Index _ | A | C | D | E | F | G | H | I | L | M | N | O | P | R | S | T | U | V | W _ _add_root_attrs() (CoolDSSingleMatrixWriter method), [1] _chrom_sum_iterator() (in module schicluster.loop.merge_raw_matrix) _init_zarr() (CoolDSSingleMatrixWriter method), [1] _is_2d_blacklist() (in module schicluster.cool.remove_blacklist) _read_chrom_info() (CoolDSSingleMatrixWriter method), [1] _read_cool_table() (CoolDSSingleMatrixWriter method), [1] _run_snakemake() (in module schicluster.loop.snakemake) _save_cool_to_temp_zarr() (CoolDSSingleMatrixWriter method), [1] _save_single_bin_chunk() (CoolDSSingleMatrixWriter method), [1] _save_single_bin_chunk_worker() (CoolDSSingleMatrixWriter static method), [1] _save_single_matrix_type() (in module schicluster.loop.merge_raw_matrix) _save_small_sample_chunks() (CoolDSSingleMatrixWriter method), [1] _save_small_sample_chunks_ds_to_final_zarr() (CoolDSSingleMatrixWriter method), [1] _str_to_bool() (in module schicluster.__main__) _t_score() (in module schicluster.loop.shuffle_fdr) _write_data() (CoolDSSingleMatrixWriter method), [1] A aggregate_boundary() (in module schicluster.domain.call_domain) aggregate_cells() (in module schicluster.cool) (in module schicluster.cool.utilities) aggregate_chromosomes() (in module schicluster.cool) (in module schicluster.cool.utilities) aggregate_chromosomes_internal_subparser() (in module schicluster._hicluster_internal) aggregate_compartment() (in module schicluster.compartment.call_compartment) aggregate_insulation() (in module schicluster.domain.call_domain) C calc_diag_stats() (in module schicluster.loop.loop_bkg) calc_sparsity() (in module schicluster.impute.impute_chromosome) calculate_chrom_background_normalization() (in module schicluster.loop.loop_bkg) calculate_loop_matrix_internal_subparser() (in module schicluster._hicluster_internal) call_compartment_register_subparser() (in module schicluster.__main__) call_domain_and_insulation() (in module schicluster.domain.call_domain) call_domain_register_subparser() (in module schicluster.__main__) call_loop() (in module schicluster.loop) (in module schicluster.loop.snakemake) call_loop_internal_subparser() (in module schicluster._hicluster_internal) call_loop_single_chrom() (in module schicluster.loop.loop_calling) call_loops() (in module schicluster.loop.loop_calling) cell_chunk() (in module schicluster.cool) (in module schicluster.cool.utilities) check_chunk_dir_finish() (in module schicluster.loop.snakemake) chrflankpv() (in module schicluster.schicluster) chrom (in module schicluster.loop.compare_loop) chrom_ave_iterator() (in module schicluster.loop.merge_group) chrom_iterator() (in module schicluster.cool) (in module schicluster.cool.utilities) chrom_sum_iterator() (in module schicluster.loop.merge_cell_to_group) comp_comp() (in module schicluster.schicluster) comp_concatcell_chr module comp_concatcell_chr() (in module comp_concatcell_chr) comp_concatcell_chr_register_subparser() (in module schicluster.__main__) comp_cpg_cell module comp_cpg_cell() (in module comp_cpg_cell) comp_cpg_cell_register_subparser() (in module schicluster.__main__) compartment() (in module schicluster.schicluster) compartment_strength() (in module schicluster.compartment.call_compartment) COMPRESSOR_C_LEVEL (in module schicluster.zarr.cool_ds) compute_decay() (in module schicluster.cool.contact_distance) compute_t() (in module schicluster.loop.shuffle_fdr) concat_cell() (in module schicluster.dev.concat_cell) contact_distance() (in module schicluster.cool.contact_distance) contact_distance_register_subparser() (in module schicluster.__main__) CoolDSSingleMatrixWriter (class in schicluster.zarr) (class in schicluster.zarr.cool_ds) cpg_ratio_register_subparser() (in module schicluster.__main__) create_loop_ds() (in module schicluster.zarr.loop_ds) D decay() (in module schicluster.schicluster) DESCRIPTION (in module schicluster.