| ._Brick_Add_Ranges_ |
Source code
|
| ._Brick_Get_Something_ |
Source code
|
| ._Brick_Put_Something_ |
Source code
|
| ._Brick_WriteArray_ |
Source code
|
| ._Brick_WriteDataFrame_ |
Source code
|
| ._Brick_do_on_ComplexSelection_ |
Source code
|
| ._Check_numeric |
Source code
|
| ._ColIndexError_ |
Source code
|
| ._Compute_various_col_matrix_metrics |
Source code
|
| ._Compute_various_matrix_metrics |
Source code
|
| ._Do_on_vector_ComputeMinMax_ |
Source code
|
| ._Do_on_vector_ComputeRowSums_ |
Source code
|
| ._Do_on_vector_PercentGTZero_ |
Source code
|
| ._Do_on_vector_SparsityIndex_ |
Source code
|
| ._Do_rbind_on_matrices_of_different_sizes_ |
Source code
|
| ._Figure_out_genomic_scale |
Source code
|
| ._FindLineNumbers_ |
Source code
|
| ._GenerateRandomName_ |
Source code
|
| ._GetDimensions |
Source code
|
| ._Get_Brick_hashname |
Source code
|
| ._Parse_genomic_coordinates |
Source code
|
| ._ProcessMatrix_ |
Source code
|
| ._Process_matrix_by_distance |
Source code
|
| ._format_by_charlen |
Source code
|
| ._get_first_nonzero_bin |
Source code
|
| ._get_sparsity_index |
Source code
|
| ._mcool_bintable_ranges |
Source code
|
| ._mcool_remap_chromosomes |
Source code
|
| .add_metrics |
Source code
|
| .add_to_hdf_array |
Source code
|
| .check_column_classes |
Source code
|
| .check_if_rangekey_exists_and_do_something |
Source code
|
| .check_if_rangekey_not_exists_and_do_something |
Source code
|
| .check_upper_triangle |
Source code
|
| .convert_chr_to_chunks |
Source code
|
| .create_bintable_group_path |
Source code
|
| .create_brick |
Source code
|
| .create_chr1_indexes |
Source code
|
| .create_configuration_header |
Source code
|
| .create_configuration_matrix_info |
Source code
|
| .create_file_connection |
Source code
|
| .create_file_list |
Source code
|
| .create_indexes_group_path |
Source code
|
| .create_matrix_group_path |
Source code
|
| .create_mcool_chr1_indexes |
Source code
|
| .fetch_data |
Source code
|
| .fetch_upper_tri_value_by_row |
Source code
|
| .final_metrics_processing |
Source code
|
| .format_resolution |
Source code
|
| .get_instance_biocparallel |
Source code
|
| .make_chr1_chr2_pairs |
Source code
|
| .make_chunks_from_bin_offset |
Source code
|
| .make_configuration_path |
Source code
|
| .make_coords_list |
Source code
|
| .make_iterations |
Source code
|
| .make_mcool_iterations |
Source code
|
| .normalize_by_distance_values |
Source code
|
| .populate_with_empty_metrics |
Source code
|
| .prepare_BrickContainer |
Source code
|
| .prepare_ranges_df_for_add |
Source code
|
| .prepare_ranges_metadata_list |
Source code
|
| .prepare_ranges_metadata_mcols |
Source code
|
| .process_mcool |
Source code
|
| .process_tsv |
Source code
|
| .remove_nas |
Source code
|
| .replace_chr1_row_indexes |
Source code
|
| .return_bias_vector |
Source code
|
| .return_chr1_chr2_pairs |
Source code
|
| .return_chromosomes_list |
Source code
|
| .return_file_list |
Source code
|
| .return_offsets |
Source code
|
| .return_table_df |
Source code
|
| .return_values_list |
Source code
|
| .send_message |
Source code
|
| .write_configuration_file |
Source code
|
| Backwards.Difference |
Source code
|
| BrickContainer_change_experiment_name |
Man page
Source code
|
| BrickContainer_change_output_directory |
Man page
Source code
|
| BrickContainer_class_check |
Source code
|
| BrickContainer_get_path_to_file |
Man page
Source code
|
| BrickContainer_list_chromosomes |
Man page
Source code
|
| BrickContainer_list_experiment_name |
Man page
Source code
|
| BrickContainer_list_files |
Man page
Source code
|
| BrickContainer_list_matrices |
Source code
|
| BrickContainer_list_output_directory |
Man page
Source code
|
| BrickContainer_list_rangekeys |
Source code
|
| BrickContainer_list_resolutions |
Man page
Source code
|
| BrickContainer_resolution_check |
Source code
|
| BrickContainer_unlink_resolution |
Man page
Source code
|
| Brick_add_ranges |
Man page
Source code
|
| Brick_call_compartments |
Man page
Source code
|
