Index A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | U | V | W | Z A absolute_error() (in module gunz_cm.visualizations) add_array() (gunz_cm.GZCMWriter method) (gunz_cm.io.GZCMWriter method) add_compressed_tile() (gunz_cm.GZCMWriter method) (gunz_cm.io.GZCMWriter method) add_rand_ligation_noise() (in module gunz_cm.preprocs) add_rand_ligation_noise_coo() (in module gunz_cm.preprocs) add_rand_ligation_noise_df() (in module gunz_cm.preprocs) add_rand_ligation_noise_mat() (in module gunz_cm.preprocs) ALL_LOCI (gunz_cm.loaders.Region attribute) B Backend (class in gunz_cm) backend (gunz_cm.structs.LoaderConfig attribute), [1] Balancing (class in gunz_cm) (class in gunz_cm.loaders) balancing (gunz_cm.structs.LoaderConfig attribute), [1] bin_size_bp (gunz_cm.ContactMatrix attribute), [1] (gunz_cm.structs.LoaderConfig attribute), [1] BP (gunz_cm.BpFrag attribute) (gunz_cm.loaders.BpFrag attribute) BpFrag (class in gunz_cm) (class in gunz_cm.loaders) BscCmcDecoder (class in gunz_cm.compressions) BscCmcEncoder (class in gunz_cm.compressions) BscDecoder (class in gunz_cm.compressions) (class in gunz_cm.compressions.bsc_decoder) BscEncoder (class in gunz_cm.compressions) (class in gunz_cm.compressions.bsc_encoder) build_centered_logarithmic_norm() (in module gunz_cm.visualizations) C chromname() (gunz_cm.loaders.Region method) chromosome (gunz_cm.loaders.Region attribute) chromosome1 (gunz_cm.ContactMatrix attribute), [1] chromosome2 (gunz_cm.ContactMatrix attribute), [1] chunksize (gunz_cm.structs.LoaderConfig attribute), [1] CmcDecoder (class in gunz_cm.compressions) (class in gunz_cm.compressions.cmc_decoder) CmcEncoder (class in gunz_cm.compressions) (class in gunz_cm.compressions.cmc_encoder) CmcZstdDecoder (class in gunz_cm.compressions) (class in gunz_cm.compressions.cmc_zstd_decoder) CmcZstdEncoder (class in gunz_cm.compressions) (class in gunz_cm.compressions.cmc_zstd_encoder) CmFrameSchema (class in gunz_cm.structs) Codec (class in gunz_cm.compressions) codec_available() (in module gunz_cm.compressions) CodecUnavailableError col_col (gunz_cm.structs.CmFrameSchema attribute) comp_contacts() (in module gunz_cm.preprocs.transforms) comp_contacts_torch() (in module gunz_cm.preprocs.transforms) comp_edm() (in module gunz_cm.preprocs.transforms) comp_edm_from_p() (in module gunz_cm.preprocs.transforms) comp_edm_torch() (in module gunz_cm.preprocs.transforms) comp_gram_mat() (in module gunz_cm.preprocs.transforms) comp_gram_mat_torch() (in module gunz_cm.preprocs.transforms) comp_hic_spector_coo() (in module gunz_cm) comp_hicrep_coo() (in module gunz_cm) comp_single_graph_adj_mat() (in module gunz_cm.preprocs) comp_sparse_wish_dist() (in module gunz_cm.preprocs) comp_sparse_wish_dist_rc_ids() (in module gunz_cm.preprocs) comp_superrec_obj_perf() (in module gunz_cm) comp_trace_P() (in module gunz_cm.preprocs.transforms) ContactMatrix (class in gunz_cm) convert_all_intra_to_cm_coo() (in module gunz_cm) convert_to_cm_coo() (in module gunz_cm) convert_to_gzcm() (in module gunz_cm) convert_to_memmap() (in module gunz_cm) COO (gunz_cm.DataStructure attribute) (gunz_cm.Format attribute) (gunz_cm.loaders.DataStructure attribute) (gunz_cm.loaders.Format attribute) COOLER (gunz_cm.Backend attribute) (gunz_cm.Format attribute) (gunz_cm.loaders.Format attribute) count_col (gunz_cm.structs.CmFrameSchema attribute) Counts (class in gunz_cm) (class in gunz_cm.loaders) coverage_ratio (gunz_cm.ContactMatrix attribute), [1] create_band_matrix() (in module gunz_cm.preprocs) create_pipeline() (in module gunz_cm) (in module gunz_cm.pipeline) create_triu_matrix() (in module gunz_cm.preprocs) CSV (gunz_cm.Format attribute) (gunz_cm.loaders.Format attribute) D data (gunz_cm.ContactMatrix property) DataStructure (class in gunz_cm) (class in gunz_cm.loaders) decode_compressed_tile() (gunz_cm.GZCMReader method) (gunz_cm.io.GZCMReader method) decode_tile() (gunz_cm.compressions.bsc_decoder.BscDecoder method) (gunz_cm.compressions.BscCmcDecoder method) (gunz_cm.compressions.BscDecoder method) (gunz_cm.compressions.cmc_decoder.CmcDecoder method) (gunz_cm.compressions.cmc_zstd_decoder.CmcZstdDecoder method) (gunz_cm.compressions.CmcDecoder method) (gunz_cm.compressions.CmcZstdDecoder method) (gunz_cm.compressions.Codec method) (gunz_cm.compressions.Lz4Decoder method) (gunz_cm.compressions.zstd_decoder.ZstdDecoder method) (gunz_cm.compressions.ZstdDecoder method) decode_tiles() (gunz_cm.compressions.bsc_decoder.BscDecoder method) (gunz_cm.compressions.BscCmcDecoder method) (gunz_cm.compressions.BscDecoder method) (gunz_cm.compressions.cmc_decoder.CmcDecoder method) (gunz_cm.compressions.cmc_zstd_decoder.CmcZstdDecoder method) (gunz_cm.compressions.CmcDecoder method) (gunz_cm.compressions.CmcZstdDecoder method) (gunz_cm.compressions.Lz4Decoder method) (gunz_cm.compressions.zstd_decoder.ZstdDecoder method) (gunz_cm.compressions.ZstdDecoder method) DF (gunz_cm.DataStructure attribute) (gunz_cm.loaders.DataStructure attribute) display_compartment_map() (in module gunz_cm.visualizations) display_contact_map() (in module gunz_cm.visualizations) downsample_points() (in module gunz_cm.preprocs) E effective_resolution_bp (gunz_cm.ContactMatrix attribute), [1] encode_tile() (gunz_cm.compressions.bsc_encoder.BscEncoder method) (gunz_cm.compressions.BscCmcEncoder method) (gunz_cm.compressions.BscEncoder method) (gunz_cm.compressions.cmc_encoder.CmcEncoder method) (gunz_cm.compressions.cmc_zstd_encoder.CmcZstdEncoder method) (gunz_cm.compressions.CmcEncoder method) (gunz_cm.compressions.CmcZstdEncoder method) (gunz_cm.compressions.Codec method) (gunz_cm.compressions.Lz4Encoder method) (gunz_cm.compressions.zstd_encoder.ZstdEncoder method) (gunz_cm.compressions.ZstdEncoder method) encode_tiles() (gunz_cm.compressions.bsc_encoder.BscEncoder method) (gunz_cm.compressions.BscCmcEncoder method) (gunz_cm.compressions.BscEncoder method) (gunz_cm.compressions.cmc_encoder.CmcEncoder method) (gunz_cm.compressions.cmc_zstd_encoder.CmcZstdEncoder method) (gunz_cm.compressions.CmcEncoder method) (gunz_cm.compressions.CmcZstdEncoder method) (gunz_cm.compressions.Lz4Encoder