repository open issue

Index

_

_ (in module ALLCools.api), [1], [2], [3], [4], [5], [6], [7], [8], [9] __add_data_panel() (Session method) __add_feature_panel() (Session method) __add_other_routine() (Session method) __add_refseq_gene() (Session method) __add_resource() (Session method) __add_resources() (Session method) __add_sequence_track() (Session method) __del__() (Closing method) __enter__() (Closing method) __exit__() (Closing method) __iter__() (PipedBamReader method) (PipedGzipReader method) (ReadGtf method) __next__() (ReadGtf method) __setitem__() (MultiDict method) __slots__ (MCDS attribute), [1] (RegionDS attribute), [1] __version__ (in module ALLCools) _aggregate_count_df() (in module ALLCools._bam_to_allc) _aggregate_enrichment() (in module ALLCools.clustering.feature_selection.feature_enrichment) _aggregate_motif_beds() (in module ALLCools.sandbox.motif.fimo) _aggregate_motif_clusters() (MotifSet method), [1] _aggregate_region_count_to_mcds() (in module ALLCools.count_matrix.mcds) _ALLC (class in ALLCools._merge_allc) _allc_to_bedgraph() (in module ALLCools._allc_to_bigwig) _annotate_by_beds_worker() (in module ALLCools.mcds.region_ds) _annotate_by_bigwigs_worker() (in module ALLCools.mcds.region_ds) _bam_to_allc_worker() (in module ALLCools._bam_to_allc) _batch_merge_allc_files_tabix() (in module ALLCools._merge_allc) _bed_intersection() (in module ALLCools.mcds.region_ds) _bedgraph_to_bigwig() (in module ALLCools._allc_to_bigwig) _bedtools_map() (in module ALLCools._allc_to_region_count) _bigwig_over_bed() (in module ALLCools.mcds.region_ds) _bin_count_table_to_csr_npz() (in module ALLCools.count_matrix.h5ad) _calculate_cell_final_values() (in module ALLCools.clustering.doublets.coverage_doublets) _calculate_cell_record() (in module ALLCools.clustering.doublets.coverage_doublets) _calculate_enrichment_score() (in module ALLCools.clustering.feature_selection.feature_enrichment) _calculate_enrichment_score_cytograph() (in module ALLCools.clustering.feature_selection.feature_enrichment) _calculate_goodness_of_fit() (in module ALLCools.dmr.rms_test) _calculate_pseudo_group() (in module ALLCools.pseudo_cell.pseudo_cell_kmeans) _call_dmr_single_chrom() (in module ALLCools.dmr.call_dmr) _call_enhancer_region() (in module ALLCools.reptile.reptile) _check_out_format_parameter() (in module ALLCools._extract_allc) _check_strandness_parameter() (in module ALLCools._extract_allc) _chunk_annotation_executor() (RegionDS method), [1] _cleanup() (PairwiseDMG method), [1] _construct_tree() (ClusterMerge method), [1] _continuous_color_palette() (in module ALLCools.plot.color) _convert_to_id() (Gtf method), [1] _corr() (in module ALLCools.mcds.correlation) _corr_preprocess() (in module ALLCools.mcds.correlation) _count_data_to_xarray() (in module ALLCools.sandbox.motif.motif_scan) _count_single_allc() (in module ALLCools.count_matrix.mcad) _count_single_cmotif_bin_on_multiple_allc() (in module ALLCools.sandbox.motif.motif_scan) _create_model() (ConsensusClustering method), [1] _create_query_dmr_ds() (in module ALLCools.reptile.reptile) _create_query_region_ds() (in module ALLCools.reptile.reptile) _create_train_dmr_ds() (in module ALLCools.reptile.reptile) _create_train_region_ds() (in module ALLCools.reptile.reptile) _csr_matrix_to_anndata() (in module ALLCools.count_matrix.h5ad) _csr_matrix_to_dataarray() (in module ALLCools.count_matrix.mcds) _density_based_sample() (in module ALLCools.plot.utilities) _downsample_sample_count() (in module ALLCools.dmr.rms_test) _dump_sample() (REPTILE method), [1] _enhancer_bed() (ABCModel method), [1] _extract_allc_parallel() (in module ALLCools._extract_allc) _extract_coords() (in module ALLCools.plot.utilities) _filter_na_train() (REPTILE method), [1] _fimo_runner() (in module ALLCools.sandbox.motif.fimo) _fisher_exact() (in module ALLCools.mcds.region_ds) _generate_c_motif_database() (in module ALLCools.sandbox.motif.cmotif) _get_bam_chrom_index() (in module ALLCools._bam_to_allc) _get_chromosome_sequence_upper() (in module ALLCools._bam_to_allc) _get_data_and_label() (in module ALLCools.reptile.reptile) _get_e() (in module ALLCools.dmr.rms_test)

