() (in module _utils) extract_batch() (_preffect.Preffect method)

F

factory() (in module preffect_factory) factory_setup() (in module preffect_factory) FFPE_dataset (class in _data_loader) filter_NaNs_from_COO() (_data_loader.FFPE_dataset method)

find_inference_in_register() (_preffect.Preffect method) forward() (_model.VAE method) from_anndata_2_numpy() (_data_loader.FFPE_dataset method) from_numpy_2_tensors() (_data_loader.FFPE_dataset method)

G

generate_and_save_visualizations() (in module preffect_factory)

get_ghost_indices() (_data_loader.FFPE_dataset method)

H

harmonize_samples() (_data_loader.FFPE_dataset method)

I

impute_values() (_inference.Inference method) Inference (class in _inference) init_weights() (_model.Decoder method) (_model.Encoder method) (_model.LibDecoder method) (_model.LibEncoder method)

init_weights_vae() (_model.VAE method)

L

LibDecoder (class in _model) LibEncoder (class in _model) load_anndata() (_data_loader.FFPE_dataset method) load_pretrained_model() (_model.VAE method) log_nb_positive() (in module _distributions)

log_prob() (_distributions.NegativeBinomial method) (_distributions.ZeroInflatedNegativeBinomial method) log_zinb_positive() (in module _distributions) logging_helper() (in module _utils) logging_tensor() (in module _utils) loss() (_model.VAE method)

M

MCAR() (_data_loader.FFPE_dataset method) mean() (_distributions.NegativeBinomial method) (_distributions.ZeroInflatedNegativeBinomial method) module _config _data_loader _distributions _error _inference _logger_config _model _preffect _utils preffect_cli preffect_factory wrappers._cluster wrappers._ZINBEstimator

multi_logging_tensor() (in module _utils)

N

NegativeBinomial (class in _distributions)

O

one_hot_encode() (in module _utils)

P

pad_adjacency_matrices() (_data_loader.FFPE_dataset method) plot_progression() (in module _utils) plot_progression_all() (in module _utils) Poisson (class in _distributions) Preffect (class in _preffect) preffect_cli module preffect_factory module

PreffectError prep_batch_iterator() (_data_loader.FFPE_dataset method) prep_from_existing_session() (_preffect.Preffect method) prep_new_session() (_preffect.Preffect method) prepare_latent_space_with_korrection_vars() (_model.Decoder method) (_model.Encoder method) (_model.LibDecoder method) (_model.LibEncoder method) print_loss_table() (in module _utils)

R

read_config_file() (in module preffect_cli) reconstruct_from_minibatches() (_inference.Inference method) register_cluster() (wrappers._cluster.Cluster method) register_inference_run() (_inference.Inference method) remove_ghost_samples() (_model.VAE method)

reparameterize() (_model.VAE method) reparameterize_gaussian() (in module _utils) return_counts_as_anndata() (_inference.Inference method) return_latent_space_as_anndata() (_inference.Inference method) run_inference() (_inference.Inference method)

S

sample() (_distributions.NegativeBinomial method) (_distributions.ZeroInflatedNegativeBinomial method) sanity_check_on_configs() (in module _utils) save() (_inference.Inference method) (_preffect.Preffect method) save_visualization() (_inference.Inference method) select_genes() (_data_loader.FFPE_dataset method) select_samples() (_data_loader.FFPE_dataset method)

selective_one_hot() (in module _utils) set_parameter_requires_grad() (_model.VAE method) set_seeds() (in module _utils) setup_categorical_variables() (_data_loader.FFPE_dataset method) setup_cuda() (in module preffect_factory) setup_loggers() (in module _logger_config) str2bool() (in module preffect_cli) support (_distributions.NegativeBinomial attribute), [1] (_distributions.ZeroInflatedNegativeBinomial attribute)

T

target_specific_one_hot() (in module _utils) To() (in module _utils) torch_mtx_unbatching() (in module _utils) train() (_preffect.Preffect method)

training (_model.Decoder attribute) (_model.Encoder attribute) (_model.LibDecoder attribute) (_model.LibEncoder attribute) (_model.VAE attribute)

U

umap_draw_latent() (in module _utils)

update_composite_configs() (in module _utils)

V

VAE (class in _model) variance() (_distributions.NegativeBinomial method) (_distributions.ZeroInflatedNegativeBinomial method) visualize_batch_adjustment() (_inference.Inference method)

visualize_fraction_pi_per_gene() (_inference.Inference method) visualize_gene_scatterplot() (_inference.Inference method) visualize_latent_recons_umap() (_inference.Inference method) visualize_lib_size() (_inference.Inference method) visualize_libsize_and_dispersion() (_inference.Inference method)

W

wrappers._cluster module

wrappers._ZINBEstimator module

Z

ZeroInflatedNegativeBinomial (class in _distributions) zi_logits() (_distributions.ZeroInflatedNegativeBinomial method)

zi_probs() (_distributions.ZeroInflatedNegativeBinomial method) ZINB_expected_value() (in module _utils) ZINBEstimator (class in wrappers._ZINBEstimator)