Index

A

add_array() (gunz_cm.io.gnz.GnzWriter method) (gunz_cm.io.GnzWriter method) add_rand_ligation_noise() (in module gunz_cm.preprocs.noises) add_rand_ligation_noise_coo() (in module gunz_cm.preprocs.noises) add_rand_ligation_noise_df() (in module gunz_cm.preprocs.noises) add_rand_ligation_noise_mat() (in module gunz_cm.preprocs.noises)

aligned_target (gunz_cm.reconstructions.objectives.procrustes.ProcrustesResult attribute) ALL_LOCI (gunz_cm.loaders.Region attribute) (gunz_cm.loaders.utils.Region attribute) any_transformation() (gunz_cm.resolution_enhancements.datasets.memmap_v1.MemmapDatasetV1 method) (gunz_cm.resolution_enhancements.datasets.ren_memmap_v1.RENMemmapDatasetV1 method) append_root_dir() (in module gunz_cm.utils.path) available_norms (gunz_cm.loaders.hic_loader.HiCFooter attribute)

B

Backend (class in gunz_cm.consts) Balancing (class in gunz_cm.consts) (class in gunz_cm.loaders) binnify() (in module gunz_cm.utils.intervals)

BP (gunz_cm.consts.BpFrag attribute) (gunz_cm.loaders.BpFrag attribute) BpFrag (class in gunz_cm.consts) (class in gunz_cm.loaders) bstr2int() (in module gunz_cm.utils.stream)

C

centered_input (gunz_cm.reconstructions.objectives.procrustes.ProcrustesResult attribute) centered_target (gunz_cm.reconstructions.objectives.procrustes.ProcrustesResult attribute) chromname() (gunz_cm.loaders.Region method) (gunz_cm.loaders.utils.Region method) chromosomes (gunz_cm.loaders.hic_loader.HiCHeader attribute) clamp() (in module gunz_cm.resolution_enhancements.preprocs.normalize) ClosedInterval (class in gunz_cm.loaders.utils) comp_flamingo_obj_perf() (in module gunz_cm.reconstructions.third_party.flamingo) comp_h3dg_obj_perf() (in module gunz_cm.reconstructions.third_party.h3dg) comp_hic_spector_coo() (in module gunz_cm.metrics.ren.hic_spector) comp_hic_spector_third_party() (in module gunz_cm.metrics.ren.third_parties.hic_spector_wrapper) comp_hicrep_coo() (in module gunz_cm.metrics.ren.hicrep) comp_hicrep_third_party() (in module gunz_cm.metrics.ren.third_parties.hicrep_wrapper) comp_norm_laplacian_mat_coo() (in module gunz_cm.metrics.ren.hic_spector) comp_shneigh_obj_perf() (in module gunz_cm.reconstructions.third_party.shneigh) comp_single_graph_adj_mat() (in module gunz_cm.preprocs.graphs) comp_sparse_wish_dist() (in module gunz_cm.preprocs.sparse_wish_dist) comp_sparse_wish_dist_rc_ids() (in module gunz_cm.preprocs.sparse_wish_dist) comp_superrec_obj_perf() (in module gunz_cm.reconstructions.third_party.superrec) Constant (class in gunz_cm.loaders.utils) ConversionFailedError convert_all_intra_to_cm_coo() (in module gunz_cm.converters.coo) convert_to_cm_coo() (in module gunz_cm.converters.coo)

