Index _ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | Q | R | S | T | U | V | W | Z _ _factor (scMultiBatchNrmls attribute) (stSmoother attribute) _from_scmodel (stSmoother attribute) _functional (crossModel attribute) (scModel attribute) (stModel attribute) _gener_graph (CrossModalityNrmls attribute) (stSmoother attribute) _indices (MaskedDataset attribute) _integrated (CrossDataset attribute) _mask (MaskedDataset attribute) _num_batches (CrossModalityNrmls attribute) (stSmoother attribute) _rout (CrossModalityNrmls attribute) _smooth (TranscriptFormer attribute) A act (BatchAwareLayerNorm attribute) (BatchAwareScale attribute) (TopNAttention attribute) adata (BaseDataset attribute) (crossModel attribute) (Saver attribute) (scModel attribute) (stModel attribute) adata_sc (PseudoST attribute) adata_st (PseudoST attribute) add_embed() (ModelOps method) add_embed_st() (CrossModalityNrmls method) alpha (Mixer attribute) anchors (Mixer attribute) arg_constraints (NegativeBinomial attribute) (ZeroInflatedNegativeBinomial attribute) args (NrmlsBC attribute) (ProbDecoder attribute) (TranscriptFormer attribute) Attention (class in step.modules.transformer) aver_items_by_ct() (in module step.utils.misc) B BaseDataset (class in step.utils.dataset) batch_emb_dim (NrmlsBC attribute) batch_embedding (NrmlsBC attribute) batch_key (BaseDataset attribute) (CrossDataset attribute) (PseudoST attribute) batch_readout (NrmlsBC attribute) BatchAwareLayerNorm (class in step.models.extension) BatchAwareScale (class in step.models.extension) C category_random_split() (in module step.functionality.comps.trainer) cell_type_key (PseudoST attribute) ch (in module step.manager) check_early_stop() (Trainer method) class_key (CrossDataset attribute) (ScDataset attribute) clear() (Readout method) cls_token (TranscriptFormer attribute) clsf() (scMultiBatchNrmls method) clsf_() (scMultiBatchNrmls method) cluster() (crossModel method) (stModel method) ClusterGeneric (class in step.models.clust) compute_selfattention() (in module step.utils.misc) coord_keys (CrossDataset attribute) (StDataset attribute) coords_key (PseudoST attribute) copy() (NrmlsBC method) (ProbDecoder method) (TranscriptFormer method) copy_dec() (NrmlsBC method) CrossDataset (class in step.utils.dataset) CrossModalityNrmls (class in step.functionality.cross_funcmodel) crossModel (class in step.integration) cum_loss() (Trainer method) CustomFormatter (class in step.manager) D dataset (crossModel attribute) (Saver attribute) (scModel attribute) (stModel attribute) decode() (NrmlsBC method) (TranscriptFormer method) decode_() (NrmlsBC method) decode_skip() (NrmlsBC method) decode_ts() (NrmlsBC method) (TranscriptFormer method) decoder (TranscriptFormer attribute) decoder_type (TranscriptFormer attribute) deconv() (CrossModalityNrmls method) defualt_lcfg (Trainer attribute) demodule() (GeneModuler method) device (FunctionalBase attribute) domain_wise (Mixer attribute) domains (StDataset attribute) downsapmle_size (PseudoST attribute) drop_edge (in module step.models.transcriptformer) dropout_() (ProbDecoder method) E early_stopping (Trainer attribute) EarlyStopping (class in step.functionality.comps.trainer) edge_clip (CrossModalityNrmls attribute) embed() (ModelOps method) (scMultiBatchNrmls method) (stSmoother method) embed_dim (TopNAttention attribute) encode() (NrmlsBC method) (TranscriptFormer method) encode_ts() (NrmlsBC method) (TranscriptFormer method) exists() (in module step.modules.transformer) Exp (class in step.modules.decoder) expand (TranscriptFormer attribute) extract_selfattention_maps() (in module step.utils.misc) extractor (GeneModuler attribute) F FeedForward (class in step.modules.transformer) ffn_() (ProbDecoder method) filtered (BaseDataset attribute) format() (CustomFormatter method) format_loss_dict() (Trainer method) formatter (in module step.manager) forward() (Attention method) (BatchAwareLayerNorm method) (BatchAwareScale method) (Exp method) (FeedForward method) (GAT method) (GCN method) (GeneModuler method) (Linear2D method) (Mixer method) (NrmlsBC