__main__) (in module schicluster._hicluster_internal) diff_bound() (in module schicluster.diff.domain) diff_dom() (in module schicluster.schicluster) dist (in module schicluster.loop.compare_loop) domain_concatcell_chr module domain_concatcell_chr() (in module domain_concatcell_chr) domain_concatcell_chr_register_subparser() (in module schicluster.__main__) domain_df_to_boundary() (in module schicluster.domain.call_domain) domain_insulation_cell module domain_insulation_cell() (in module domain_insulation_cell) domain_insulation_cell_register_subparser() (in module schicluster.__main__) ds_pca() (in module schicluster.schicluster) E embed_concatcell_chr module embed_concatcell_chr() (in module embed_concatcell_chr) embed_concatcell_chr_register_subparser() (in module schicluster.__main__) embed_mergechr module embed_mergechr() (in module embed_mergechr) embed_mergechr_register_subparser() (in module schicluster.__main__) embedding() (in module schicluster.embedding) (in module schicluster.embedding.calc_embedding) embedding_register_subparser() (in module schicluster.__main__) EPILOG (in module schicluster.__main__) (in module schicluster._hicluster_internal) execute() (CoolDSSingleMatrixWriter method), [1] F fetch_chrom() (in module schicluster.loop.loop_calling) filter_bins() (in module schicluster.schicluster) filter_by_background() (in module schicluster.loop.loop_calling) filter_contacts() (in module schicluster.cool.remove_blacklist) filter_contacts_register_subparser() (in module schicluster.__main__) filter_contacts_wrapper() (in module schicluster.cool.remove_blacklist) filter_loops() (in module schicluster.loop.loop_calling) find_summit() (in module schicluster.loop.loop_calling) format() (NiceFormatter method) G gene_score module gene_score() (in module gene_score) gene_score_impute() (in module gene_score) gene_score_raw() (in module gene_score) gene_score_register_subparser() (in module schicluster.__main__) generate_cool_ds() (in module schicluster.zarr) (in module schicluster.zarr.cool_ds) generate_matrix() (in module schicluster.dev.generate_matrix) GENERATE_MATRIX_CHUNK_TEMPLATE (in module schicluster.loop.snakemake) GENERATE_MATRIX_SCOOL_TEMPLATE (in module schicluster.loop.snakemake) generate_scool() (in module schicluster.cool) (in module schicluster.cool.scool) generate_scool_batch_data() (in module schicluster.cool.scool) generate_scool_register_subparser() (in module schicluster.__main__) generate_scool_single_resolution() (in module schicluster.cool.scool) generatematrix_cell module generatematrix_cell() (in module generatematrix_cell) generatematrix_cell_register_subparser() (in module schicluster.__main__) get_chrom_offsets() (in module schicluster.cool) (in module schicluster.cool.utilities) get_cpg_profile() (in module schicluster.compartment) (in module schicluster.compartment.call_compartment) H hg19dim (in module schicluster.dev.imputecell) hg38dim (in module schicluster.dev.imputecell) hicluster_cpu() (in module schicluster.schicluster) hicluster_gpu() (in module schicluster.schicluster) I impute_cell module impute_cell() (in module impute_cell) (in module schicluster.dev.imputecell) impute_cell_register_subparser() (in module schicluster.__main__) impute_chromosome() (in module schicluster.impute.impute_chromosome) impute_chromosome_internal_subparser() (in module schicluster._hicluster_internal) impute_cpu() (in module schicluster.schicluster) impute_gpu() (in module schicluster.schicluster) init_empty_loop_array() (in module schicluster.zarr.loop_ds) install_r_package() (in module schicluster.domain.call_domain) internal_main() (in module schicluster._hicluster_internal) L load_boundary() (in module domain_concatcell_chr) load_cell_csv_to_csr() (in module schicluster.cool.merge) load_cool_ds_chrom() (in module schicluster.zarr.loop_ds) load_cpg() (in module comp_concatcell_chr) load_insulation() (in module domain_concatcell_chr) log (in module schicluster.