method) (gunz_cm.compressions.zstd_encoder.ZstdEncoder method) (gunz_cm.compressions.ZstdEncoder method) eps (gunz_cm.reconstructions.objectives.MDSConfig attribute) (gunz_cm.reconstructions.objectives.WMDSConfig attribute) expand_with_nans() (in module gunz_cm.preprocs) EXPECTED (gunz_cm.Counts attribute) (gunz_cm.loaders.Counts attribute) F fformat (gunz_cm.structs.LoaderConfig attribute), [1] filter_bimodal_outliers() (in module gunz_cm.preprocs.matrices) filter_by_raw_counts() (in module gunz_cm) (in module gunz_cm.preprocs) filter_by_weights_quantile_df() (in module gunz_cm.preprocs) filter_common_empty_rowcols() (in module gunz_cm.preprocs) filter_empty_rowcols() (in module gunz_cm.preprocs) filter_points() (in module gunz_cm.preprocs) filter_valid_points() (in module gunz_cm.preprocs) Format (class in gunz_cm) (class in gunz_cm.loaders) format_bytes() (in module gunz_cm.visualizations) format_seconds() (in module gunz_cm.visualizations) fpath (gunz_cm.structs.LoaderConfig attribute), [1] FRAG (gunz_cm.BpFrag attribute) (gunz_cm.loaders.BpFrag attribute) fragment_resolution_bp (gunz_cm.ContactMatrix attribute), [1] from_legacy_flags() (in module gunz_cm.structs) from_string() (gunz_cm.loaders.Region static method) G gen_h3dg_coo() (in module gunz_cm) gen_memmap_fpaths() (in module gunz_cm.loaders) gen_shneigh_coo() (in module gunz_cm) general_error_loss() (in module gunz_cm.reconstructions.objectives) GeneralErrorConfig (class in gunz_cm.reconstructions.objectives) GenomeBuild (class in gunz_cm) (class in gunz_cm.loaders) get_array() (gunz_cm.GZCMReader method) (gunz_cm.io.GZCMReader method) get_array_writable() (gunz_cm.GZCMWriter method) (gunz_cm.io.GZCMWriter method) get_balancing() (in module gunz_cm) (in module gunz_cm.loaders) get_bin_size_bps() (in module gunz_cm) (in module gunz_cm.loaders) get_bins() (in module gunz_cm) (in module gunz_cm.loaders) get_chrom_infos() (in module gunz_cm) (in module gunz_cm.loaders) get_codec() (in module gunz_cm.compressions) get_compartment_boundaries() (in module gunz_cm.visualizations) get_compartment_matrix() (in module gunz_cm.visualizations) get_compartment_name() (in module gunz_cm.visualizations) get_compartment_sizes() (in module gunz_cm.visualizations) get_compressed_tile() (gunz_cm.GZCMReader method) (gunz_cm.io.GZCMReader method) get_compression_info() (gunz_cm.compressions.bsc_encoder.BscEncoder method) (gunz_cm.compressions.BscCmcEncoder method) (gunz_cm.compressions.BscEncoder method) (gunz_cm.compressions.cmc_encoder.CmcEncoder method) (gunz_cm.compressions.cmc_zstd_encoder.CmcZstdEncoder method) (gunz_cm.compressions.CmcEncoder method) (gunz_cm.compressions.CmcZstdEncoder method) (gunz_cm.compressions.Lz4Encoder method) (gunz_cm.compressions.zstd_encoder.ZstdEncoder method) (gunz_cm.compressions.ZstdEncoder method) get_genomic_mask() (in module gunz_cm.preprocs) get_metadata() (gunz_cm.GZCMReader method) (gunz_cm.io.GZCMReader method) get_optimization_mask() (in module gunz_cm.preprocs) get_resolutions() (in module gunz_cm) (in module gunz_cm.loaders) get_unified_mask() (in module