_get_motif_threshold() (in module ALLCools.motif.motifs) _hclust_to_scipy_linkage() (in module ALLCools.clustering.pvclust) _increase_soft_fd_limit() (in module ALLCools._merge_allc) _is_sqlite3() (in module ALLCools.plot.genome_track.GtfTrack) _kmeans_division() (in module ALLCools.pseudo_cell.pseudo_cell_kmeans) _leiden_runner() (in module ALLCools.clustering.ConsensusClustering) _make_count_table() (in module ALLCools.dmr.call_dms) _make_hypo_hyper_matrix() (in module ALLCools.dmr.parse_methylpy) _make_permutation_table() (in module ALLCools.dmr.rms_test) _make_tiny_axis_label() (in module ALLCools.plot.utilities) _map_to_sparse_chrom_bin() (in module ALLCools._allc_to_region_count) _mean() (in module ALLCools.mcds.correlation) _merge_allc_files_tabix() (in module ALLCools._merge_allc) _merge_allc_files_tabix_with_snp_info() (in module ALLCools._merge_allc) _merge_cg_strand() (in module ALLCools._extract_allc) _merge_gz_files() (in module ALLCools._extract_allc) _merge_pair() (ClusterMerge method), [1] _merge_pseudo_cell() (in module ALLCools.pseudo_cell.pseudo_cell_kmeans) _multi_seq_motif_scores() (MotifSet method), [1] _normalize_per_cell() (in module ALLCools.clustering.incremental_pca) _one_vs_rest_dmr_runner() (in module ALLCools.clustering.dmg) _open_single_dataset() (RegionDS class method), [1] _pairwise_dmg() (PairwiseDMG method), [1] _perform_rms_batch() (in module ALLCools.dmr.call_dms) _plot_cluster_dist() (MethylScrublet method), [1] _plot_enrichment_result() (in module ALLCools.clustering.feature_selection.feature_enrichment) _predict() (REPTILE method), [1] _predict_sample() (in module ALLCools.reptile.reptile) _prepare_track_config() (in module ALLCools.plot.genome_track._pygenometrack) _promoter_and_enhancer_bed() (ABCModel method), [1] _promoter_bed() (ABCModel method), [1] _r1_normalize() (in module ALLCools.clustering.ConsensusClustering) _r2_normalize() (in module ALLCools.clustering.ConsensusClustering) _raise_if_error() (PipedBamReader method) (PipedGzipReader method) _read_faidx() (in module ALLCools._bam_to_allc) _read_region_bed() (in module ALLCools.count_matrix.mcad) _read_single_allc() (in module ALLCools.dmr.call_dms) _read_snap_bins() (in module ALLCools.count_matrix.snap) _read_snap_genes() (in module ALLCools.count_matrix.snap) _read_snap_meta() (in module ALLCools.count_matrix.snap) _region_bed_sorted() (in module ALLCools.mcds.region_ds) _region_count_table_to_csr_npz() (in module ALLCools.count_matrix.mcds) _run_motif_scan_chunks() (MotifSet method), [1] _sample_fruit() (ContractedExamplerSampler method) _sample_pulp_dist() (ContractedExamplerSampler method) _save_cluster_adata() (PairwiseDMG method), [1] _scan_motif_local() (RegionDS method), [1] _scan_motif_over_fasta() (in module ALLCools.sandbox.motif.fimo) _scan_motifs_snakemake() (RegionDS method), [1] _select_corr_cutoff() (in module ALLCools.mcds.correlation) _select_dist_thresh() (ContractedExamplerSampler method) _select_longest_id() (Gtf method), [1] _single_ame_runner() (in module ALLCools.sandbox.motif.ame) _single_chrom_abc_score() (ABCModel method), [1] _single_chrom_activity_score() (ABCModel method), [1] _single_ovr_dmg() (in module ALLCools.clustering.dmg) _single_pairwise_dmg() (in module ALLCools.clustering.dmg) _single_seq_single_motif_max_score() (in module ALLCools.motif.motifs) _split_train_test_per_group() (in module ALLCools.clustering.ConsensusClustering) _standard_bed() (ABCModel method), [1] _std() (in module ALLCools.mcds.correlation) _str_to_bool() (in module ALLCools.__main__) _summarize_multi_leiden() (ConsensusClustering method), [1] _text_anno_scatter() (in module ALLCools.plot.text_anno_scatter) _train() (REPTILE method), [1] _transfer_bin_size() (in module ALLCools.utilities) _transform_single_h5ad() (in module ALLCools.count_matrix.h5ad) _translate_coord_name() (in module ALLCools.plot.utilities) _traverse() (ClusterMerge static method), [1] _tss_bed() (ABCModel method), [1] _tss_bin() (ABCModel method), [1] _unique (MultiDict attribute) _validate_region_name() (REPTILE method), [1] _verify_correlation_da() (in module ALLCools.mcds.correlation) _verify_dim() (MCDS method), [1]

A

ABCModel (class in ALLCools.abc) (class in ALLCools.abc.abc_score) activity_score_atac_mcg() (in module ALLCools.abc.abc_score) adata_to_df() (in module ALLCools.count_matrix.snap) add() (ContextCounter method) (StrandContextCounter method) add_ax_box() (in module ALLCools.plot) (in module ALLCools.plot.utilities) add_cell_metadata() (MCDS method), [1] add_data() (ConsensusClustering method), [1] add_data_range() (DataTrack method) add_data_track() (Session method) add_feature_cov_mean() (MCDS method), [1] add_feature_track() (Session method) add_mc_frac() (MCDS method), [1] add_mc_rate() (MCDS method), [1] aggregate_pairwise_dmg() (PairwiseDMG method), [1] aggregate_region_count_to_paired_anndata() (in module ALLCools.count_matrix.h5ad) allc_motif_scan() (in module ALLCools.sandbox.motif.motif_scan) allc_path_doc (in module ALLCools._doc) allc_paths_doc (in module ALLCools._doc) allc_table_doc (in module ALLCools._doc) allc_to_bigwig() (in module ALLCools._allc_to_bigwig) (in module ALLCools._allc_to_bigwig_new) allc_to_bigwig_register_subparser() (in module ALLCools.__main__) allc_to_region_count() (in module ALLCools._allc_to_region_count) allc_to_region_count_register_subparser() (in module ALLCools.__main__) ALLCools module ALLCools.__main__ module ALLCools._allc_to_bigwig module ALLCools._allc_to_bigwig_new module ALLCools._allc_to_region_count module ALLCools._bam_to_allc module ALLCools._doc module ALLCools._extract_allc module ALLCools._merge_allc module ALLCools._open module ALLCools._version module ALLCools.abc module ALLCools.abc.abc_score module ALLCools.api module ALLCools.clustering module ALLCools.clustering.art_of_tsne module ALLCools.clustering.balanced_pca module ALLCools.clustering.ClusterMerging module ALLCools.clustering.ConsensusClustering module ALLCools.clustering.dmg module ALLCools.clustering.doublets module ALLCools.clustering.doublets.coverage_doublets module ALLCools.clustering.doublets.scrublet module ALLCools.clustering.feature_selection module ALLCools.clustering.feature_selection.feature_enrichment module ALLCools.clustering.feature_selection.gene_panel_design module ALLCools.clustering.incremental_pca module ALLCools.clustering.mcad module ALLCools.clustering.pvclust module ALLCools.count_matrix module ALLCools.count_matrix.atac module ALLCools.count_matrix.dataset module ALLCools.count_matrix.h5ad module ALLCools.count_matrix.mcad module ALLCools.count_matrix.mcds module ALLCools.count_matrix.snap module ALLCools.count_matrix.zarr module ALLCools.dmr module ALLCools.dmr.call_dmr module ALLCools.dmr.call_dms module ALLCools.dmr.parse_methylpy module ALLCools.dmr.rms_test module ALLCools.gtf module ALLCools.gtf.Gtf module ALLCools.gtf.utilities module ALLCools.integration module ALLCools.integration.cca module

