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scdori
Welcome & Executive Summary
Model Overview & Architecture
Hyperparameter Configuration Guide
scDoRI Data Preprocessing
scDoRI Model Training
scDoRI Downstream Analysis
API
Core
scdori.compute_activator_tf_activity_per_cell
scdori.compute_atac_grn_activator_with_significance
scdori.compute_atac_grn_repressor_with_significance
scdori.compute_neighbors_umap
scdori.compute_repressor_tf_activity_per_cell
scdori.compute_significant_grn
scdori.compute_topic_gene_matrix
scdori.compute_topic_peak_umap
scdori.get_latent_topics
scdori.get_latent_topics
scdori.get_tf_expression
scdori.get_top_activators_per_topic
scdori.get_top_repressor_per_topic
scdori.initialize_scdori_parameters
scdori.load_best_model
scdori.load_scdori_inputs
scdori.save_regulons
scdori.scDoRI
scdori.train_model_grn
scdori.train_scdori_phases
scdori.trainConfig
Preprocessing
scdori.compute_gene_peak_distance_matrix
scdori.compute_hvgs_and_tfs
scdori.compute_in_silico_chipseq
scdori.compute_motif_scores
scdori.create_dir_if_not_exists
scdori.create_extended_gene_bed
scdori.create_metacells
scdori.download_genome_references
scdori.filter_protein_coding_genes
scdori.intersect_cells
scdori.keep_promoters_and_select_hv_peaks
scdori.load_anndata
scdori.load_gtf
scdori.load_motif_database
scdori.ppConfig
scdori.remove_mitochondrial_genes
scdori.run_bedtools_intersect
scdori.save_processed_datasets
Plotting
scdori.plot_downstream_targets
scdori.plot_topic_activation_heatmap
Changelog
Contributing guide
References
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