gunz_cm.preprocs) GINTERACTIONS (gunz_cm.Format attribute) (gunz_cm.loaders.Format attribute) gunz_cm module gunz_cm.cli module gunz_cm.compressions module gunz_cm.compressions.bsc_decoder module gunz_cm.compressions.bsc_encoder module gunz_cm.compressions.cmc_decoder module gunz_cm.compressions.cmc_encoder module gunz_cm.compressions.cmc_zstd_decoder module gunz_cm.compressions.cmc_zstd_encoder module gunz_cm.compressions.zstd_decoder module gunz_cm.compressions.zstd_encoder module gunz_cm.converters module gunz_cm.datasets module gunz_cm.io module gunz_cm.loaders module gunz_cm.metrics module gunz_cm.metrics.reconstruction module gunz_cm.metrics.ren module gunz_cm.metrics.ren.third_parties module gunz_cm.pipeline module gunz_cm.preprocs module gunz_cm.preprocs.matrices module gunz_cm.preprocs.points module gunz_cm.preprocs.transforms module gunz_cm.reconstructions module gunz_cm.reconstructions.implementations module gunz_cm.reconstructions.objectives module gunz_cm.reconstructions.preprocs module gunz_cm.reconstructions.utils module gunz_cm.resolution_enhancements module gunz_cm.resolution_enhancements.datasets module gunz_cm.resolution_enhancements.preprocs module gunz_cm.resolution_enhancements.transforms module gunz_cm.samplers module gunz_cm.structs module gunz_cm.utils module gunz_cm.visualizations module GZCMDataset (class in gunz_cm.datasets) GzcmDataset (in module gunz_cm.datasets) GZCMReader (class in gunz_cm) (class in gunz_cm.io) GzcmTileDataset (class in gunz_cm.datasets) GZCMWriter (class in gunz_cm) (class in gunz_cm.io) H has_raw_count() (gunz_cm.structs.CmFrameSchema method) HG19 (gunz_cm.GenomeBuild attribute) (gunz_cm.loaders.GenomeBuild attribute) HG38 (gunz_cm.GenomeBuild attribute) (gunz_cm.loaders.GenomeBuild attribute) HIC (gunz_cm.Format attribute) (gunz_cm.loaders.Format attribute) HiCDataset (class in gunz_cm.datasets) HiCSparseDataset (in module gunz_cm.datasets) HICSTRAW (gunz_cm.Backend attribute) HiCTileDataset (class in gunz_cm.datasets) HICTK (gunz_cm.Backend attribute) I index (gunz_cm.datasets.TileDataset property) infer_mat_shape() (in module gunz_cm.preprocs) init_compressed_tile_stream() (gunz_cm.GZCMWriter method) (gunz_cm.io.GZCMWriter method) init_streaming_array() (gunz_cm.GZCMWriter method) (gunz_cm.io.GZCMWriter method) intersect_masks() (in module gunz_cm.preprocs) is_file_standard_cm() (in module gunz_cm.loaders) is_full_chrom() (gunz_cm.loaders.Region method) is_memmap_exists() (in module gunz_cm.loaders) K keys() (gunz_cm.GZCMReader method) (gunz_cm.io.GZCMReader method) KR (gunz_cm.Balancing attribute) (gunz_cm.loaders.Balancing attribute) kwargs (gunz_cm.structs.LazyMatrixView attribute) L LazyMatrixView (class in gunz_cm.structs) list_available_codecs() (in module gunz_cm.compressions) list_codecs() (in module gunz_cm.compressions) load_cm_data() (in module gunz_cm) (in module gunz_cm.loaders) load_memmap() (in module gunz_cm.loaders) loader (gunz_cm.structs.LazyMatrixView attribute) loader_func (gunz_cm.ContactMatrix attribute), [1] loader_kwargs (gunz_cm.ContactMatrix