Index C | D | E | F | G | I | K | L | M | P | R | S | T | U | V C compute_activator_tf_activity_per_cell() (in module scdori.downstream) compute_atac_grn_activator_with_significance() (in module scdori.downstream) compute_atac_grn_repressor_with_significance() (in module scdori.downstream) compute_eval_loss_grn() (in module scdori.train_grn) compute_eval_loss_scdori() (in module scdori.train_scdori) compute_gene_peak_distance_matrix() (in module preprocessing_pipeline.utils) compute_hvgs_and_tfs() (in module preprocessing_pipeline.gene_selection) compute_in_silico_chipseq() (in module preprocessing_pipeline.correlation) compute_motif_scores() (in module preprocessing_pipeline.motif_scanning) compute_neighbors_umap() (in module scdori.downstream) compute_repressor_tf_activity_per_cell() (in module scdori.downstream) compute_significant_grn() (in module scdori.downstream) compute_topic_gene_matrix() (in module scdori.downstream) compute_topic_peak_umap() (in module scdori.downstream) create_dir_if_not_exists() (in module preprocessing_pipeline.data_io) create_extended_gene_bed() (in module preprocessing_pipeline.utils) create_metacells() (in module preprocessing_pipeline.metacells) create_minibatch() (in module scdori.dataloader) D download_file() (in module preprocessing_pipeline.download) download_genome_references() (in module preprocessing_pipeline.download) E encode() (scdori.models.scDoRI method) F filter_protein_coding_genes() (in module preprocessing_pipeline.gene_selection) forward() (scdori.models.scDoRI method) G get_latent_topics() (in module scdori.evaluation) get_loss_weights_scdori() (in module scdori.train_scdori) get_phase_scdori() (in module scdori.train_scdori) get_tf_expression() (in module scdori.train_grn) get_top_activators_per_topic() (in module scdori.downstream) get_top_repressor_per_topic() (in module scdori.downstream) I initialize_scdori_parameters() (in module scdori.models) intersect_cells() (in module preprocessing_pipeline.filtering) K keep_promoters_and_select_hv_peaks() (in module preprocessing_pipeline.peak_selection) L load_anndata() (in module preprocessing_pipeline.data_io) load_best_model() (in module scdori.downstream) load_gtf() (in module preprocessing_pipeline.gene_selection) load_motif_database() (in module preprocessing_pipeline.motif_scanning) load_scdori_inputs() (in module scdori.data_io) log_nb_positive() (in module scdori.utils) M module preprocessing_pipeline.config preprocessing_pipeline.correlation preprocessing_pipeline.data_io preprocessing_pipeline.download preprocessing_pipeline.filtering preprocessing_pipeline.gene_selection preprocessing_pipeline.metacells preprocessing_pipeline.motif_scanning preprocessing_pipeline.peak_selection preprocessing_pipeline.utils scdori.config scdori.data_io scdori.dataloader scdori.downstream scdori.evaluation scdori.main scdori.models scdori.train_grn scdori.train_scdori scdori.utils P plot_topic_activation_heatmap() (in module scdori.downstream) preprocessing_pipeline.config module preprocessing_pipeline.correlation module preprocessing_pipeline.data_io module preprocessing_pipeline.download module preprocessing_pipeline.filtering module preprocessing_pipeline.gene_selection module preprocessing_pipeline.metacells module preprocessing_pipeline.motif_scanning module preprocessing_pipeline.peak_selection module preprocessing_pipeline.utils module R remove_mitochondrial_genes() (in module preprocessing_pipeline.filtering) resolve_genome_urls() (in module preprocessing_pipeline.download) run_bedtools_intersect() (in module preprocessing_pipeline.motif_scanning) run_scdori_pipeline() (in module scdori.main) S save_model_weights() (in module scdori.data_io) save_processed_datasets() (in module preprocessing_pipeline.data_io) save_regulons() (in module scdori.downstream) scDoRI (class in scdori.models) scdori.config module scdori.data_io module scdori.dataloader module scdori.downstream module scdori.evaluation module scdori.main module scdori.models module scdori.train_grn module scdori.train_scdori module scdori.utils module select_highly_variable_peaks_by_std() (in module preprocessing_pipeline.peak_selection) set_encoder_frozen() (in module scdori.train_grn) set_peak_gene_frozen() (in module scdori.train_grn) set_seed() (in module scdori.utils) set_topic_peak_frozen() (in module scdori.train_grn) set_topic_tf_frozen() (in module scdori.train_grn) simulate_pwm_scoring() (in module preprocessing_pipeline.motif_scanning) T train_model_grn() (in module scdori.train_grn) train_scdori_phases() (in module scdori.train_scdori) U unzip_gz() (in module preprocessing_pipeline.download) V visualize_downstream_targets() (in module scdori.downstream)