HiCBricks
Framework for Storing and Accessing Hi-C Data Through HDF Files

Package index
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Functions
232
Source code
17
Man pages
50
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HiCBricks: Framework for Storing and Accessing Hi-C Data Through HDF Files
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API

API for HiCBricks
Framework for Storing and Accessing Hi-C Data Through HDF Files

Global functions
._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
HiCBricks documentation built on Nov. 8, 2020, 7:45 p.m.

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