attribute), [1] LoaderConfig (class in gunz_cm.structs) log_scale_matrix() (in module gunz_cm.preprocs) Lz4Decoder (class in gunz_cm.compressions) Lz4Encoder (class in gunz_cm.compressions) M mask_points() (in module gunz_cm.preprocs) materialize() (in module gunz_cm.structs) MCOO (gunz_cm.Format attribute) (gunz_cm.loaders.Format attribute) MCSV (gunz_cm.Format attribute) (gunz_cm.loaders.Format attribute) mds_loss() (in module gunz_cm.reconstructions.objectives) MDSConfig (class in gunz_cm.reconstructions.objectives) mean_absolute_error() (in module gunz_cm.visualizations) mean_squared_error() (in module gunz_cm.visualizations) MEMMAP (gunz_cm.Format attribute) (gunz_cm.loaders.Format attribute) MemmapTileDataset (class in gunz_cm.datasets) metadata (gunz_cm.ContactMatrix attribute), [1] mirror_upper_to_lower_triangle() (in module gunz_cm.preprocs) mirror_upper_to_lower_triangle_coo() (in module gunz_cm.preprocs) mirror_upper_to_lower_triangle_df() (in module gunz_cm.preprocs) MM10 (gunz_cm.GenomeBuild attribute) (gunz_cm.loaders.GenomeBuild attribute) MM9 (gunz_cm.GenomeBuild attribute) (gunz_cm.loaders.GenomeBuild attribute) model_config (gunz_cm.structs.CmFrameSchema attribute) (gunz_cm.structs.LoaderConfig attribute) module gunz_cm gunz_cm.cli gunz_cm.compressions gunz_cm.compressions.bsc_decoder gunz_cm.compressions.bsc_encoder gunz_cm.compressions.cmc_decoder gunz_cm.compressions.cmc_encoder gunz_cm.compressions.cmc_zstd_decoder gunz_cm.compressions.cmc_zstd_encoder gunz_cm.compressions.zstd_decoder gunz_cm.compressions.zstd_encoder gunz_cm.converters gunz_cm.datasets gunz_cm.io gunz_cm.loaders gunz_cm.metrics gunz_cm.metrics.reconstruction gunz_cm.metrics.ren gunz_cm.metrics.ren.third_parties gunz_cm.pipeline gunz_cm.preprocs gunz_cm.preprocs.matrices gunz_cm.preprocs.points gunz_cm.preprocs.transforms gunz_cm.reconstructions gunz_cm.reconstructions.implementations gunz_cm.reconstructions.objectives gunz_cm.reconstructions.preprocs gunz_cm.reconstructions.utils gunz_cm.resolution_enhancements gunz_cm.resolution_enhancements.datasets gunz_cm.resolution_enhancements.preprocs gunz_cm.resolution_enhancements.transforms gunz_cm.samplers gunz_cm.structs gunz_cm.utils gunz_cm.visualizations mre() (in module gunz_cm.visualizations) N n_pairs (gunz_cm.ContactMatrix attribute), [1] naive_predicted_contacts() (in module gunz_cm.preprocs.matrices) name (gunz_cm.compressions.CodecUnavailableError attribute) NONE (gunz_cm.Balancing attribute) (gunz_cm.loaders.Balancing attribute) NPY (gunz_cm.Format attribute) (gunz_cm.loaders.Format attribute) O OBSERVED (gunz_cm.Counts attribute) (gunz_cm.loaders.Counts attribute) OE (gunz_cm.Counts attribute) (gunz_cm.loaders.Counts attribute) OPAQUE_PAYLOAD (gunz_cm.compressions.WireFormat attribute), [1] output_format (gunz_cm.structs.LoaderConfig attribute), [1] P pearson_corr() (in module gunz_cm.visualizations) PICKLE (gunz_cm.Format attribute) (gunz_cm.loaders.Format attribute) Pipeline (class in gunz_cm) (class in gunz_cm.pipeline) plot_chromosome_3d() (in module