ALLCools.integration.confusion module ALLCools.integration.harmony module ALLCools.mcds module ALLCools.mcds.correlation module ALLCools.mcds.mcds module ALLCools.mcds.region_ds module ALLCools.mcds.utilities module ALLCools.motif module ALLCools.motif.default_motif_set module ALLCools.motif.motifs module ALLCools.motif.parse_meme module ALLCools.motif.snakemake module ALLCools.plot module ALLCools.plot.categorical_scatter module ALLCools.plot.color module ALLCools.plot.continuous_scatter module ALLCools.plot.contour module ALLCools.plot.decomposition module ALLCools.plot.dendro module ALLCools.plot.genome_track module ALLCools.plot.genome_track._pygenometrack module ALLCools.plot.genome_track.GtfTrack module ALLCools.plot.genome_track.HiCMatrixCoolTrack module ALLCools.plot.interactive_scatter module ALLCools.plot.qc_plots module ALLCools.plot.size module ALLCools.plot.sunburst module ALLCools.plot.text_anno_scatter module ALLCools.plot.utilities module ALLCools.pseudo_cell module ALLCools.pseudo_cell.pseudo_cell_kmeans module ALLCools.pseudo_cell.pseudo_cell_knn module ALLCools.reptile module ALLCools.reptile.reptile module ALLCools.sandbox module ALLCools.sandbox.balanced_knn module ALLCools.sandbox.igv module ALLCools.sandbox.igv.BaseClass module ALLCools.sandbox.igv.defaults module ALLCools.sandbox.igv.make_session module ALLCools.sandbox.igv.Session module ALLCools.sandbox.igv.Track module ALLCools.sandbox.motif module ALLCools.sandbox.motif.ame module ALLCools.sandbox.motif.cmotif module ALLCools.sandbox.motif.fimo module ALLCools.sandbox.motif.motif_scan module ALLCools.sandbox.motif.utilities module ALLCools.sandbox.scanorama module ALLCools.sandbox.sccaf module ALLCools.schema module ALLCools.schema.mcds_schema module ALLCools.table_to_allc module ALLCools.utilities module allocate_buffers() (Harmony method) ALLOW_QUANT_TYPES (in module ALLCools.count_matrix.dataset) ALPHA (in module ALLCools.sandbox.scanorama) ame() (in module ALLCools.sandbox.motif.ame) annotate_by_beds() (RegionDS method), [1] annotate_by_bigwigs() (RegionDS method), [1] (REPTILE method), [1] APPROX (in module ALLCools.sandbox.scanorama) AROUND_REGION (in module ALLCools.plot.genome_track.GtfTrack) art_of_tsne() (in module ALLCools.clustering.art_of_tsne) assemble() (in module ALLCools.sandbox.scanorama) auto_ml() (REPTILE static method), [1]

B

balance_knn_loop() (in module ALLCools.sandbox.balanced_knn) balanced_pca() (in module ALLCools.clustering) (in module ALLCools.clustering.balanced_pca) bam_to_allc() (in module ALLCools._bam_to_allc) bam_to_allc_register_subparser() (in module ALLCools.__main__) batch_allc_to_region_count() (in module ALLCools._allc_to_region_count) batch_bias() (in module ALLCools.sandbox.scanorama) batch_correct_pc() (in module ALLCools.sandbox.scanorama) BATCH_SIZE (in module ALLCools.sandbox.scanorama) BGZIP (in module ALLCools._open) bhattacharyya_distance() (in module ALLCools.sandbox.sccaf) bhattacharyya_matrix() (in module ALLCools.sandbox.sccaf)

bin_sf() (in module ALLCools.count_matrix.dataset) (in module ALLCools.count_matrix.mcad) bin_sizes_doc (in module ALLCools._doc) binarize_doc (in module ALLCools._doc) binarize_matrix() (in module ALLCools.clustering) (in module ALLCools.clustering.mcad) binary_accuracy() (in module ALLCools.sandbox.sccaf) binary_count() (in module ALLCools.utilities) BOOLEAN_PROPERTIES (GtfTrack attribute) (HiCMatrixCoolTrack attribute) (SpacerTrack attribute) (XAxisTrack attribute) bw_bin_sizes_doc (in module ALLCools._doc)

C

calculate() (ABCModel method), [1] calculate_blacklist_region() (in module ALLCools.clustering.doublets.coverage_doublets) calculate_direct_confusion() (in module ALLCools.integration) (in module ALLCools.integration.confusion) calculate_doublet_scores() (MethylScrublet method), [1] calculate_gch_rate() (in module ALLCools.mcds.utilities) calculate_hvf() (MCDS method), [1] calculate_hvf_svr() (MCDS method), [1] calculate_posterior_mc_frac() (in module ALLCools.mcds.utilities) calculate_posterior_mc_frac_lazy() (in module ALLCools.mcds.utilities) calculate_pv() (in module ALLCools.count_matrix.dataset) calculate_residual() (in module ALLCools.dmr.rms_test) calculate_threshold() (MotifSet method), [1] call_dmr() (in module ALLCools.dmr) (in module ALLCools.dmr.call_dmr) call_dms() (in module ALLCools.dmr) (in module ALLCools.dmr.call_dms) call_doublets() (MethylScrublet method), [1] call_enhancers() (REPTILE method), [1] categorical_scatter() (in module ALLCools.plot) (in module ALLCools.plot.categorical_scatter) cell_sf() (in module ALLCools.count_matrix.dataset) ch (in module ALLCools.integration.harmony) check_convergence() (Harmony method) check_custom_dim_name_and_return() (in module ALLCools.schema.mcds_schema) check_datasets() (in module ALLCools.sandbox.scanorama) check_file_exists() (PlotTracks static method), [1] check_snakemake_success() (in module ALLCools.motif.snakemake) check_tbi_chroms() (in module ALLCools.utilities) chrom_dict_to_id_index() (in module ALLCools.utilities) chrom_size_path (RegionDS property), [1] chrom_size_path_doc (in module ALLCools._doc) clip_too_large_cov() (in module ALLCools.count_matrix.mcds) close() (_ALLC method) (Closing method) (PipedBamReader method) (PipedBamWriter method) (PipedGzipReader method) (PipedGzipWriter method)