convert_to_gnz() (in module gunz_cm.converters.gnz) convert_to_memmap() (in module gunz_cm.converters.memmap) ConverterError COO (gunz_cm.consts.DataStructure attribute) (gunz_cm.consts.Format attribute) (gunz_cm.loaders.DataStructure attribute) (gunz_cm.loaders.Format attribute) cool2pixels() (in module gunz_cm.metrics.ren.third_parties.hicrep.utils) COOLER (gunz_cm.consts.Backend attribute) (gunz_cm.consts.Format attribute) (gunz_cm.loaders.Format attribute) coolerInfo() (in module gunz_cm.metrics.ren.third_parties.hicrep.utils) CopyInputAsOutput (class in gunz_cm.resolution_enhancements.transforms.cp_input_as_output) Counts (class in gunz_cm.consts) (class in gunz_cm.loaders) cpair_info (gunz_cm.loaders.hic_loader.HiCFooter attribute) create_band_matrix() (in module gunz_cm.preprocs.band_matrix) create_pipeline() (in module gunz_cm.pipeline) (in module gunz_cm.pipeline.core) create_sprite_cm() (in module gunz_cm.pipeline.sprite.sprite_cm) create_triu_matrix() (in module gunz_cm.preprocs.triu_matrix) CSV (gunz_cm.consts.Format attribute) (gunz_cm.loaders.Format attribute)

D

DataResolutionError DatasetError DataStructure (class in gunz_cm.consts) (class in gunz_cm.loaders) DF (gunz_cm.consts.DataStructure attribute) (gunz_cm.loaders.DataStructure attribute)

diag_transform_coo() (in module gunz_cm.metrics.ren.hicrep) distance (gunz_cm.reconstructions.objectives.procrustes.ProcrustesResult attribute) downsample_points() (in module gunz_cm.reconstructions.preprocs.points) downscale_counts() (in module gunz_cm.resolution_enhancements.preprocs.downscaling) Downweighting (class in gunz_cm.pipeline.sprite.downweighting) DS (in module gunz_cm.consts)

E

end (gunz_cm.loaders.utils.ClosedInterval attribute) estimate_num_contacts() (gunz_cm.pipeline.sprite.downweighting.Downweighting method) evec_distance() (in module gunz_cm.metrics.ren.third_parties.hic_spector) (in module gunz_cm.metrics.ren.third_parties.hic_spector_ahmed)

expand_with_nans() (in module gunz_cm.preprocs.masks) EXPECTED (gunz_cm.consts.Counts attribute) (gunz_cm.loaders.Counts attribute) expected_values (gunz_cm.loaders.hic_loader.HiCFooter attribute)

F

fetch_centromeres() (in module gunz_cm.utils.resources) filter_by_raw_counts() (in module gunz_cm.preprocs.count_filters) filter_by_weights_quantile_df() (in module gunz_cm.preprocs.weight_filters) filter_common_empty_rowcols() (in module gunz_cm.preprocs.rc_filters_common) filter_empty_rowcols() (in module gunz_cm.preprocs.rc_filters) filter_points() (in module gunz_cm.reconstructions.preprocs.points) filter_valid_points() (in module gunz_cm.reconstructions.preprocs.points) find_h3dg_mapping_fpath() (in module gunz_cm.reconstructions.third_party.h3dg) find_h3dg_points_fpath() (in module gunz_cm.reconstructions.third_party.h3dg)

footer (gunz_cm.loaders.hic_loader.HiCMetadata attribute) Format (class in gunz_cm.consts) (class in gunz_cm.loaders) FormatError FRAG (gunz_cm.consts.BpFrag attribute) (gunz_cm.loaders.BpFrag attribute) from_str() (gunz_cm.pipeline.sprite.downweighting.Downweighting static method) from_string() (gunz_cm.loaders.Region static method) (gunz_cm.loaders.utils.Region static method)

