Man pages for koustav-pal/HiCBricks
Framework for Storing and Accessing Hi-C Data Through HDF Files

Brick_add_rangesStore a ranges object in the Brick store.
Brick_call_compartmentsIdentify compartments in the Hi-C data
BrickContainer_change_experiment_nameChange the location of HDF files in the BrickContainer object
BrickContainer_change_output_directoryChange the location of HDF files in the BrickContainer object
BrickContainer_get_path_to_fileGet the path to HDF files present in the Brick container.
BrickContainer_list_chromosomesReturn the descriptive name of the BrickContainer
BrickContainer_list_experiment_nameReturn the descriptive name of the BrickContainer
BrickContainer_list_filesGet the list of HDF files present in the Brick container.
BrickContainer_list_output_directoryReturn the output directory of the BrickContainer
BrickContainer_list_resolutionsReturn the descriptive name of the BrickContainer
BrickContainer_unlink_resolutionRemove links to all Hi-C matrices for a given resolution.
Brick_export_to_sparseExport an entire resolution from a given BrickContainer as a...
Brick_fetch_range_indexReturns the position of the supplied ranges in the binning...
Brick_fetch_row_vectorReturn row or col vectors.
Brick_get_bintableReturns the binning table associated to the Hi-C experiment.
Brick_get_chrominfoGet the chrominfo for the Hi-C experiment.
Brick_get_entire_matrixReturn an entire matrix for provided chromosome pair for a...
Brick_get_matrixReturn a matrix subset.
Brick_get_matrix_mcolsGet the matrix metadata columns in the Brick store.
Brick_get_matrix_within_coordsReturn a matrix subset between two regions.
Brick_get_rangesFetch the ranges associated to a rangekey or chromosome.
Brick_get_values_by_distanceReturn values separated by a certain distance.
Brick_get_vector_valuesReturn a N dimensional vector selection.
Brick_list_matricesList the matrix pairs present in the Brick store.
Brick_list_matrix_mcolsList the matrix metadata columns in the Brick store.
Brick_list_mcool_normalisationsGet all available normalisations in an mcool file.
Brick_list_mcool_resolutionsGet all available normalisations in an mcool file.
Brick_list_rangekeysList the ranges tables stored within the Brick.
Brick_list_ranges_mcolsFind out what metadata columns are associated to a ranges...
Brick_load_cis_matrix_till_distanceLoad a NxN dimensional sub-distance _cis_ matrix into the...
Brick_load_data_from_mcoolLoad a NxN dimensional matrix into the Brick store from an...
Brick_load_matrixLoad a NxM dimensional matrix into the Brick store.
Brick_local_score_differentiatorDo TAD Calls with Local Score Differentiator on a Hi-C matrix
Brick_make_rangesCreates a ranges object from provided vectors.
Brick_matrix_dimensionsReturn the dimensions of a matrix
Brick_matrix_existsCheck if a chromosome pair exists.
Brick_matrix_filenameReturn the filename of the loaded matrix
Brick_matrix_isdoneCheck if a matrix has been loaded for a chromosome pair.
Brick_matrix_issparseCheck if a matrix for a chromosome pair is sparse.
Brick_matrix_maxdistGet the maximum loaded distance from the diagonal of any...
Brick_matrix_minmaxReturn the value range of the matrix
Brick_mcool_normalisation_existsCheck if a normalisation exists in an mcool file.
Brick_rangekey_existsCheck to see if the Brick contains a ranges with a certain...
Brick_return_region_positionProvides the overlapping position (within) from the bintable.
Brick_vizart_plot_heatmapCreate the entire HDF5 structure and load the bintable
Create_many_BricksCreate the entire HDF5 structure and load the bintable
Create_many_Bricks_from_mcoolCreate the entire HDF5 structure and load the bintable from a...
HiCBricksA package for storing, accessing and plotting Hi-C data
load_BrickContainerCreate a BrickContainer object from a JSON file
koustav-pal/HiCBricks documentation built on Nov. 6, 2019, 10:19 a.m.