close_files() (PlotTracks method), [1] Closing (class in ALLCools._open) cluster() (Harmony method) cluster_adjmat() (in module ALLCools.sandbox.sccaf) cluster_enriched_features() (in module ALLCools.clustering) (in module ALLCools.clustering.feature_selection.feature_enrichment) ClusterMerge (class in ALLCools.clustering) (class in ALLCools.clustering.ClusterMerging) cm2inch() (PlotTracks static method), [1] collapse_replicates() (in module ALLCools.dmr) (in module ALLCools.dmr.call_dmr) color_long (in module ALLCools.sandbox.sccaf) COMPLIMENT_BASE (in module ALLCools.utilities) compress_level_doc (in module ALLCools._doc) compute_neighbors() (ConsensusClustering method), [1] compute_objective() (Harmony method) confusion_matrix() (in module ALLCools.sandbox.sccaf) connect() (in module ALLCools.sandbox.scanorama) ConsensusClustering (class in ALLCools.clustering) (class in ALLCools.clustering.ConsensusClustering) ContextCounter (class in ALLCools._allc_to_bigwig_new) continuous_scatter() (in module ALLCools.plot) (in module ALLCools.plot.continuous_scatter) ContractedExamplerSampler (class in ALLCools.pseudo_cell.pseudo_cell_knn) convert_mcds_to_zarr_register_subparser() (in module ALLCools.__main__) convert_to_zarr() (in module ALLCools.mcds.utilities) COORD_ALLOW_VALUES (in module ALLCools.schema.mcds_schema) corr() (in module ALLCools.mcds.correlation) correct() (in module ALLCools.sandbox.scanorama) correct_scanpy() (in module ALLCools.sandbox.scanorama) count_single_region_set() (in module ALLCools.count_matrix.dataset) count_single_zarr() (in module ALLCools.count_matrix.dataset) CountQuantifier (class in ALLCools.count_matrix.dataset) cov_cutoff_doc (in module ALLCools._doc) coverage_doublets() (in module ALLCools.clustering.doublets) (in module ALLCools.clustering.doublets.coverage_doublets) cpu_basic_doc (in module ALLCools._doc) create_gtf_db() (in module ALLCools.gtf) (in module ALLCools.gtf.Gtf) cutoff_vs_cell_remain() (in module ALLCools.plot.qc_plots)

D

DATA_TRACK_DEFAULT (in module ALLCools.sandbox.igv.defaults) dataframe_to_allc() (in module ALLCools.table_to_allc) DataRange (class in ALLCools.sandbox.igv.BaseClass) DATARANGE_DEFAULT (in module ALLCools.sandbox.igv.defaults) dataset_to_adata() (in module ALLCools.count_matrix.zarr) dataset_to_array() (in module ALLCools.count_matrix.zarr) DataTrack (class in ALLCools.sandbox.igv.Track) DEFAULT_BED_COLOR (in module ALLCools.plot.genome_track.GtfTrack) DEFAULT_DISPLAY_BED (in module ALLCools.plot.genome_track.GtfTrack) DEFAULT_FIGURE_WIDTH (in module ALLCools.plot.genome_track._pygenometrack) DEFAULT_MARGINS (in module ALLCools.plot.genome_track._pygenometrack) DEFAULT_MATRIX_COLORMAP (in module ALLCools.plot.genome_track.HiCMatrixCoolTrack) DEFAULT_MAX_ALLC (in module ALLCools._merge_allc) DEFAULT_MCDS_DTYPE (in module ALLCools.count_matrix.mcds) DEFAULT_MOTIF_DIR (in module ALLCools.motif.parse_meme) DEFAULT_TRACK_HEIGHT (in module ALLCools.plot.genome_track._pygenometrack) DEFAULT_WIDTH_RATIOS (in module ALLCools.plot.genome_track._pygenometrack) DEFAULTS_PROPERTIES (GtfTrack attribute) (HiCMatrixCoolTrack attribute) (SpacerTrack attribute) (XAxisTrack attribute)

Dendrogram (class in ALLCools.clustering) (class in ALLCools.clustering.pvclust) density_contour() (in module ALLCools.plot.contour) DESCRIPTION (in module ALLCools.__main__) determine_datasets() (in module ALLCools.count_matrix.dataset) determine_engine() (in module ALLCools.mcds.utilities) dict_greedy_search() (in module ALLCools.clustering.feature_selection.gene_panel_design) dimensionality_reduce() (in module ALLCools.sandbox.scanorama) DIMRED (in module ALLCools.sandbox.scanorama) dispersion() (in module ALLCools.sandbox.scanorama) DISPLAY_BED_SYNONYMOUS (in module ALLCools.plot.genome_track.GtfTrack) DISPLAY_BED_VALID (in module ALLCools.plot.genome_track.GtfTrack) dmr_model (REPTILE property), [1] doc_params() (in module ALLCools._doc) downsample_table() (in module ALLCools.dmr.rms_test) dump() (ReproduciblePCA method), [1] dump_bigwigs() (REPTILE method), [1]

E

EPILOG (in module ALLCools.__main__) eu_distance() (in module ALLCools.sandbox.sccaf)

extract_allc() (in module ALLCools._extract_allc) extract_context_allc_register_subparser() (in module ALLCools.__main__)

F

FEATURE_TRACK_DEFAULT (in module ALLCools.sandbox.igv.defaults) FEATURE_TRACK_FORMATS (in module ALLCools.sandbox.igv.defaults) FeatureTrack (class in ALLCools.sandbox.igv.Track) fill_table() (in module ALLCools.sandbox.scanorama) filter_feature_by_cov_mean() (MCDS method), [1] filter_regions() (in module ALLCools.clustering) (in module ALLCools.clustering.mcad) final_evaluation() (ConsensusClustering method), [1] find_alignments() (in module ALLCools.sandbox.scanorama) find_alignments_table() (in module ALLCools.sandbox.scanorama) find_high_resolution() (in module ALLCools.sandbox.sccaf) fit() (Dendrogram method), [1] (IncrementalPCA method) (MethylScrublet method), [1] (NearestNeighbors method) (REPTILE method), [1]

fit_predict() (ClusterMerge method), [1] (ConsensusClustering method), [1] (PairwiseDMG method), [1] fit_transform() (IncrementalPCA method) FLOAT_PROPERTIES (GtfTrack attribute) (HiCMatrixCoolTrack attribute) (SpacerTrack attribute) (XAxisTrack attribute) FORMAT (in module ALLCools.plot.genome_track._pygenometrack) format() (NiceFormatter method) formatter (in module ALLCools.integration.harmony) from_bed() (RegionDS class method), [1]