G

gen_h3dg_coo() (in module gunz_cm.reconstructions.third_party.h3dg) gen_h3dg_domain() (in module gunz_cm.reconstructions.third_party.h3dg) gen_memmap_fpaths() (in module gunz_cm.loaders) (in module gunz_cm.loaders.memmap_loader) gen_shneigh_coo() (in module gunz_cm.reconstructions.third_party.shneigh) gen_superrec_coo() (in module gunz_cm.reconstructions.third_party.superrec) GeneralError (class in gunz_cm.reconstructions.objectives.general_error) genome (gunz_cm.loaders.hic_loader.HiCHeader attribute) GenomeBuild (class in gunz_cm.consts) (class in gunz_cm.loaders) get_array() (gunz_cm.io.gnz.GnzReader method) (gunz_cm.io.GnzReader method) get_array_writable() (gunz_cm.io.gnz.GnzWriter method) (gunz_cm.io.GnzWriter method) get_assembly() (in module gunz_cm.loaders.cool_loader) get_balancing() (in module gunz_cm.cli.loaders) (in module gunz_cm.loaders) get_balancing_methods() (in module gunz_cm.loaders.hic_loader) get_balancing_weights() (in module gunz_cm.loaders.cool_loader) get_bins() (in module gunz_cm.cli.loaders) (in module gunz_cm.loaders) (in module gunz_cm.loaders.cool_loader) (in module gunz_cm.loaders.hic_loader) get_chrom_infos() (in module gunz_cm.cli.loaders) (in module gunz_cm.loaders) (in module gunz_cm.loaders.cool_loader) (in module gunz_cm.loaders.hic_loader) (in module gunz_cm.loaders.narrowpeaks) get_genomic_mask() (in module gunz_cm.preprocs.masks) get_hic_spector_test() (in module gunz_cm.metrics.ren.third_parties.hic_spector_ahmed) get_hic_spector_train() (in module gunz_cm.metrics.ren.third_parties.hic_spector_ahmed) get_ipr() (in module gunz_cm.metrics.ren.third_parties.hic_spector) (in module gunz_cm.metrics.ren.third_parties.hic_spector_ahmed) get_Laplacian() (in module gunz_cm.metrics.ren.third_parties.hic_spector) (in module gunz_cm.metrics.ren.third_parties.hic_spector_ahmed) get_metadata() (gunz_cm.io.gnz.GnzReader method) (gunz_cm.io.GnzReader method) get_optimization_mask() (in module gunz_cm.preprocs.masks) get_reproducibility() (in module gunz_cm.metrics.ren.third_parties.hic_spector) get_resolutions() (in module gunz_cm.cli.loaders) (in module gunz_cm.loaders) (in module gunz_cm.loaders.cool_loader) (in module gunz_cm.loaders.hic_loader) get_root_dir() (in module gunz_cm.utils.path) get_score() (in module gunz_cm.metrics.ren.third_parties.hic_spector_ahmed) get_sparsity() (in module gunz_cm.loaders.cool_loader) (in module gunz_cm.loaders.hic_loader) get_unified_mask() (in module gunz_cm.preprocs.masks) getSubCoo() (in module gunz_cm.metrics.ren.third_parties.hicrep.utils) GINTERACTIONS (gunz_cm.consts.Format attribute) (gunz_cm.loaders.Format attribute) GnzReader (class in gunz_cm.io) (class in gunz_cm.io.gnz) GnzSparseDataset (class in gunz_cm.datasets.gnz) GnzWriter (class in gunz_cm.io) (class in gunz_cm.io.gnz) gunz_cm module gunz_cm.cli module gunz_cm.cli.converters module gunz_cm.cli.loaders module gunz_cm.cli.main module gunz_cm.consts module gunz_cm.converters module gunz_cm.converters.coo module gunz_cm.converters.gnz module gunz_cm.converters.memmap module gunz_cm.datasets module gunz_cm.datasets.gnz module gunz_cm.datasets.hic module gunz_cm.datasets.memmap module gunz_cm.exceptions module gunz_cm.io module gunz_cm.io.gnz module gunz_cm.loaders module gunz_cm.loaders.cool_loader module gunz_cm.loaders.csv_loader module gunz_cm.loaders.ginteractions_loader module gunz_cm.loaders.hic_loader module gunz_cm.loaders.memmap_loader module gunz_cm.loaders.narrowpeaks module gunz_cm.loaders.pickle_loader module gunz_cm.loaders.utils module gunz_cm.metrics module gunz_cm.metrics.reconstruction module gunz_cm.metrics.reconstruction.n_way_interactions module gunz_cm.metrics.ren module gunz_cm.metrics.ren.hic_spector module gunz_cm.metrics.ren.hicrep module gunz_cm.metrics.ren.stat_test module gunz_cm.metrics.ren.third_parties module gunz_cm.metrics.ren.third_parties.hic_spector module gunz_cm.metrics.ren.third_parties.hic_spector_ahmed module