__main__) (in module schicluster._hicluster_internal) loop0 (in module schicluster.loop.compare_loop) loop1 (in module schicluster.loop.compare_loop), [1] loop2 (in module schicluster.loop.compare_loop), [1] loop_background() (in module schicluster.loop.loop_calling) loop_bkg_cell module loop_bkg_cell() (in module loop_bkg_cell) loop_bkg_cell_register_subparser() (in module schicluster.__main__) loop_mergechr module loop_mergechr() (in module loop_mergechr) loop_mergechr_register_subparser() (in module schicluster.__main__) loop_sc() (in module schicluster.dev.loop_sc) loop_sumcell_chr module loop_sumcell_chr() (in module loop_sumcell_chr) loop_sumcell_chr_register_subparser() (in module schicluster.__main__) M main() (in module schicluster.__main__) make_chrom_matrix() (in module schicluster.embedding.calc_embedding) make_idx() (in module schicluster.embedding.calc_embedding) make_raw_matrix_cell_table() (in module schicluster.loop.merge_raw_matrix) merge_cell() (in module schicluster.dev.merge_cell) merge_cell_impute_matrix_internal_subparser() (in module schicluster._hicluster_internal) merge_cell_loop_bkg_internal_subparser() (in module schicluster._hicluster_internal) merge_cell_raw() (in module schicluster.cool.merge) merge_cell_raw_register_subparser() (in module schicluster.__main__) merge_cells_for_single_chromosome() (in module schicluster.impute.merge_cell_to_group) (in module schicluster.loop.merge_cell_to_group) merge_cool() (in module schicluster.loop.merge_cell_to_group) merge_cool_register_subparser() (in module schicluster.__main__) merge_cpu() (in module schicluster.schicluster) merge_gpu() (in module schicluster.schicluster) merge_group_chunks_internal_subparser() (in module schicluster._hicluster_internal) merge_group_chunks_to_group_cools() (in module schicluster.loop.merge_cell_to_group) merge_group_to_bigger_group_cools() (in module schicluster.loop.merge_cell_to_group) (in module schicluster.loop.merge_group) merge_groups() (in module schicluster.diff.loop) merge_loop() (in module schicluster.loop.snakemake) merge_raw_scool_by_cluster() (in module schicluster.loop.merge_raw_matrix) merge_raw_scool_internal_subparser() (in module schicluster._hicluster_internal) mm10dim (in module schicluster.dev.imputecell) module comp_concatcell_chr comp_cpg_cell domain_concatcell_chr domain_insulation_cell embed_concatcell_chr embed_mergechr gene_score generatematrix_cell impute_cell loop_bkg_cell loop_mergechr loop_sumcell_chr schicluster schicluster.__main__ schicluster._hicluster_internal schicluster._version schicluster.compartment schicluster.compartment.call_compartment schicluster.cool schicluster.cool.contact_distance schicluster.cool.merge schicluster.cool.remove_blacklist schicluster.cool.scool schicluster.cool.utilities schicluster.dev schicluster.dev.concat_cell schicluster.dev.generate_matrix schicluster.dev.imputecell schicluster.dev.loop_sc schicluster.dev.merge_cell schicluster.diff schicluster.diff.domain schicluster.diff.loop schicluster.domain schicluster.domain.call_domain schicluster.embedding schicluster.embedding.calc_embedding schicluster.impute schicluster.impute.impute_chromosome schicluster.impute.merge_cell_to_group schicluster.impute.snakemake schicluster.loop schicluster.loop.compare_loop schicluster.loop.loop_bkg schicluster.loop.loop_calling schicluster.loop.merge_cell_to_group schicluster.loop.merge_group schicluster.loop.merge_raw_matrix schicluster.loop.shuffle_fdr schicluster.loop.snakemake schicluster.schicluster schicluster.zarr schicluster.zarr.cool_ds schicluster.zarr.loop_ds multiple_call_domain_and_insulation() (in module schicluster.domain) (in module schicluster.domain.call_domain) multiple_cell_compartment() (in module schicluster.compartment) (in module schicluster.compartment.call_compartment) N neighbor_ave_cpu() (in module schicluster.schicluster) neighbor_ave_gpu() (in module schicluster.schicluster) NiceFormatter (class in schicluster.