G

generate_chrom_bin_bed_dataframe() (in module ALLCools.utilities) generate_cmotif_database() (in module ALLCools.sandbox.motif.cmotif) generate_dataset() (in module ALLCools.count_matrix.dataset) generate_dataset_chunk_size_doc (in module ALLCools._doc) generate_dataset_doc (in module ALLCools._doc) generate_dataset_obs_dim_doc (in module ALLCools._doc) generate_dataset_quantifiers_doc (in module ALLCools._doc) generate_dataset_regions_doc (in module ALLCools._doc) generate_dataset_register_subparser() (in module ALLCools.__main__) generate_mcad() (in module ALLCools.count_matrix.mcad) generate_mcad_register_subparser() (in module ALLCools.__main__) generate_mcds() (in module ALLCools.count_matrix.mcds) generate_mcds_register_subparser() (in module ALLCools.__main__) generate_pseudo_cells() (in module ALLCools.pseudo_cell.pseudo_cell_kmeans) (in module ALLCools.pseudo_cell.pseudo_cell_knn) generate_pseudo_cells_kmeans() (in module ALLCools.pseudo_cell) generate_pseudo_cells_knn() (in module ALLCools.pseudo_cell) generate_region_ds() (REPTILE method), [1] genome_region_chunks() (in module ALLCools.utilities) get_adata() (MCDS method), [1] get_allc_chroms() (in module ALLCools.utilities) get_available_tracks() (PlotTracks static method), [1] get_bed() (RegionDS method), [1] get_bed_handler() (GtfTrack method) get_bed_interval() (ReadGtf method) get_bin_id() (in module ALLCools.utilities) get_connection_matrix() (in module ALLCools.sandbox.sccaf) get_context() (in module ALLCools.table_to_allc) get_coords() (RegionDS method), [1] get_corr_table() (in module ALLCools.mcds.correlation) get_default_motif_set() (in module ALLCools.motif) (in module ALLCools.motif.parse_meme)

get_distance_matrix() (in module ALLCools.sandbox.sccaf) get_fasta() (RegionDS method), [1] get_feature() (RegionDS method), [1] get_feature_bed() (MCDS method), [1] get_gene_exons() (Gtf method), [1] get_gene_feature() (Gtf method), [1] get_gene_id_by_name() (Gtf method), [1] get_gene_length() (Gtf method), [1] get_gene_name() (Gtf method), [1] get_gene_promoter() (Gtf method), [1] get_gene_transcripts() (Gtf method), [1] get_gene_tss() (Gtf method), [1] get_hypo_hyper_index() (RegionDS method), [1] get_knn_graph() (MethylScrublet method), [1] get_kv_dict() (in module ALLCools.plot.color) get_md5() (in module ALLCools.utilities) get_mean_dispersion() (in module ALLCools.mcds.utilities) get_pairwise_differential_index() (RegionDS method), [1] get_panel_int() (in module ALLCools.sandbox.igv.Session) get_pc_centers() (in module ALLCools.clustering) (in module ALLCools.clustering.balanced_pca) get_score_adata() (MCDS method), [1] get_strand() (in module ALLCools.table_to_allc) get_strand_and_context() (in module ALLCools.table_to_allc) get_topmarkers() (in module ALLCools.sandbox.sccaf) get_tracks_height() (PlotTracks method), [1] gs_idxs (in module ALLCools.sandbox.scanorama) Gtf (class in ALLCools.gtf) (class in ALLCools.gtf.Gtf) GtfTrack (class in ALLCools.plot.genome_track.GtfTrack) guess_filetype() (PlotTracks static method), [1]

H

handle_zeros_in_scale() (in module ALLCools.sandbox.scanorama) harmonize() (Harmony method) Harmony (class in ALLCools.integration.harmony) has_bai() (in module ALLCools._open) has_tabix() (in module ALLCools._open)

hex_to_rgb_text() (in module ALLCools.sandbox.igv.make_session) HiCMatrixCoolTrack (class in ALLCools.plot.genome_track.HiCMatrixCoolTrack) HiddenAttributes (class in ALLCools.sandbox.igv.BaseClass) highly_variable_methylation_feature() (in module ALLCools.mcds.utilities) HVG (in module ALLCools.sandbox.scanorama)

I

idx_doc (in module ALLCools._doc) incremental_cca() (in module ALLCools.integration) (in module ALLCools.integration.cca) IncrementalPCA (class in ALLCools.clustering.incremental_pca) init_cluster() (Harmony method) install_r_package() (in module ALLCools.clustering.pvclust) INTEGER_PROPERTIES (GtfTrack attribute) (HiCMatrixCoolTrack attribute) (SpacerTrack attribute) (XAxisTrack attribute)

integrate() (in module ALLCools.sandbox.scanorama) integrate_scanpy() (in module ALLCools.sandbox.scanorama) interactive_scatter() (in module ALLCools.plot) (in module ALLCools.plot.interactive_scatter) interpret_alignments() (in module ALLCools.sandbox.scanorama) is_gz_file() (in module ALLCools.utilities) iter_array() (RegionDS method), [1] iter_index() (RegionDS method), [1] IUPAC_TABLE (in module ALLCools.utilities)

J

jensen_shannon_distance() (in module ALLCools.sandbox.balanced_knn)

jensen_shannon_divergence() (in module ALLCools.sandbox.balanced_knn)

K

kneighbors() (NearestNeighbors method) kneighbors_graph() (NearestNeighbors method)

KNN (in module ALLCools.sandbox.scanorama) knn_balance() (in module ALLCools.sandbox.balanced_knn)

L

leiden_centroids() (in module ALLCools.integration.harmony) level_one_palette() (in module ALLCools.plot.color) level_two_palette() (in module ALLCools.plot.color) location (RegionDS property), [1] log (in module ALLCools.__main__) (in module ALLCools._allc_to_bigwig) (in module ALLCools._bam_to_allc) (in module ALLCools._merge_allc) (in module ALLCools.mcds.utilities) (in module ALLCools.plot.genome_track._pygenometrack) (in module ALLCools.plot.genome_track.HiCMatrixCoolTrack)

log_scale() (in module ALLCools.clustering) (in module ALLCools.clustering.balanced_pca) logger (in module ALLCools.integration.harmony) lsi() (in module ALLCools.clustering) (in module ALLCools.clustering.mcad)