gunz_cm.metrics.ren.third_parties.hic_spector_wrapper module gunz_cm.metrics.ren.third_parties.hicrep module gunz_cm.metrics.ren.third_parties.hicrep.hicrep module gunz_cm.metrics.ren.third_parties.hicrep.utils module gunz_cm.metrics.ren.third_parties.hicrep_wrapper module gunz_cm.pipeline module gunz_cm.pipeline.core module gunz_cm.pipeline.sprite module gunz_cm.pipeline.sprite.downweighting module gunz_cm.pipeline.sprite.sprite_cm module gunz_cm.preprocs module gunz_cm.preprocs.band_matrix module gunz_cm.preprocs.commons module gunz_cm.preprocs.converters module gunz_cm.preprocs.count_filters module gunz_cm.preprocs.graphs module gunz_cm.preprocs.infer_shape module gunz_cm.preprocs.linear_scaler module gunz_cm.preprocs.log_scaler module gunz_cm.preprocs.masks module gunz_cm.preprocs.mirrors module gunz_cm.preprocs.noises module gunz_cm.preprocs.rc_filters module gunz_cm.preprocs.rc_filters_common module gunz_cm.preprocs.resamples module gunz_cm.preprocs.sparse_wish_dist module gunz_cm.preprocs.triu_matrix module gunz_cm.preprocs.weight_filters module gunz_cm.reconstructions module gunz_cm.reconstructions.objectives module gunz_cm.reconstructions.objectives.consts module gunz_cm.reconstructions.objectives.general_error module gunz_cm.reconstructions.objectives.mds module gunz_cm.reconstructions.objectives.procrustes module gunz_cm.reconstructions.preprocs module gunz_cm.reconstructions.preprocs.points module gunz_cm.reconstructions.third_party module gunz_cm.reconstructions.third_party.flamingo module gunz_cm.reconstructions.third_party.h3dg module gunz_cm.reconstructions.third_party.shneigh module gunz_cm.reconstructions.third_party.superrec module gunz_cm.resolution_enhancements module gunz_cm.resolution_enhancements.datasets module gunz_cm.resolution_enhancements.datasets.memmap_v1 module gunz_cm.resolution_enhancements.datasets.memmap_v2 module gunz_cm.resolution_enhancements.datasets.ren_memmap_v1 module gunz_cm.resolution_enhancements.preprocs module gunz_cm.resolution_enhancements.preprocs.downscaling module gunz_cm.resolution_enhancements.preprocs.normalize module gunz_cm.resolution_enhancements.preprocs.thresholding module gunz_cm.resolution_enhancements.transforms module gunz_cm.resolution_enhancements.transforms.cp_input_as_output module gunz_cm.resolution_enhancements.transforms.rand_downsample module gunz_cm.samplers module gunz_cm.samplers.spatial module gunz_cm.structs module gunz_cm.utils module gunz_cm.utils.intervals module gunz_cm.utils.logger module gunz_cm.utils.matrix module gunz_cm.utils.path module gunz_cm.utils.resources module gunz_cm.utils.stream module GunzCMError

H

header (gunz_cm.loaders.hic_loader.HiCMetadata attribute) HG19 (gunz_cm.consts.GenomeBuild attribute) (gunz_cm.loaders.GenomeBuild attribute) HG38 (gunz_cm.consts.GenomeBuild attribute) (gunz_cm.loaders.GenomeBuild attribute) HIC (gunz_cm.consts.Format attribute) (gunz_cm.loaders.Format attribute) hic2cool() (in module gunz_cm.cli.converters)