__main__) O one_way_anova() (in module schicluster.diff.loop) output_sparse() (in module schicluster.schicluster) output_topdom() (in module schicluster.schicluster) P PACKAGE_DIR (in module schicluster.domain.call_domain) (in module schicluster.impute.snakemake) (in module schicluster.loop.snakemake) paired_t_test() (in module schicluster.loop.loop_calling) parser (in module schicluster.dev.merge_cell) permute_fdr() (in module schicluster.loop.shuffle_fdr) prepare_2d_blacklist_dict() (in module schicluster.cool.remove_blacklist) prepare_dir() (in module schicluster.loop.snakemake) prepare_imputation_register_subparser() (in module schicluster.__main__) prepare_impute() (in module schicluster.impute) (in module schicluster.impute.snakemake) prepare_loop_snakemake() (in module schicluster.loop.snakemake) R random_walk_cpu() (in module schicluster.dev.imputecell) (in module schicluster.impute.impute_chromosome) (in module schicluster.schicluster) random_walk_gpu() (in module schicluster.schicluster) raw_pca() (in module schicluster.schicluster) read_chrom() (in module schicluster.impute.merge_cell_to_group) read_single_cool_chrom() (in module schicluster.loop.merge_cell_to_group) res (in module schicluster.loop.compare_loop) run_svd() (in module schicluster.dev.concat_cell) S save_sample_chunk() (in module schicluster.zarr.loop_ds) save_single_matrix_type() (in module schicluster.loop.merge_cell_to_group) (in module schicluster.loop.merge_group) scan_kernel() (in module schicluster.loop.loop_calling) schicluster module schicluster.__main__ module schicluster._hicluster_internal module schicluster._version module schicluster.compartment module schicluster.compartment.call_compartment module schicluster.cool module schicluster.cool.contact_distance module schicluster.cool.merge module schicluster.cool.remove_blacklist module schicluster.cool.scool module schicluster.cool.utilities module schicluster.dev module schicluster.dev.concat_cell module schicluster.dev.generate_matrix module schicluster.dev.imputecell module schicluster.dev.loop_sc module schicluster.dev.merge_cell module schicluster.diff module schicluster.diff.domain module schicluster.diff.loop module schicluster.domain module schicluster.domain.call_domain module schicluster.embedding module schicluster.embedding.calc_embedding module schicluster.impute module schicluster.impute.impute_chromosome module schicluster.impute.merge_cell_to_group module schicluster.impute.snakemake module schicluster.loop module schicluster.loop.compare_loop module schicluster.loop.loop_bkg module schicluster.loop.loop_calling module schicluster.loop.merge_cell_to_group module schicluster.loop.merge_group module schicluster.loop.merge_raw_matrix module schicluster.loop.shuffle_fdr module schicluster.loop.snakemake module schicluster.schicluster module schicluster.zarr module schicluster.zarr.cool_ds module schicluster.zarr.loop_ds module select_loop_candidates() (in module schicluster.loop.loop_calling) setup_logging() (in module schicluster.__main__) single_cell_compartment() (in module schicluster.compartment.call_compartment) single_chrom_calculate_insulation_score() (in module schicluster.domain.call_domain) single_chrom_compartment() (in module schicluster.compartment.call_compartment) SMALL_SAMPLE_CHUNK (in module schicluster.zarr.cool_ds) svd() (in module schicluster.embedding.calc_embedding) T tmp1 (in module schicluster.loop.compare_loop) tot (in module schicluster.loop.compare_loop) U update_fdr_qval() (in module schicluster.loop.shuffle_fdr) V validate_environment() (in module schicluster.__main__) W write_coo() (in module schicluster.cool) (in module schicluster.cool.utilities)