Index A | C | D | F | G | H | I | L | M | P | R | S | T | V | W A AbstractArray (class in modality.reduction) aggregate_bygroup() (modality.contig_dataset.ContigDataset method) assign_fractions() (modality.contig_dataset.ContigDataset method) assign_text_nucleotide_contexts() (modality.contig_dataset.ContigDataset method) at_mincoverage() (modality.contig_dataset.ContigDataset method) C call_dmrs() (in module modality.dmr) cast_result() (in module modality.contig_dataset) cast_xrattr() (in module modality.contig_dataset) catplot() (in module modality.plot_features) chunk_ranges_core() (in module modality.reduction) chunked_generator() (in module modality.utils) combine_dataset_attrs() (in module modality.contig_dataset) compose_dataset_ranges() (in module modality.utils) compute_correlation_matrix() (modality.contig_dataset.ContigDataset method) compute_histogram() (modality.contig_dataset.ContigDataset method) compute_pearson_matrix() (modality.contig_dataset.ContigDataset method) concat_contig_datasets() (in module modality.contig_dataset) conditional_dataframe_to_pyranges() (in module modality.annotation) ContigDataset (class in modality.contig_dataset) count_non_nan() (in module modality.reduction) create_trinucleotide_dict() (in module modality.utils) D dataframe_to_pyranges() (in module modality.annotation) default_position_mask() (in module modality.ranges) displot() (in module modality.plot_features) dmr_wrapper() (in module modality.dmr) ds (modality.contig_dataset.ContigDataset attribute) F filter_warnings() (in module modality.utils) from_dict() (modality.contig_dataset.ContigDataset class method) from_run_configs() (modality.contig_dataset.ContigDataset class method) from_zarrz() (modality.contig_dataset.ContigDataset class method) G get_annotation() (in module modality.annotation) get_cds() (in module modality.annotation) get_confpath() (in module modality.utils) get_context_positions_pyranges() (in module modality.reference) get_contig_dtype() (in module modality.genomes) get_cpg_islands() (in module modality.annotation) get_cpg_shelves() (in module modality.annotation) get_cpg_shores() (in module modality.annotation) get_exons() (in module modality.annotation) get_five_prime_utrs() (in module modality.annotation) get_fixed_windows() (in module modality.ranges) get_gencode_url() (in module modality.annotation) get_genes() (in module modality.annotation) get_genomes_config() (in module modality.genomes) get_introns() (in module modality.annotation) get_lncRNAs() (in module modality.annotation) get_miRNAs() (in module modality.annotation) get_nansum() (in module modality.reduction) get_promoters() (in module modality.annotation) get_protein_coding_def() (in module modality.annotation) get_protocadherin_cluster() (in module modality.annotation) get_reference_name() (in module modality.reference) get_sorted_contigs() (in module modality.genomes) get_start_codons() (in module modality.annotation) get_temporary_name() (modality.contig_dataset.ContigDataset method) get_three_prime_utrs() (in module modality.annotation) get_tile_index() (in module modality.reduction) get_transcription_end_region() (in module modality.annotation) get_transcripts() (in module modality.annotation) get_tss_dist() (in module modality.annotation) get_tss_region() (in module modality.annotation) get_ucsc_df() (in module modality.annotation) get_ucsc_rest_url() (in module modality.annotation) granges2rows() (modality.contig_dataset.ContigDataset method) H hstack() (modality.contig_dataset.ContigDataset method) I insert() (modality.contig_dataset.ContigDataset method) is_bgzip() (in module modality.index) is_jsonable() (in module modality.utils) is_newer() (in module modality.index) items() (modality.contig_dataset.ContigDataset method) L lmplot() (in module modality.plot_features) load_biomodal_dataset() (in module modality.datasets) load_dataset_description() (in module modality.datasets) load_ese14_methylation_data() (in module modality.datasets) load_giab_methylation_data() (in module modality.datasets) logistic_regression_llr() (in module modality.dmr) M make_name_unique() (in module modality.utils) masked_array_fromranges() (in module modality.ranges) mean_imputation() (in module modality.pca) merge_annotation() (modality.contig_dataset.ContigDataset method) merge_meta() (modality.contig_dataset.ContigDataset method) merge_ranges() (in module modality.ranges) modality.annotation module modality.contig_dataset module modality.contig_slices module modality.datasets module modality.dmr module modality.genomes module modality.index module modality.pca module modality.plot_features module modality.ranges module modality.reduction module modality.reference module modality.utils module module modality.annotation modality.contig_dataset modality.contig_slices modality.datasets modality.dmr modality.genomes modality.index modality.pca modality.plot_features modality.ranges modality.reduction modality.reference modality.utils P package_in_editable_mode() (in module modality.utils) parse_config() (in module modality.genomes) parse_tuple_string() (in module modality.contig_dataset) plot_correlation_heatmaps() (modality.contig_dataset.ContigDataset method) plot_correlation_scatter() (modality.contig_dataset.ContigDataset method) plot_coverage_distribution() (modality.contig_dataset.ContigDataset method) plot_histogram() (modality.contig_dataset.ContigDataset method) plot_methylation_tile() (modality.contig_dataset.ContigDataset method) plot_methylation_trace() (modality.contig_dataset.ContigDataset method) plot_pca_scatter() (in module modality.pca) plot_pca_scree() (in module modality.pca) plot_pearson_matrix() (modality.contig_dataset.ContigDataset method) plot_six_base_ternary() (modality.contig_dataset.ContigDataset method) plot_wrapper() (in module modality.plot_features) prep_index_factory() (in module modality.index) prepare_data() (in module modality.plot_features) pyranges_columns_mapping() (in module modality.annotation) pyranges_to_dataframe() (in module modality.annotation) R ranges_loader() (in module modality.ranges) rechunk_dataset() (in module modality.utils) reduce_block_bytile() (in module modality.reduction) reduce_bybins() (modality.contig_dataset.ContigDataset method) reduce_bycolumn_core() (in module modality.reduction) reduce_byranges() (modality.contig_dataset.ContigDataset method) reduce_byslices_core_float() (in module modality.reduction) reduce_byslices_core_int() (in module modality.reduction) relplot() (in module modality.plot_features) remove_majority_nan() (in module modality.pca) rename_samples() (modality.contig_dataset.ContigDataset method) retrieve() (modality.reduction.AbstractArray method) run_pca() (in module modality.pca) S sampled_generator() (in module modality.utils) select_samples() (modality.contig_dataset.ContigDataset method) set_contig_slices() (in module modality.contig_slices) slices (modality.contig_dataset.ContigDataset property) slices_are_valid() (in module modality.contig_slices) standardise_contig() (in module modality.annotation) subset_bycoverage() (modality.contig_dataset.ContigDataset method) subset_byranges() (modality.contig_dataset.ContigDataset method) subtract_from_genes() (in module modality.utils) summary() (modality.contig_dataset.ContigDataset method) summary_cpg_coverage() (modality.contig_dataset.ContigDataset method) T to_bedgraph() (modality.contig_dataset.ContigDataset method) to_bedmethyl() (modality.contig_dataset.ContigDataset method) to_bismark_cov_report() (modality.contig_dataset.ContigDataset method) to_quant() (modality.contig_dataset.ContigDataset method) to_zarrz() (modality.contig_dataset.ContigDataset method) V vstack() (modality.contig_dataset.ContigDataset method) W where() (modality.contig_dataset.ContigDataset method)