HiCFooter (class in gunz_cm.loaders.hic_loader) HiCHeader (class in gunz_cm.loaders.hic_loader) HiCMetadata (class in gunz_cm.loaders.hic_loader) hicrepSCC() (in module gunz_cm.metrics.ren.third_parties.hicrep.hicrep) HiCSparseDataset (class in gunz_cm.datasets) (class in gunz_cm.datasets.hic) HICSTRAW (gunz_cm.consts.Backend attribute) HICTK (gunz_cm.consts.Backend attribute)

I

infer_mat_shape() (in module gunz_cm.preprocs.infer_shape) init_streaming_array() (gunz_cm.io.gnz.GnzWriter method) (gunz_cm.io.GnzWriter method) int2bstr() (in module gunz_cm.utils.stream) intersect_masks() (in module gunz_cm.preprocs.masks) InvalidRegionFormatError

IOError IRLS (gunz_cm.reconstructions.objectives.procrustes.Method attribute) is_file_standard_cm() (in module gunz_cm.loaders) is_full_chrom() (gunz_cm.loaders.Region method) (gunz_cm.loaders.utils.Region method) is_memmap_exists() (in module gunz_cm.loaders) (in module gunz_cm.loaders.memmap_loader)

K

keys() (gunz_cm.io.gnz.GnzReader method) (gunz_cm.io.GnzReader method)

KR (gunz_cm.consts.Balancing attribute) (gunz_cm.loaders.Balancing attribute)

L

limit_count() (in module gunz_cm.resolution_enhancements.preprocs.thresholding) load_cm_data() (in module gunz_cm.loaders) load_cooler() (in module gunz_cm.loaders.cool_loader) load_csv() (in module gunz_cm.loaders.csv_loader) load_data() (gunz_cm.resolution_enhancements.datasets.memmap_v1.MemmapDatasetV1 method) (gunz_cm.resolution_enhancements.datasets.memmap_v2.MemmapDatasetV2 method) (gunz_cm.resolution_enhancements.datasets.ren_memmap_v1.RENMemmapDatasetV1 method) (in module gunz_cm.cli.loaders)

load_ginteractions() (in module gunz_cm.loaders.ginteractions_loader) load_h3dg_points() (in module gunz_cm.reconstructions.third_party.h3dg) load_hic() (in module gunz_cm.loaders.hic_loader) load_memmap() (in module gunz_cm.loaders) (in module gunz_cm.loaders.memmap_loader) load_narrowpeak() (in module gunz_cm.loaders.narrowpeaks) load_pickle() (in module gunz_cm.loaders.pickle_loader) LoaderError log_scale_matrix() (in module gunz_cm.preprocs.log_scaler)

