unravel.allen_institute.abca package

• unravel.allen_institute.abca.cache module
• unravel.allen_institute.abca.merfish package
  • unravel.allen_institute.abca.merfish.utils module
    • filter_neurons()
    • load_cell_metadata()
    • load_cell_metadata_og()
    • join_reconstructed_coords()
    • join_cluster_details()
    • join_cluster_colors()
    • join_parcellation_annotation()
    • join_parcellation_color()
    • filter_brain_section()
    • load_expression_data()
    • select_gene()
    • join_expression_to_section()
    • genes_in_merfish_data()
    • genes_in_imputed_merfish_data()
    • prepare_cells_table()
    • build_neuron_subset()
    • slice_index_dict()
    • load_region_boundaries()
    • auto_zoom()
    • plot_slice_color()
    • plot_slice_gene()
  • unravel.allen_institute.abca.merfish.merfish module
    • Usage for gene expression:
    • Usage for color:
    • parse_args()
    • load_cell_metadata()
    • join_reconstructed_coords()
    • join_cluster_details()
    • join_cluster_colors()
    • join_parcellation_annotation()
    • join_parcellation_color()
    • filter_brain_section()
    • load_region_boundaries()
    • load_expression_data()
    • filter_expression_data()
    • create_expression_dataframe()
    • genes_in_merfish_data()
    • genes_in_imputed_merfish_data()
    • slice_index_dict()
    • section_to_zindex()
    • plot_section()
    • points_to_img_sum()
    • main()
  • unravel.allen_institute.abca.merfish.merfish_slice module
    • Usage for color mode (choose cell_metadata.csv color column):
    • Usage for gene expression mode:
    • Usage for overlaying neurons:
    • parse_args()
    • join_cell_metadata()
    • legend_prep()
    • main()
  • unravel.allen_institute.abca.merfish.merfish_filter module
    • Usage:
    • parse_args()
    • sanitize_filename()
    • save_filtered_value()
    • filter_all_values()
    • filter_dataframe()
    • main()
  • unravel.allen_institute.abca.merfish.merfish_filter_by_mask module
    • Usage:
    • parse_args()
    • check_cells_in_mask()
    • merfish_filter_by_mask()
    • main()
  • unravel.allen_institute.abca.merfish.merfish_cells_to_nii module
    • Usage:
    • parse_args()
    • merfish_cells_to_img()
    • main()
  • unravel.allen_institute.abca.merfish.merfish_expression_to_nii module
    • Notes:
    • Usage:
    • Usage for one gene:
    • Usage for selected genes:
    • Usage for all genes:
    • GeneJobResult
    • parse_args()
    • unique_preserve_order()
    • get_requested_genes_from_args()
    • format_gene_preview()
    • find_expression_h5ad()
    • default_output_path()
    • get_var_symbols()
    • get_gene_to_cols()
    • load_and_prepare_cell_metadata()
    • infer_cell_id_column()
    • align_cells_to_adata()
    • precompute_linear_indices()
    • load_X_fully_into_memory()
    • subset_matrix_after_memory_load()
    • get_gene_values()
    • expression_values_to_img()
    • save_nii()
    • process_gene_job()
    • run_gene_jobs()
    • main()
  • unravel.allen_institute.abca.merfish.merfish_join_expression module
    • Usage:
    • parse_args()
    • main()
  • unravel.allen_institute.abca.merfish.merfish_check_genes module
    • Usage:
    • parse_args()
    • normalize_gene_names()
    • main()
  • unravel.allen_institute.abca.merfish.merfish_regions module
    • Usage:
    • Usage with piping to grep:
    • parse_args()
    • main()
• unravel.allen_institute.abca.sunburst package
  • unravel.allen_institute.abca.sunburst.sunburst module
    • Usage:
    • parse_args()
    • filter_non_neuronal_cells()
    • main()
  • unravel.allen_institute.abca.sunburst.sunburst_expression module
    • Usage:
    • parse_args()
    • main()
  • unravel.allen_institute.abca.sunburst.sunburst_filter_by_expression module
    • Usage for first run:
    • Usage to apply filtering from another dataset:
    • parse_args()
    • main()
  • unravel.allen_institute.abca.sunburst.sunburst_filter_by_proportion module
    • Usage:
    • parse_args()
    • main()
  • unravel.allen_institute.abca.sunburst.mean_expression_color_scale module
    • Usage:
    • parse_args()
    • main()
  • unravel.allen_institute.abca.sunburst.percent_expression_color_scale module
    • Usage:
    • parse_args()
    • main()
• unravel.allen_institute.abca.scRNA_seq package
  • unravel.allen_institute.abca.scRNA_seq.expression module
    • Usage:
    • Usage for humans:
    • Usage for mice:
    • parse_args()
    • load_RNAseq_cell_metadata()
    • load_RNAseq_gene_metadata()
    • extract_gene_expression()
    • get_gene_data_wo_cache_and_chunking()
    • load_annotated_cell_metadata()
    • join_cell_metadata()
    • main()
  • unravel.allen_institute.abca.scRNA_seq.filter module
    • Usage:
    • parse_args()
    • filter_by_cell_type()
    • main()
  • unravel.allen_institute.abca.scRNA_seq.expression_summary module
    • Usage for mouse:
    • Usage for human:
    • Usage for parallel processing:
    • parse_args()
    • infer_species()
    • infer_genes()
    • format_number()
    • natural_sort_text()
    • load_expression_data()
    • source_paths_dataframe()
    • summarize_level()
    • save_outputs()
    • main()
  • unravel.allen_institute.abca.scRNA_seq.expression_plot module
    • Usage (sorting by mean expression by default):
    • Usage for selected cell types and genes (ranked by mean expression and sorted by cell count):
    • Usage for the 50 most abundant cell types sorted by abundance:
    • Usage for parallel processing:
    • parse_args()
    • safe_name()
    • natural_sort_text()
    • color_cell_type_tick_labels()
    • detect_genes()
    • validate_and_select_genes()
    • row_rank()
    • prepare_plot_dataframe()
    • summary_context()
    • default_title()
    • automatic_figure_size()
    • matrix_for_metric()
    • finite_max()
    • save_figure()
    • plot_dotplot()
    • plot_heatmap()
    • main()