gunz_cm.visualizations) plot_chromosome_3d_with_ellipsoid() (in module gunz_cm.visualizations) plot_structure_grid() (in module gunz_cm.visualizations) protocol_type (gunz_cm.ContactMatrix attribute), [1] R rand_downsample() (in module gunz_cm.preprocs) raw_count_col (gunz_cm.structs.CmFrameSchema attribute) RC (gunz_cm.DataStructure attribute) (gunz_cm.loaders.DataStructure attribute) RCV (gunz_cm.DataStructure attribute) (gunz_cm.loaders.DataStructure attribute) re() (in module gunz_cm.visualizations) reason (gunz_cm.compressions.CodecUnavailableError attribute) reduction (gunz_cm.reconstructions.objectives.GeneralErrorConfig attribute) (gunz_cm.reconstructions.objectives.MDSConfig attribute) (gunz_cm.reconstructions.objectives.WMDSConfig attribute) Region (class in gunz_cm.loaders) region (gunz_cm.loaders.Region attribute) region1 (gunz_cm.structs.LoaderConfig attribute) region2 (gunz_cm.structs.LoaderConfig attribute) register_codec() (in module gunz_cm.compressions) return_raw_counts (gunz_cm.structs.LoaderConfig attribute), [1] root_mean_squared_error() (in module gunz_cm.visualizations) row_col (gunz_cm.structs.CmFrameSchema attribute) run() (gunz_cm.Pipeline method) (gunz_cm.pipeline.Pipeline method) S scale_matrix() (in module gunz_cm.preprocs) select_informative_contacts() (in module gunz_cm.preprocs.matrices) SELF_DESCRIBING (gunz_cm.compressions.WireFormat attribute), [1] set_metadata() (gunz_cm.GZCMWriter method) (gunz_cm.io.GZCMWriter method) sparse_collate_fn() (in module gunz_cm.datasets) SpatialBatchSampler (class in gunz_cm.samplers) spearman_corr() (in module gunz_cm.visualizations) split_compartments() (in module gunz_cm.visualizations) squared_error() (in module gunz_cm.visualizations) STRAW (gunz_cm.Backend attribute) T term (gunz_cm.reconstructions.objectives.GeneralErrorConfig attribute) (gunz_cm.reconstructions.objectives.MDSConfig attribute) (gunz_cm.reconstructions.objectives.WMDSConfig attribute) TileDataset (class in gunz_cm.datasets) to_coo_matrix() (in module gunz_cm) (in module gunz_cm.preprocs) to_dataframe() (in module gunz_cm) (in module gunz_cm.preprocs) transform_to_gaussian() (in module gunz_cm.preprocs) TSV (gunz_cm.Format attribute) (gunz_cm.loaders.Format attribute) U unavailable_reason() (in module gunz_cm.compressions) uniform_resample_mat() (in module gunz_cm.preprocs) UnknownCodecError V VC (gunz_cm.Balancing attribute) (gunz_cm.loaders.Balancing attribute) VC_SQRT (gunz_cm.Balancing attribute) (gunz_cm.loaders.Balancing attribute) W weight_exp (gunz_cm.reconstructions.objectives.WMDSConfig attribute) wire_format (gunz_cm.compressions.Codec property) WireFormat (class in gunz_cm.compressions) wmds_loss() (in module gunz_cm.reconstructions.objectives) WMDSConfig (class in gunz_cm.reconstructions.objectives) write() (gunz_cm.GZCMWriter method) (gunz_cm.io.GZCMWriter method) write_vtk_points() (in module gunz_cm.visualizations) Z ZstdDecoder (class in gunz_cm.compressions) (class in gunz_cm.compressions.zstd_decoder) ZstdEncoder (class in gunz_cm.compressions) (class in gunz_cm.compressions.zstd_encoder)