M

main() (in module gunz_cm.cli.main) (in module gunz_cm.metrics.ren.third_parties.hic_spector) (in module gunz_cm.metrics.ren.third_parties.hicrep) mask_points() (in module gunz_cm.reconstructions.preprocs.points) master_index (gunz_cm.loaders.hic_loader.HiCHeader attribute) MCOO (gunz_cm.consts.Format attribute) (gunz_cm.loaders.Format attribute) MCSV (gunz_cm.consts.Format attribute) (gunz_cm.loaders.Format attribute) mean_filter_coo_mat() (in module gunz_cm.metrics.ren.hicrep) meanFilterSparse() (in module gunz_cm.metrics.ren.third_parties.hicrep.utils) measure_nways_interaction_found() (in module gunz_cm.metrics.reconstruction.n_way_interactions) MEMMAP (gunz_cm.consts.Format attribute) (gunz_cm.loaders.Format attribute) MemmapDatasetV1 (class in gunz_cm.resolution_enhancements.datasets.memmap_v1) MemmapDatasetV2 (class in gunz_cm.resolution_enhancements.datasets.memmap_v2) MemmapSparseDataset (class in gunz_cm.datasets.memmap) metadata (gunz_cm.loaders.hic_loader.HiCHeader attribute) Method (class in gunz_cm.reconstructions.objectives.procrustes) MetricError min_max_norm() (in module gunz_cm.resolution_enhancements.preprocs.normalize) mirror_upper_to_lower_triangle() (in module gunz_cm.preprocs.mirrors) mirror_upper_to_lower_triangle_coo() (in module gunz_cm.preprocs.mirrors) mirror_upper_to_lower_triangle_df() (in module gunz_cm.preprocs.mirrors) MM10 (gunz_cm.consts.GenomeBuild attribute) (gunz_cm.loaders.GenomeBuild attribute) MM9 (gunz_cm.consts.GenomeBuild attribute) (gunz_cm.loaders.GenomeBuild attribute) module gunz_cm gunz_cm.cli gunz_cm.cli.converters gunz_cm.cli.loaders gunz_cm.cli.main gunz_cm.consts gunz_cm.converters gunz_cm.converters.coo gunz_cm.converters.gnz gunz_cm.converters.memmap gunz_cm.datasets gunz_cm.datasets.gnz gunz_cm.datasets.hic gunz_cm.datasets.memmap gunz_cm.exceptions gunz_cm.io gunz_cm.io.gnz gunz_cm.loaders gunz_cm.loaders.cool_loader gunz_cm.loaders.csv_loader gunz_cm.loaders.ginteractions_loader gunz_cm.loaders.hic_loader gunz_cm.loaders.memmap_loader gunz_cm.loaders.narrowpeaks gunz_cm.loaders.pickle_loader gunz_cm.loaders.utils gunz_cm.metrics gunz_cm.metrics.reconstruction gunz_cm.metrics.reconstruction.n_way_interactions gunz_cm.metrics.ren gunz_cm.metrics.ren.hic_spector gunz_cm.metrics.ren.hicrep gunz_cm.metrics.ren.stat_test gunz_cm.metrics.ren.third_parties gunz_cm.metrics.ren.third_parties.hic_spector gunz_cm.metrics.ren.third_parties.hic_spector_ahmed gunz_cm.metrics.ren.third_parties.hic_spector_wrapper gunz_cm.metrics.ren.third_parties.hicrep gunz_cm.metrics.ren.third_parties.hicrep.hicrep gunz_cm.metrics.ren.third_parties.hicrep.utils gunz_cm.metrics.ren.third_parties.hicrep_wrapper gunz_cm.pipeline gunz_cm.pipeline.core gunz_cm.pipeline.sprite gunz_cm.pipeline.sprite.downweighting gunz_cm.pipeline.sprite.sprite_cm gunz_cm.preprocs gunz_cm.preprocs.band_matrix gunz_cm.preprocs.commons gunz_cm.preprocs.converters gunz_cm.preprocs.count_filters gunz_cm.preprocs.graphs gunz_cm.preprocs.infer_shape gunz_cm.preprocs.linear_scaler gunz_cm.preprocs.log_scaler gunz_cm.preprocs.masks gunz_cm.preprocs.mirrors gunz_cm.preprocs.noises gunz_cm.preprocs.rc_filters gunz_cm.preprocs.rc_filters_common gunz_cm.preprocs.resamples gunz_cm.preprocs.sparse_wish_dist gunz_cm.preprocs.triu_matrix gunz_cm.preprocs.weight_filters gunz_cm.reconstructions gunz_cm.reconstructions.objectives gunz_cm.reconstructions.objectives.consts gunz_cm.reconstructions.objectives.general_error gunz_cm.reconstructions.objectives.mds gunz_cm.reconstructions.objectives.procrustes gunz_cm.reconstructions.preprocs gunz_cm.reconstructions.preprocs.points gunz_cm.reconstructions.third_party gunz_cm.reconstructions.third_party.flamingo gunz_cm.reconstructions.third_party.h3dg gunz_cm.reconstructions.third_party.shneigh gunz_cm.reconstructions.third_party.superrec gunz_cm.resolution_enhancements gunz_cm.resolution_enhancements.datasets gunz_cm.resolution_enhancements.datasets.memmap_v1 gunz_cm.resolution_enhancements.datasets.memmap_v2 gunz_cm.resolution_enhancements.datasets.ren_memmap_v1 gunz_cm.resolution_enhancements.preprocs gunz_cm.resolution_enhancements.preprocs.downscaling gunz_cm.resolution_enhancements.preprocs.normalize gunz_cm.resolution_enhancements.preprocs.thresholding gunz_cm.resolution_enhancements.transforms gunz_cm.resolution_enhancements.transforms.cp_input_as_output gunz_cm.resolution_enhancements.transforms.rand_downsample gunz_cm.samplers gunz_cm.samplers.spatial gunz_cm.structs gunz_cm.utils gunz_cm.utils.intervals gunz_cm.utils.logger gunz_cm.utils.matrix gunz_cm.utils.path gunz_cm.utils.resources gunz_cm.utils.stream