M

main() (in module ALLCools.__main__) make_obs_df_var_df() (in module ALLCools.mcds.mcds) make_session() (in module ALLCools.sandbox.igv.make_session) make_unique() (in module ALLCools.sandbox.sccaf) mc_context_mcad_doc (in module ALLCools._doc) mc_contexts_doc (in module ALLCools._doc) mc_gene_panel_greedy_search() (in module ALLCools.clustering.feature_selection.gene_panel_design) MCDS (class in ALLCools.mcds) (class in ALLCools.mcds.mcds) mcds_to_adata() (ReproduciblePCA method), [1] mcds_to_adata_with_pc() (ReproduciblePCA method), [1] meme_motif_file_to_dict() (in module ALLCools.sandbox.motif.utilities) meme_to_homer() (in module ALLCools.sandbox.motif.utilities) meme_to_pfm_dict() (in module ALLCools.sandbox.motif.utilities) merge_allc_files() (in module ALLCools._merge_allc) merge_allc_register_subparser() (in module ALLCools.__main__) merge_cluster() (in module ALLCools.sandbox.sccaf) (MCDS method), [1] merge_datasets() (in module ALLCools.sandbox.scanorama) methylpy_to_region_ds() (in module ALLCools.dmr) (in module ALLCools.dmr.parse_methylpy) MethylScrublet (class in ALLCools.clustering.doublets) (class in ALLCools.clustering.doublets.scrublet) mnn_graph() (NearestNeighbors method) mode_mc_cov() (in module ALLCools.table_to_allc) mode_mc_frac_cov() (in module ALLCools.table_to_allc) mode_mc_frac_mc() (in module ALLCools.table_to_allc) mode_mc_frac_pseudo_count() (in module ALLCools.table_to_allc) mode_mc_frac_uc() (in module ALLCools.table_to_allc) mode_mc_uc() (in module ALLCools.table_to_allc) mode_uc_cov() (in module ALLCools.table_to_allc) module ALLCools ALLCools.__main__ ALLCools._allc_to_bigwig ALLCools._allc_to_bigwig_new ALLCools._allc_to_region_count ALLCools._bam_to_allc ALLCools._doc ALLCools._extract_allc ALLCools._merge_allc ALLCools._open ALLCools._version ALLCools.abc ALLCools.abc.abc_score ALLCools.api ALLCools.clustering ALLCools.clustering.art_of_tsne ALLCools.clustering.balanced_pca ALLCools.clustering.ClusterMerging ALLCools.clustering.ConsensusClustering ALLCools.clustering.dmg ALLCools.clustering.doublets ALLCools.clustering.doublets.coverage_doublets ALLCools.clustering.doublets.scrublet ALLCools.clustering.feature_selection ALLCools.clustering.feature_selection.feature_enrichment ALLCools.clustering.feature_selection.gene_panel_design ALLCools.clustering.incremental_pca ALLCools.clustering.mcad ALLCools.clustering.pvclust ALLCools.count_matrix ALLCools.count_matrix.atac ALLCools.count_matrix.dataset ALLCools.count_matrix.h5ad ALLCools.count_matrix.mcad ALLCools.count_matrix.mcds ALLCools.count_matrix.snap ALLCools.count_matrix.zarr ALLCools.dmr ALLCools.dmr.call_dmr ALLCools.dmr.call_dms ALLCools.dmr.parse_methylpy ALLCools.dmr.rms_test ALLCools.gtf ALLCools.gtf.Gtf ALLCools.gtf.utilities ALLCools.integration ALLCools.integration.cca ALLCools.integration.confusion ALLCools.integration.harmony ALLCools.mcds ALLCools.mcds.correlation ALLCools.mcds.mcds ALLCools.mcds.region_ds ALLCools.mcds.utilities ALLCools.motif ALLCools.motif.default_motif_set ALLCools.motif.motifs ALLCools.motif.parse_meme ALLCools.motif.snakemake ALLCools.plot ALLCools.plot.categorical_scatter ALLCools.plot.color ALLCools.plot.continuous_scatter ALLCools.plot.contour ALLCools.plot.decomposition ALLCools.plot.dendro ALLCools.plot.genome_track ALLCools.plot.genome_track._pygenometrack ALLCools.plot.genome_track.GtfTrack ALLCools.plot.genome_track.HiCMatrixCoolTrack ALLCools.plot.interactive_scatter ALLCools.plot.qc_plots ALLCools.plot.size ALLCools.plot.sunburst ALLCools.plot.text_anno_scatter ALLCools.plot.utilities ALLCools.pseudo_cell ALLCools.pseudo_cell.pseudo_cell_kmeans ALLCools.pseudo_cell.pseudo_cell_knn ALLCools.reptile ALLCools.reptile.reptile ALLCools.sandbox ALLCools.sandbox.balanced_knn ALLCools.sandbox.igv ALLCools.sandbox.igv.BaseClass ALLCools.sandbox.igv.defaults ALLCools.sandbox.igv.make_session ALLCools.sandbox.igv.Session ALLCools.sandbox.igv.Track ALLCools.sandbox.motif ALLCools.sandbox.motif.ame ALLCools.sandbox.motif.cmotif ALLCools.sandbox.motif.fimo ALLCools.sandbox.motif.motif_scan ALLCools.sandbox.motif.utilities ALLCools.sandbox.scanorama ALLCools.sandbox.sccaf ALLCools.schema ALLCools.schema.mcds_schema ALLCools.table_to_allc ALLCools.utilities

moe_correct_ridge() (in module ALLCools.integration.harmony) Motif (class in ALLCools.motif.motifs) motif_enrichment() (RegionDS method), [1] MotifSet (class in ALLCools.motif) (class in ALLCools.motif.motifs) msample() (in module ALLCools.sandbox.sccaf) multi_leiden_clustering() (ConsensusClustering method), [1] MultiDict (class in ALLCools.plot.genome_track._pygenometrack)

N

N_ITER (in module ALLCools.sandbox.scanorama) n_samples (NearestNeighbors property) N_SITES_PATTERN (in module ALLCools.motif.parse_meme) NearestNeighbors (class in ALLCools.sandbox.balanced_knn) NECESSARY_PROPERTIES (GtfTrack attribute) (HiCMatrixCoolTrack attribute) (SpacerTrack attribute) (XAxisTrack attribute)

NiceFormatter (class in ALLCools.__main__) nn() (in module ALLCools.sandbox.scanorama) nn_approx() (in module ALLCools.sandbox.scanorama) normalize_confmat1() (in module ALLCools.sandbox.sccaf) normalize_confmat2() (in module ALLCools.sandbox.sccaf)