method) (PreNorm method) (ProbDecoder method) (Readout method) (TopNAttention method) (TranscriptFormer method) (Transformer method) from_spatial_graph() (CrossModalityNrmls method) (stSmoother method) funcmodel (Saver attribute) FunctionalBase (class in step.functionality.base) G g (Mixer attribute) gargs (TranscriptFormer attribute) GAT (class in step.modules.gnn) GCN (class in step.modules.gnn) geary_c() (in module step.utils.metrics) gembed() (stSmoother method) GeneModuler (class in step.models.transcriptformer) generate() (ModelOps method) generate_adj() (in module step.utils.misc) generate_domains() (CrossModalityNrmls method) geneset (BaseDataset attribute) get() (BaseDataset method) get_anchors() (scMultiBatchNrmls method) get_batch_ohenc() (ModelOps method) get_de_genes() (in module step.utils.misc) get_gene_modules() (ModelOps method) get_instance() (Saver class method) get_prop() (CrossModalityNrmls method) (Mixer method) get_px() (ModelOps method) get_px_r() (TranscriptFormer method) get_pz() (CrossModalityNrmls method) get_scores() (CrossModalityNrmls method) (Mixer method) get_signatures() (CrossModalityNrmls method) (ModelOps method) H h_feats (GCN attribute) handle_ginput_tuple() (CrossModalityNrmls method) (stSmoother method) (Trainer method) handle_input_tuple() (scMultiBatchNrmls method) (scSingleBatch method) (stSmoother method) (Trainer method) hard_anchors (Mixer attribute) hidden_dim (GeneModuler attribute) (Mixer attribute) (TranscriptFormer attribute) hvg_method (BaseDataset attribute) I impute() (ModelOps method) (scMultiBatchNrmls method) in_feats (GCN attribute) inf_pz() (Mixer method) info_key (PseudoST attribute) init_anchor() (NrmlsBC method) init_optimizer() (Trainer method) init_smoother() (TranscriptFormer method) init_smoother_with_builtin() (TranscriptFormer method) input_dim (GeneModuler attribute) (TranscriptFormer attribute) integrate() (CrossModalityNrmls method) is_human (BaseDataset attribute) K k_hop (PseudoST attribute) kl_loss() (Readout method) kmeans() (in module step.models.clust) knn_random_coords() (in module step.models.knn_map) kv (TopNAttention attribute) L layer_key (BaseDataset attribute) (PseudoST attribute) layernorm (BatchAwareLayerNorm attribute) (GeneModuler attribute) Linear2D (class in step.models.transcriptformer) load() (crossModel class method) (scModel class method) (stModel class method) load_checkpoint() (CrossModalityNrmls method) (FunctionalBase method) (scModel method) local_smooth() (TranscriptFormer method) log_mixture_nb() (in module step.models.distributions) log_nb_positive() (in module step.models.distributions) log_prob() (NegativeBinomial method) (ZeroInflatedNegativeBinomial method) log_transformed (BaseDataset attribute) log_zinb_positive() (in module step.models.distributions) logarithm_first (BaseDataset attribute) logger (in module step.manager) logvar (Readout attribute) loss() (ModelOps method) (scMultiBatchNrmls method) loss_fn() (ModelOps method) loss_gbatch() (ModelOps method) (stSmoother method) lossconfig (Trainer attribute) lr_scheduler (Trainer attribute) M make_loaders() (Trainer static method) mask_prop() (Mixer method) MaskedDataset (class in step.utils.dataset) max_ct_per_spot (Mixer attribute) max_neighs (CrossModalityNrmls attribute) mclust_R() (in module step.models.clust) mean (BatchAwareLayerNorm attribute) (Readout attribute) method (ClusterGeneric attribute) Mixer (class in step.models.deconv) mixer (CrossModalityNrmls attribute) mode (BaseDataset attribute) (CrossDataset attribute) (ScDataset attribute) (StDataset attribute) mode_switch_to_train() (Trainer method) model (FunctionalBase attribute) (ModelOps attribute) (scMultiBatchNrmls attribute) (scSingleBatch attribute) (stSmoother attribute) (Trainer attribute) ModelOps (class in step.functionality.comps.model_ops) module step step.functionality step.functionality.base step.functionality.comps step.functionality.comps.model_ops step.functionality.comps.trainer step.functionality.cross_funcmodel step.functionality.sc_funcmodel step.functionality.st_funcmodel