MultiDimensionalScaling (class in gunz_cm.reconstructions.objectives.mds)

N

N_MINUS_ONE (gunz_cm.pipeline.sprite.downweighting.Downweighting attribute) NONE (gunz_cm.consts.Balancing attribute) (gunz_cm.loaders.Balancing attribute) (gunz_cm.pipeline.sprite.downweighting.Downweighting attribute)

norm_factors (gunz_cm.loaders.hic_loader.HiCFooter attribute) norm_info (gunz_cm.loaders.hic_loader.HiCFooter attribute) NPY (gunz_cm.consts.Format attribute) (gunz_cm.loaders.Format attribute)

O

OBSERVED (gunz_cm.consts.Counts attribute) (gunz_cm.loaders.Counts attribute) OE (gunz_cm.consts.Counts attribute) (gunz_cm.loaders.Counts attribute)

one_sided_gt_wilcoxon() (in module gunz_cm.metrics.ren.stat_test) one_sided_lt_wilcoxon() (in module gunz_cm.metrics.ren.stat_test)

P

parse_h3dg_mapping() (in module gunz_cm.reconstructions.third_party.h3dg) parse_h3dg_points() (in module gunz_cm.reconstructions.third_party.h3dg) Parse_matrix() (in module gunz_cm.metrics.ren.third_parties.hic_spector) Parse_matrix_hic() (in module gunz_cm.metrics.ren.third_parties.hic_spector) Parse_matrix_lieberman() (in module gunz_cm.metrics.ren.third_parties.hic_spector) PICKLE (gunz_cm.consts.Format attribute) (gunz_cm.loaders.Format attribute) Pipeline (class in gunz_cm.pipeline) (class in gunz_cm.pipeline.core)

pixels2Coo() (in module gunz_cm.metrics.ren.third_parties.hicrep.utils) plot_points() (in module gunz_cm.reconstructions.preprocs.points) PreprocError preprocess_matrices_coo() (in module gunz_cm.metrics.ren.hicrep) procrustes_analysis() (in module gunz_cm.reconstructions.objectives.procrustes) ProcrustesError ProcrustesResult (class in gunz_cm.reconstructions.objectives.procrustes)

R

rand_downsample() (in module gunz_cm.preprocs.resamples) RandomDownsampleCM (class in gunz_cm.resolution_enhancements.transforms.rand_downsample) RC (gunz_cm.consts.DataStructure attribute) (gunz_cm.loaders.DataStructure attribute) RCV (gunz_cm.consts.DataStructure attribute) (gunz_cm.loaders.DataStructure attribute) read_hic_metadata() (in module gunz_cm.loaders.hic_loader) read_str() (in module gunz_cm.utils.stream) readMcool() (in module gunz_cm.metrics.ren.third_parties.hicrep.utils) ReconstructionError

Region (class in gunz_cm.loaders) (class in gunz_cm.loaders.utils) RENMemmapDatasetV1 (class in gunz_cm.resolution_enhancements.datasets.ren_memmap_v1) resample() (in module gunz_cm.metrics.ren.third_parties.hicrep.utils) resample_coo_mat() (in module gunz_cm.metrics.ren.hicrep) resolutions (gunz_cm.loaders.hic_loader.HiCHeader attribute) ROBUST_L1 (gunz_cm.reconstructions.objectives.procrustes.Method attribute) rotation_matrix (gunz_cm.reconstructions.objectives.procrustes.ProcrustesResult attribute) run() (gunz_cm.pipeline.core.Pipeline method) (gunz_cm.pipeline.Pipeline method)

