API Reference

• Preprocessing Pipeline
  • create_dir_if_not_exists()
  • load_anndata()
  • save_processed_datasets()
  • intersect_cells()
  • remove_mitochondrial_genes()
  • compute_in_silico_chipseq()
  • compute_gene_peak_distance_matrix()
  • create_extended_gene_bed()
  • keep_promoters_and_select_hv_peaks()
  • select_highly_variable_peaks_by_std()
  • compute_motif_scores()
  • load_motif_database()
  • run_bedtools_intersect()
  • simulate_pwm_scoring()
  • create_metacells()
  • compute_hvgs_and_tfs()
  • filter_protein_coding_genes()
  • load_gtf()
  • download_file()
  • download_genome_references()
  • resolve_genome_urls()
  • unzip_gz()
• scDORI training
  • compute_eval_loss_grn()
  • get_tf_expression()
  • set_encoder_frozen()
  • set_peak_gene_frozen()
  • set_topic_peak_frozen()
  • set_topic_tf_frozen()
  • train_model_grn()
  • Attributes
  • initialize_scdori_parameters()
  • scDoRI
    • scDoRI.encode()
    • scDoRI.forward()
  • run_scdori_pipeline()
  • log_nb_positive()
  • set_seed()
  • compute_eval_loss_scdori()
  • get_loss_weights_scdori()
  • get_phase_scdori()
  • train_scdori_phases()
  • get_latent_topics()
  • compute_activator_tf_activity_per_cell()
  • compute_atac_grn_activator_with_significance()
  • compute_atac_grn_repressor_with_significance()
  • compute_neighbors_umap()
  • compute_repressor_tf_activity_per_cell()
  • compute_significant_grn()
  • compute_topic_gene_matrix()
  • compute_topic_peak_umap()
  • get_top_activators_per_topic()
  • get_top_repressor_per_topic()
  • load_best_model()
  • plot_topic_activation_heatmap()
  • save_regulons()
  • visualize_downstream_targets()
  • create_minibatch()
  • load_scdori_inputs()
  • save_model_weights()