step.integration step.manager step.manager.save step.models step.models.clust step.models.deconv step.models.distributions step.models.extension step.models.knn_map step.models.nnls step.models.transcriptformer step.modules step.modules.decoder step.modules.gnn step.modules.transformer step.scmodel step.stmodel step.utils step.utils.dataset step.utils.gbolt step.utils.metrics step.utils.misc step.utils.plotting step.utils.synthetics step.utils.synthetics.pseudo_st module (TranscriptFormer attribute) module_dim (TranscriptFormer attribute) moduler (NrmlsBC attribute) (TranscriptFormer attribute) moran_i() (in module step.utils.metrics) multi_batches (ScMode attribute), [1] (StMode attribute), [1] multi_batches_with_ct (ScMode attribute), [1] MultiGraphsAllNodesSampler (class in step.utils.gbolt) N n_graphs (MultiGraphsAllNodesSampler attribute) n_layers (GCN attribute) (Mixer attribute) n_modules (GeneModuler attribute) (TranscriptFormer attribute) n_spots (Mixer attribute) n_top_genes (BaseDataset attribute) need_anchor (CrossModalityNrmls attribute) NegativeBinomial (class in step.models.distributions) net (BatchAwareScale attribute) (Readout attribute) nnls_deconv() (CrossModalityNrmls method) (in module step.models.nnls) node_sampler() (MultiGraphsAllNodesSampler method) NrmlsBC (class in step.models.extension) num_batches (BaseDataset attribute) (NrmlsBC attribute) num_classes (BaseDataset attribute) (CrossDataset attribute) (ScDataset attribute) num_heads (TopNAttention attribute) O optimizer (Trainer attribute) original_dataset (MaskedDataset attribute) out (Readout attribute) (TopNAttention attribute) P p_hat() (Mixer method) pair() (in module step.modules.transformer) params() (Mixer method) pearson_residuals() (NegativeBinomial method) phat_params() (Mixer method) plot_domain_summary() (in module step.utils.plotting) plot_domain_summary_single_ct() (in module step.utils.plotting) plot_posterior_mu_vs_data() (in module step.utils.plotting) plot_single_domain_summary() (in module step.utils.plotting) plot_spatial_pie_charts() (in module step.utils.plotting) plot_trajectory() (in module step.utils.plotting) plot_trajectory_curve() (in module step.utils.plotting) PreNorm (class in step.modules.transformer) ProbDecoder (class in step.modules.decoder) process() (BaseDataset method) process_fields (BaseDataset attribute), [1] (CrossDataset attribute), [1] PROCESS_FIELDS (in module step.utils.dataset) process_fields (ScDataset attribute), [1] (StDataset attribute) PseudoST (class in step.utils.synthetics.pseudo_st) px_r (TranscriptFormer attribute) Q q (TopNAttention attribute) R random_permute() (GeneModuler method) rate (Mixer attribute) read() (BaseDataset class method) (CrossDataset class method) read_fields (BaseDataset attribute), [1] READ_FIELDS (in module step.utils.dataset) read_fields (ScDataset attribute), [1] (StDataset attribute), [1] read_folder (BaseDataset attribute) (ScDataset attribute), [1] (StDataset attribute), [1] read_folder() (BaseDataset method) read_visium_hd() (in module step.utils.misc) Readout (class in step.models.transcriptformer) readout (TranscriptFormer attribute) readout_() (NrmlsBC method) (TranscriptFormer method) readout_batch() (NrmlsBC method) recieve_fields (BaseDataset attribute), [1] (CrossDataset attribute), [1] RECIEVE_FIELDS (in module step.utils.dataset) recieve_fields (ScDataset attribute), [1] (StDataset attribute) reference_map() (CrossModalityNrmls method) refine() (scMultiBatchNrmls method) regress_out() (ModelOps method) rep (CrossDataset attribute) (StDataset attribute) reset_model() (ModelOps method) (scMultiBatchNrmls method) (stSmoother method) rsample() (NegativeBinomial method) (ZeroInflatedNegativeBinomial method) run() (CrossModalityNrmls method) (FunctionalBase method) (scMultiBatchNrmls method) (stSmoother method) S sample() (NegativeBinomial method) (ZeroInflatedNegativeBinomial method) save() (crossModel method) (PseudoST method) (Saver method) (scModel method) (stModel method) Saver (class in step.manager.save) sc_consistency() (Mixer method) scale (BatchAwareLayerNorm attribute) ScDataset (class in step.utils.dataset) ScMode (class in step.utils.dataset) scModel (class in step.scmodel) scMultiBatchNrmls (class in step.functionality.sc_funcmodel) scSingleBatch (class in step.functionality.sc_funcmodel) seed (ClusterGeneric attribute) set_beta() (ModelOps method) set_cmap() (in module step.utils.plotting) set_domains() (StDataset method) set_kl_cutoff() (ModelOps method) set_kl_start() (ModelOps method) set_lr_scheduler() (Trainer method) set_mode() (CrossDataset method) (MaskedDataset method) (ScDataset method) (StDataset method) set_prior_coef() (StDataset method) set_rep() (CrossDataset method) set_seed() (in module step.utils.misc) set_verbosity() (in module step.manager) setup_early_stopping() (Trainer method) show_attn_maps() (ModelOps method) signatures (Mixer attribute) simulate() (PseudoST method) single_batch (ScMode attribute), [1] (StMode attribute), [1] single_st (CrossModalityNrmls attribute) smoother (Mixer attribute) (NrmlsBC attribute) (TranscriptFormer attribute) smoother_type (TranscriptFormer attribute) softmax_one() (in module step.modules.transformer) solver (Mixer attribute) spatial_plot() (crossModel method) (in module step.utils.plotting) (stModel method) split_rate (FunctionalBase attribute) split_X() (Trainer method) st_adata (CrossDataset attribute) (crossModel attribute) st_decoder (CrossModalityNrmls attribute) st_impute() (CrossModalityNrmls method) st_sample_names (CrossDataset attribute) StDataset (class in step.utils.dataset) step module step.functionality module step.functionality.base module step.functionality.comps module step.functionality.comps.model_ops module step.functionality.comps.trainer module step.functionality.cross_funcmodel module step.functionality.sc_funcmodel module step.functionality.st_funcmodel module step.integration module step.manager module step.manager.save module step.models module step.models.clust module step.models.deconv module step.models.distributions module step.models.extension module step.models.knn_map module step.models.nnls module step.models.transcriptformer module step.modules module step.modules.decoder module step.modules.gnn module step.modules.transformer module step.scmodel module step.stmodel module step.utils module step.utils.dataset module step.utils.gbolt module step.utils.metrics module step.utils.misc module step.utils.plotting module step.utils.synthetics module step.utils.synthetics.pseudo_st module StMode (class in step.utils.dataset) stModel (class in step.stmodel) stSmoother (class in step.functionality.st_funcmodel) sub_cluster() (crossModel method) (stModel method) sub_type_key (PseudoST attribute) subset() (BaseDataset method) (MaskedDataset method) subset_st() (CrossDataset method) summarize_domain() (crossModel method) (stModel method) summarize_single_domain() (crossModel method) (stModel method) support (NegativeBinomial attribute) (ZeroInflatedNegativeBinomial attribute) switch_layer() (BaseDataset method) T T (Mixer attribute) (TopNAttention attribute) top_n (TopNAttention attribute) TopNAttention (class in step.models.deconv) train() (scMultiBatchNrmls method) (Trainer method) train_batch() (Trainer method) train_graph_batch() (Trainer method) train_loop_formatter() (in module step.functionality.comps.trainer) train_node_sampler() (Trainer method) Trainer (class in step.functionality.comps.trainer) TranscriptFormer (class in step.models.transcriptformer) Transformer (class in step.modules.transformer) ts_forward() (Mixer method) U update_model_params() (Trainer method) use_earlystop (FunctionalBase attribute) (stSmoother attribute) use_smoother (Mixer attribute) V validate_gloader() (Trainer method) validate_loader() (Trainer method) validate_X() (Trainer method) variational (Readout attribute) W with_domains (StMode attribute), [1] with_edge (GCN attribute) with_rep (StMode attribute), [1] Z ZeroInflatedNegativeBinomial (class in step.models.distributions) zi_logits() (ZeroInflatedNegativeBinomial method) zi_probs() (ZeroInflatedNegativeBinomial method)