O

obj_to_str() (in module ALLCools.mcds.utilities) object_coords_to_string() (RegionDS method), [1] obs_dim (MCDS property), [1] obs_names (MCDS property), [1] one_vs_rest_dmg() (in module ALLCools.clustering) (in module ALLCools.clustering.dmg) open() (MCDS class method), [1] (RegionDS class method), [1]

open_allc() (in module ALLCools._open) open_bam() (in module ALLCools._open) open_gz() (in module ALLCools._open) open_zarr() (in module ALLCools.count_matrix.zarr) OPTIONS_TXT (GtfTrack attribute) (HiCMatrixCoolTrack attribute)

P

PACKAGE_DIR (in module ALLCools.motif.parse_meme) pairwise_dmr_motif_enrichment() (RegionDS method), [1] PairwiseDMG (class in ALLCools.clustering) (class in ALLCools.clustering.dmg) PairwiseDMGCriterion (class in ALLCools.clustering) (class in ALLCools.clustering.ClusterMerging) palplot() (in module ALLCools.plot.color) Panel (class in ALLCools.sandbox.igv.BaseClass) PanelLayout (class in ALLCools.sandbox.igv.BaseClass) parse_chrom_size() (in module ALLCools.utilities) parse_dtype() (in module ALLCools.utilities) parse_file_paths() (in module ALLCools.utilities) parse_header_lines() (in module ALLCools.motif.parse_meme) parse_mc_pattern() (in module ALLCools.utilities) parse_meme_database() (in module ALLCools.motif.parse_meme) parse_motif() (in module ALLCools.motif.parse_meme) parse_tracks() (PlotTracks method), [1] pc_transform() (ReproduciblePCA method), [1] pca() (MethylScrublet method), [1] pcolormesh_45deg() (HiCMatrixCoolTrack method) per_cell_accuracy() (in module ALLCools.sandbox.sccaf) per_cluster_accuracy() (in module ALLCools.sandbox.sccaf) permute_root_mean_square_test() (in module ALLCools.dmr.rms_test) PERPLEXITY (in module ALLCools.sandbox.scanorama) PIGZ (in module ALLCools._open) PipedBamReader (class in ALLCools._open) PipedBamWriter (class in ALLCools._open) PipedGzipReader (class in ALLCools._open) PipedGzipWriter (class in ALLCools._open) plot() (HiCMatrixCoolTrack method) (MethylScrublet method), [1] (PlotTracks method), [1] (SpacerTrack method) (XAxisTrack method) plot_before_after() (ConsensusClustering method), [1] plot_color_legend() (in module ALLCools.plot.color)

plot_colorbar() (in module ALLCools.plot.color) plot_decomp_scatters() (in module ALLCools.plot) (in module ALLCools.plot.decomposition) plot_dendrogram() (in module ALLCools.plot) (in module ALLCools.plot.dendro) plot_dispersion() (in module ALLCools.plot.qc_plots) plot_hvf_selection() (in module ALLCools.plot.qc_plots) plot_leiden_cases() (ConsensusClustering method), [1] plot_merge_process() (ConsensusClustering method), [1] plot_on_plate() (in module ALLCools.plot.qc_plots) plot_pfm() (in module ALLCools.sandbox.motif.utilities) plot_sizebar() (in module ALLCools.plot.size) plot_steps() (ConsensusClustering method), [1] plot_vlines() (PlotTracks method), [1] plot_y_axis() (HiCMatrixCoolTrack method) (SpacerTrack method) (XAxisTrack method) PlotTracks (class in ALLCools.plot.genome_track) (class in ALLCools.plot.genome_track._pygenometrack) POSSIBLE_PROPERTIES (GtfTrack attribute) (HiCMatrixCoolTrack attribute) (SpacerTrack attribute) (XAxisTrack attribute) predict() (PairwiseDMGCriterion method), [1] (REPTILE method), [1] prepare_config() (in module ALLCools.plot.genome_track) (in module ALLCools.plot.genome_track._pygenometrack) prepare_motif_scan_snakemake() (in module ALLCools.motif.snakemake) prepare_training_input() (REPTILE method), [1] preprocess_bed() (in module ALLCools.abc.abc_score) PRESERVED_DIMS (in module ALLCools.schema.mcds_schema) print_elapsed() (PlotTracks static method), [1] PROCESS (in module ALLCools._merge_allc) process_data() (in module ALLCools.sandbox.scanorama) profile_allc() (in module ALLCools.utilities) profile_allc_register_subparser() (in module ALLCools.__main__)

Q

Quant (class in ALLCools.count_matrix.dataset)

query_dmr_ds (REPTILE property), [1] query_region_ds (REPTILE property), [1]

R

read() (PipedBamReader method) (PipedGzipReader method) read_gtf() (in module ALLCools.gtf) (in module ALLCools.gtf.utilities) read_line() (CountQuantifier method) read_snap() (in module ALLCools.count_matrix.snap) ReadGtf (class in ALLCools.plot.genome_track.GtfTrack) readline() (_ALLC method) (PipedBamReader method) (PipedGzipReader method) reduce_dimensionality() (in module ALLCools.sandbox.scanorama) reference_fasta_doc (in module ALLCools._doc) region_bed_names_doc (in module ALLCools._doc) region_bed_path_mcad_doc (in module ALLCools._doc) region_bed_paths_doc (in module ALLCools._doc) region_correlation() (in module ALLCools.mcds.correlation) region_dim (RegionDS property), [1] region_doc (in module ALLCools._doc) region_model (REPTILE property), [1]

RegionDS (class in ALLCools.mcds) (class in ALLCools.mcds.region_ds) remove_additional_chrom_doc (in module ALLCools._doc) remove_black_list_region() (in module ALLCools.clustering) (in module ALLCools.clustering.mcad) (MCDS method), [1] remove_chromosome() (MCDS method), [1] ReproduciblePCA (class in ALLCools.clustering) (class in ALLCools.clustering.balanced_pca) REPTILE (class in ALLCools.reptile) (class in ALLCools.reptile.reptile) Resource (class in ALLCools.sandbox.igv.BaseClass) Resources (class in ALLCools.sandbox.igv.BaseClass) result() (Harmony method) reverse_complement() (in module ALLCools.utilities) rna_table_doc (in module ALLCools._doc) rnn_graph() (NearestNeighbors method) run_BayesianGaussianMixture() (in module ALLCools.sandbox.sccaf) run_harmony() (in module ALLCools.integration.harmony)