S

scale_matrix() (in module gunz_cm.preprocs.linear_scaler) scaled_input (gunz_cm.reconstructions.objectives.procrustes.ProcrustesResult attribute) sccByDiag() (in module gunz_cm.metrics.ren.third_parties.hicrep.hicrep) sccOfDiag() (in module gunz_cm.metrics.ren.third_parties.hicrep.hicrep) set_metadata() (gunz_cm.io.gnz.GnzWriter method) (gunz_cm.io.GnzWriter method) set_transformations() (gunz_cm.resolution_enhancements.datasets.ren_memmap_v1.RENMemmapDatasetV1 method) setup_logging() (in module gunz_cm.cli.main) (in module gunz_cm.utils.logger)

shape (gunz_cm.resolution_enhancements.datasets.memmap_v1.MemmapDatasetV1 property) (gunz_cm.resolution_enhancements.datasets.ren_memmap_v1.RENMemmapDatasetV1 property) sparse_collate_fn() (in module gunz_cm.datasets) (in module gunz_cm.datasets.hic) SpatialBatchSampler (class in gunz_cm.samplers) (class in gunz_cm.samplers.spatial) start (gunz_cm.loaders.utils.ClosedInterval attribute) STRAW (gunz_cm.consts.Backend attribute) subtract() (in module gunz_cm.utils.intervals) symmetrize_edges() (in module gunz_cm.preprocs.mirrors)

T

to_bigmat() (in module gunz_cm.cli.converters) to_coo() (in module gunz_cm.cli.converters) to_coo_matrix() (in module gunz_cm.preprocs.converters) to_dataframe() (in module gunz_cm.preprocs.converters) to_intra_cm_coos() (in module gunz_cm.cli.converters) transform_item() (gunz_cm.resolution_enhancements.datasets.memmap_v1.MemmapDatasetV1 method) (gunz_cm.resolution_enhancements.datasets.ren_memmap_v1.RENMemmapDatasetV1 method)

transform_to_gaussian() (in module gunz_cm.preprocs.linear_scaler) trimDiags() (in module gunz_cm.metrics.ren.third_parties.hicrep.utils) TSV (gunz_cm.consts.Format attribute) (gunz_cm.loaders.Format attribute) TWO_OVER_N (gunz_cm.pipeline.sprite.downweighting.Downweighting attribute)

U

uniform_resample_mat() (in module gunz_cm.preprocs.resamples) UNKNOWN (gunz_cm.pipeline.sprite.downweighting.Downweighting attribute)

UnsupportedLoaderFeatureError upperDiagCsr() (in module gunz_cm.metrics.ren.third_parties.hicrep.utils)

V

VANILLA (gunz_cm.reconstructions.objectives.procrustes.Method attribute) variance_stabilizing_transform_variance() (in module gunz_cm.metrics.ren.hicrep) varVstran() (in module gunz_cm.metrics.ren.third_parties.hicrep.utils) VC (gunz_cm.consts.Balancing attribute) (gunz_cm.loaders.Balancing attribute)

VC_SQRT (gunz_cm.consts.Balancing attribute) (gunz_cm.loaders.Balancing attribute) vec_calc_eig_vec_dist() (in module gunz_cm.metrics.ren.hic_spector) vec_comp_ipr4() (in module gunz_cm.metrics.ren.hic_spector) version (gunz_cm.loaders.hic_loader.HiCHeader attribute)

W

WeightedMultiDimensionalScaling (class in gunz_cm.reconstructions.objectives.mds)

write() (gunz_cm.io.gnz.GnzWriter method) (gunz_cm.io.GnzWriter method)