gunz_cm#
- gunz_cm package
- gunz_cm.cli
- gunz_cm.compressions
- Submodules
BscCmcDecoderBscCmcEncoderBscDecoderBscEncoderCmcDecoderCmcEncoderCmcZstdDecoderCmcZstdEncoderCodecCodecUnavailableErrorLz4DecoderLz4EncoderUnknownCodecErrorWireFormatZstdDecoderZstdEncodercodec_available()get_codec()list_available_codecs()list_codecs()register_codec()unavailable_reason()- gunz_cm.compressions.bsc_encoder
- gunz_cm.compressions.bsc_decoder
- gunz_cm.compressions.cmc_encoder
- gunz_cm.compressions.cmc_decoder
- gunz_cm.compressions.cmc_zstd_encoder
- gunz_cm.compressions.cmc_zstd_decoder
- gunz_cm.compressions.zstd_encoder
- gunz_cm.compressions.zstd_decoder
- Submodules
- gunz_cm.converters
- gunz_cm.datasets
- gunz_cm.io
- gunz_cm.loaders
- gunz_cm.metrics package
- gunz_cm.pipeline
- gunz_cm.preprocs package
- gunz_cm.preprocs.matrices
- gunz_cm.preprocs.points
- gunz_cm.preprocs.transforms
add_rand_ligation_noise()add_rand_ligation_noise_coo()add_rand_ligation_noise_df()add_rand_ligation_noise_mat()comp_single_graph_adj_mat()comp_sparse_wish_dist()comp_sparse_wish_dist_rc_ids()create_band_matrix()create_triu_matrix()downsample_points()expand_with_nans()filter_by_raw_counts()filter_by_weights_quantile_df()filter_common_empty_rowcols()filter_empty_rowcols()filter_points()filter_valid_points()get_genomic_mask()get_optimization_mask()get_unified_mask()infer_mat_shape()intersect_masks()log_scale_matrix()mask_points()mirror_upper_to_lower_triangle()mirror_upper_to_lower_triangle_coo()mirror_upper_to_lower_triangle_df()rand_downsample()scale_matrix()to_coo_matrix()to_dataframe()transform_to_gaussian()uniform_resample_mat()
- gunz_cm.reconstructions package
- gunz_cm.resolution_enhancements package
- gunz_cm.samplers
- gunz_cm.structs package
- gunz_cm.utils
- gunz_cm.visualizations
- Module contents
absolute_error()build_centered_logarithmic_norm()display_compartment_map()display_contact_map()format_bytes()format_seconds()get_compartment_boundaries()get_compartment_matrix()get_compartment_name()get_compartment_sizes()mean_absolute_error()mean_squared_error()mre()pearson_corr()plot_chromosome_3d()plot_chromosome_3d_with_ellipsoid()plot_structure_grid()re()root_mean_squared_error()spearman_corr()split_compartments()squared_error()write_vtk_points()
- Module contents
- Commonly Used Exports
BackendBalancingBpFragContactMatrixContactMatrix.chromosome1ContactMatrix.bin_size_bpContactMatrix.loader_funcContactMatrix.loader_kwargsContactMatrix.chromosome2ContactMatrix.metadataContactMatrix.n_pairsContactMatrix.coverage_ratioContactMatrix.effective_resolution_bpContactMatrix.fragment_resolution_bpContactMatrix.protocol_typeContactMatrix.bin_size_bpContactMatrix.chromosome1ContactMatrix.chromosome2ContactMatrix.coverage_ratioContactMatrix.dataContactMatrix.effective_resolution_bpContactMatrix.fragment_resolution_bpContactMatrix.loader_funcContactMatrix.loader_kwargsContactMatrix.metadataContactMatrix.n_pairsContactMatrix.protocol_type
CountsDataStructureFormatGZCMReaderGZCMWriterGenomeBuildPipelinecomp_hic_spector_coo()comp_hicrep_coo()comp_superrec_obj_perf()convert_all_intra_to_cm_coo()convert_to_cm_coo()convert_to_gzcm()convert_to_memmap()create_pipeline()filter_by_raw_counts()gen_h3dg_coo()gen_shneigh_coo()get_balancing()get_bin_size_bps()get_bins()get_chrom_infos()get_resolutions()load_cm_data()to_coo_matrix()to_dataframe()