| Brick_export_to_sparse |
Man page
Source code
|
| Brick_fetch_range_index |
Man page
Source code
|
| Brick_fetch_row_vector |
Man page
Source code
|
| Brick_get_bintable |
Man page
Source code
|
| Brick_get_chrominfo |
Man page
Source code
|
| Brick_get_entire_matrix |
Man page
Source code
|
| Brick_get_matrix |
Man page
Source code
|
| Brick_get_matrix_mcols |
Man page
Source code
|
| Brick_get_matrix_within_coords |
Man page
Source code
|
| Brick_get_ranges |
Man page
Source code
|
| Brick_get_values_by_distance |
Man page
Source code
|
| Brick_get_vector_values |
Man page
Source code
|
| Brick_list_matrices |
Man page
Source code
|
| Brick_list_matrix_mcols |
Man page
Source code
|
| Brick_list_mcool_normalisations |
Man page
Source code
|
| Brick_list_mcool_resolutions |
Man page
Source code
|
| Brick_list_rangekeys |
Man page
Source code
|
| Brick_list_ranges_mcols |
Man page
Source code
|
| Brick_load_cis_matrix_till_distance |
Man page
Source code
|
| Brick_load_data_from_mcool |
Man page
Source code
|
| Brick_load_data_from_sparse |
Man page
Source code
|
| Brick_load_matrix |
Man page
Source code
|
| Brick_local_score_differentiator |
Man page
Source code
|
| Brick_make_ranges |
Man page
Source code
|
| Brick_matrix_dimensions |
Man page
Source code
|
| Brick_matrix_exists |
Man page
Source code
|
| Brick_matrix_filename |
Man page
Source code
|
| Brick_matrix_isdone |
Man page
Source code
|
| Brick_matrix_issparse |
Man page
Source code
|
| Brick_matrix_maxdist |
Man page
Source code
|
| Brick_matrix_minmax |
Man page
Source code
|
| Brick_mcool_normalisation_exists |
Man page
Source code
|
| Brick_rangekey_exists |
Man page
Source code
|
| Brick_return_region_position |
Man page
Source code
|
| Brick_vizart_plot_heatmap |
Man page
Source code
|
| CheckContinuousRanges |
Source code
|
| CloseH5Con |
Source code
|
| ComputeDirectionalityIndex |
Source code
|
| ComputeOutlierOverIQRInsideWindow |
Source code
|
| CreateAttributes |
Source code
|
| CreateDataset |
Source code
|
| CreateDomainlist |
Source code
|
| CreateGroups |
Source code
|
| Create_Path |
Source code
|
| Create_many_Bricks |
Man page
Source code
|
| Create_many_Bricks_from_mcool |
Man page
Source code
|
| Format_boundaries_normal_heatmap |
Source code
|
| Forwards.Difference |
Source code
|
| GetAttributes |
Source code
|
| Get_heatmap_theme |
Source code
|
| Get_heatmap_titles |
Source code
|
| Get_one_or_two_brick_regions |
Source code
|
| HiCBricks |
Man page
|
| MakeBoundaries |
Source code
|
| Make_axis_labels |
Source code
|
| Make_colours |
Source code
|
| Read_bintable |
Source code
|
| ReturnH5Attribute |
Source code
|
| ReturnH5FileConnection |
Source code
|
| ReturnH5Handler |
Source code
|
| RotateHeatmap |
Source code
|
| RotatePixels |
Source code
|
| Split_genomic_coordinates |
Source code
|
| Validate_table |
Source code
|
| WriteAttributes |
Source code
|
| add_to_data |
Source code
|
| configuration_class_check |
Source code
|
| configuration_length_check |
Source code
|
| configuration_na_check |
Source code
|
| configuration_null_check |
Source code
|
| create_configuration_object |
Source code
|
| get_chrom_info |
Source code
|
| get_directionality_index_by_chunks |
Source code
|
| get_legend_breaks |
Source code
|
| humanize_size |
Source code
|
| insert_data_and_computemetrics_both_matrices |
Source code
|
| load_BrickContainer |
Man page
Source code
|
| make_axis_coord_breaks |
Source code
|
| make_boundaries_for_heatmap |
Source code
|
| make_boundaries_for_rotated_heatmap |
Source code
|
| make_colour_breaks |
Source code
|
| mcool_list_resolutions |
Source code
|
| prepare_empty_metrics_list |
Source code
|
| read_configuration_file |
Source code
|
| rescale_values_for_colours |
Source code
|
| return_chrominfo_df |
Source code
|
| return_chromosome_lengths |
Source code
|
| return_chromosome_pairs |
Source code
|
| return_chromosomes |
Source code
|
| return_experiment_name |
Source code
|
| return_output_directory |
Source code
|
| return_resolutions |
Source code
|
