SCOTCH

• NMTF module
  • NMTF
    • NMTF.assign_X_data()
    • NMTF.assign_cluster()
    • NMTF.fit()
    • NMTF.print_USV()
    • NMTF.print_output()
    • NMTF.recluster_V()
    • NMTF.save_cluster()
    • NMTF.send_to_cpu()
    • NMTF.send_to_gpu()
    • NMTF.update()
    • NMTF.update_unit()
    • NMTF.visualize_clusters()
    • NMTF.visualize_clusters_sorted()
    • NMTF.visualize_factors()
    • NMTF.visualize_factors_sorted()
    • NMTF.write_gif()
• SCOTCH module
  • SCOTCH
    • SCOTCH.add_data_from_adata()
    • SCOTCH.add_data_from_file()
    • SCOTCH.add_scotch_embeddings_to_adata()
    • SCOTCH.combined_embedding_visualization()
    • SCOTCH.combined_enrichment_visualization()
    • SCOTCH.make_adata_from_scotch()
    • SCOTCH.make_top_regulators_list()
    • SCOTCH.plot_S_matrix()
    • SCOTCH.plot_cooccurrence_proportions()
    • SCOTCH.plot_element_count_heatmap()
    • SCOTCH.plot_reconstruction_error()
    • SCOTCH.run_enrich_analyzer()
    • SCOTCH.visualize_enrichment_bubbleplots()
    • SCOTCH.visualize_marker_gene_bubbleplot_per_cell_cluster()
    • SCOTCH.visualize_marker_gene_bubbleplot_per_gene_cluster()
• initialize module
  • nnsvd_nmf_initialize()
  • nnsvd_nmtf_initialize()