S

safe_entropy() (in module ALLCools.integration.harmony) sample_contracted_examplers() (ContractedExamplerSampler method) sample_dmr_motif_enrichment() (RegionDS method), [1] sample_pseudo_cells() (in module ALLCools.pseudo_cell.pseudo_cell_knn) save() (ConsensusClustering method), [1] (Dendrogram method), [1] (RegionDS method), [1] save_motif_chunks() (in module ALLCools.motif.snakemake) scale() (ReproduciblePCA method), [1] scan_motifs() (MotifSet method), [1] (RegionDS method), [1] scan_single_bw() (in module ALLCools.abc.abc_score) SCCAF_assessment() (in module ALLCools.sandbox.sccaf) SCCAF_optimize() (in module ALLCools.sandbox.sccaf) SCCAF_optimize_all() (in module ALLCools.sandbox.sccaf) select_confusion_pairs() (in module ALLCools.clustering) (in module ALLCools.clustering.ConsensusClustering) self_projection() (in module ALLCools.sandbox.sccaf) Session (class in ALLCools.sandbox.igv.Session) set_properties_defaults() (GtfTrack method) (HiCMatrixCoolTrack method) setup_logging() (in module ALLCools.__main__) SIGMA (in module ALLCools.sandbox.scanorama) significant_pc_test() (in module ALLCools.clustering) (in module ALLCools.clustering.balanced_pca) simple_cca() (in module ALLCools.integration) (in module ALLCools.integration.cca) simple_violin() (in module ALLCools.plot.qc_plots) simulate_doublets() (MethylScrublet method), [1] single_meme_txt_to_pfm_df() (in module ALLCools.sandbox.motif.utilities) single_supervise_evaluation() (in module ALLCools.clustering.ConsensusClustering) smart_number_format() (in module ALLCools.plot.utilities) SNAP_BD_FIELDS (in module ALLCools.count_matrix.snap)

snap_to_xarray() (in module ALLCools.count_matrix.snap) snap_to_zarr() (in module ALLCools.count_matrix.snap) snp_doc (in module ALLCools._doc) sort_df_by_order_dict() (in module ALLCools.sandbox.igv.make_session) SPACE_PATTERN (in module ALLCools.motif.parse_meme) SpacerTrack (class in ALLCools.plot.genome_track._pygenometrack) split_meme_motif_file() (in module ALLCools.sandbox.motif.utilities) split_strand_doc (in module ALLCools._doc) standardize_allc() (in module ALLCools.utilities) standardize_allc_register_subparser() (in module ALLCools.__main__) straight_branch() (in module ALLCools.plot.dendro) StrandContextCounter (class in ALLCools._allc_to_bigwig_new) strandness_doc (in module ALLCools._doc) STRING_PROPERTIES (GtfTrack attribute) (HiCMatrixCoolTrack attribute) (SpacerTrack attribute) (XAxisTrack attribute) subset_db() (Gtf method), [1] subset_gtf() (in module ALLCools.gtf) (in module ALLCools.gtf.utilities) success_vs_fail() (in module ALLCools.plot.qc_plots) summary() (CountQuantifier method) sunbrust() (in module ALLCools.plot) (in module ALLCools.plot.sunburst) supervise_learning() (ConsensusClustering method), [1] SUPPORTED_ENDINGS (GtfTrack attribute) (HiCMatrixCoolTrack attribute) (SpacerTrack attribute) (XAxisTrack attribute) SYNONYMOUS_PROPERTIES (GtfTrack attribute) (HiCMatrixCoolTrack attribute) (SpacerTrack attribute) (XAxisTrack attribute)

T

tabix_allc() (in module ALLCools.utilities) tabix_allc_register_subparser() (in module ALLCools.__main__) TABLE_REQUIRED_FIELDS (in module ALLCools.sandbox.igv.defaults) table_to_allc() (in module ALLCools.table_to_allc) table_to_allc_add_chr (in module ALLCools._doc) table_to_allc_chrom (in module ALLCools._doc) table_to_allc_chunk_size (in module ALLCools._doc) table_to_allc_context (in module ALLCools._doc) table_to_allc_cov (in module ALLCools._doc) table_to_allc_doc (in module ALLCools._doc) table_to_allc_fasta_path (in module ALLCools._doc) table_to_allc_header (in module ALLCools._doc) table_to_allc_input_path (in module ALLCools._doc) table_to_allc_mc (in module ALLCools._doc) table_to_allc_mc_frac (in module ALLCools._doc) table_to_allc_num_downstream_bases (in module ALLCools._doc) table_to_allc_num_upstream_bases (in module ALLCools._doc) table_to_allc_output_prefix (in module ALLCools._doc) table_to_allc_pos (in module ALLCools._doc) table_to_allc_pseudo_count (in module ALLCools._doc) table_to_allc_register_subparser() (in module ALLCools.__main__) table_to_allc_sep (in module ALLCools._doc)

table_to_allc_sort (in module ALLCools._doc) table_to_allc_strand (in module ALLCools._doc) table_to_allc_uc (in module ALLCools._doc) tf_idf() (in module ALLCools.clustering.mcad) tight_hue_range() (in module ALLCools.plot.continuous_scatter) (in module ALLCools.plot.utilities) to_region_ds() (MCDS method), [1] Track (class in ALLCools.sandbox.igv.BaseClass) TRACK_REQUIRED_KEYS (in module ALLCools.sandbox.igv.defaults) TRACK_TYPE (GtfTrack attribute) (HiCMatrixCoolTrack attribute) (SpacerTrack attribute) (XAxisTrack attribute) train_dmr_ds (REPTILE property), [1] train_dmr_model() (REPTILE method), [1] train_region_ds (REPTILE property), [1] train_region_model() (REPTILE method), [1] train_test_split_per_type() (in module ALLCools.sandbox.sccaf) transform() (in module ALLCools.sandbox.scanorama) (IncrementalPCA method) tsne() (in module ALLCools.clustering) (in module ALLCools.clustering.art_of_tsne)

U

update_dataset_config() (in module ALLCools.mcds.utilities)

update_R() (Harmony method)

V

validate_environment() (in module ALLCools.__main__) var_dim (MCDS property), [1] var_names (MCDS property), [1]

VERBOSE (in module ALLCools.sandbox.scanorama) version (in module ALLCools._version) version_tuple (in module ALLCools._version)

W

write() (PipedBamWriter method) (PipedGzipWriter method)

write_dataset() (MCDS method), [1] write_entry() (in module ALLCools._allc_to_bigwig_new) write_ordered_chunks() (in module ALLCools.mcds.utilities)

X

XAxisTrack (class in ALLCools.plot.genome_track._pygenometrack)

Z

zoom_ax() (in module ALLCools.plot.utilities)

zoom_min_max() (in module ALLCools.plot.utilities)