Index _ | A | C | D | E | F | G | H | I | L | M | N | P | R | S | T | V | W _ __getitem__() (modality.ContigDataset method) A append() (modality.ContigDataset method) assign_fractions() (modality.ContigDataset method) at_mincoverage() (modality.ContigDataset method) C catplot() (in module modality.analysis) clear() (modality.ContigDataset method) compute_correlation_matrix() (modality.ContigDataset method) compute_pearson_matrix() (modality.ContigDataset method) concat_contig_datasets() (in module modality) context (modality.ContigDataset property) ContigDataset (class in modality) count() (modality.ContigDataset method) D displot() (in module modality.analysis) DMRBatchWorkflow (class in modality.analysis) DMRResult (class in modality.analysis) DMRWorkflow (class in modality.analysis) E extend() (modality.ContigDataset method) F filter_dmr_results() (modality.analysis.DMRResult method) frac_c (modality.ContigDataset property) frac_hmc (modality.ContigDataset property) frac_mc (modality.ContigDataset property) frac_modc (modality.ContigDataset property) from_dmrfile() (modality.analysis.DMRResult class method) from_zarrz() (modality.ContigDataset class method) G get_annotation() (in module modality.annotation) get_cds() (in module modality.annotation) 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_feature_dist() (in module modality.annotation) get_five_prime_utrs() (in module modality.annotation) get_gencode_url() (in module modality.annotation) get_genes() (in module modality.annotation) get_introns() (in module modality.annotation) get_lncRNAs() (in module modality.annotation) get_miRNAs() (in module modality.annotation) get_promoters() (in module modality.annotation) get_protocadherin_cluster() (in module modality.annotation) get_start_codons() (in module modality.annotation) get_three_prime_utrs() (in module modality.annotation) get_transcription_end_region() (in module modality.annotation) get_transcripts() (in module modality.annotation) get_tss_dist() (in module modality.annotation) granges2rows() (modality.ContigDataset method) groupby() (modality.ContigDataset method) grouped_on (modality.ContigDataset property) H hstack() (modality.ContigDataset method) I include_headers() (modality.analysis.DMRBatchWorkflow method) index() (modality.ContigDataset method) insert() (modality.ContigDataset method) L lmplot() (in module modality.analysis) load_biomodal_dataset() (in module modality) load_dataset_description() (in module modality) M merge_annotation() (modality.ContigDataset method) merge_meta() (modality.ContigDataset method) modality.analysis module modality.annotation module module modality.analysis modality.annotation N num_contexts (modality.ContigDataset property) P plot_correlation_heatmaps() (in module modality.analysis) (modality.ContigDataset method) plot_correlation_scatter() (in module modality.analysis) (modality.ContigDataset method) plot_coverage_distribution() (in module modality.analysis) (modality.ContigDataset method) plot_histogram() (in module modality.analysis) (modality.ContigDataset method) plot_manhattan() (modality.analysis.DMRResult method) plot_methylation_tile() (in module modality.analysis) (modality.ContigDataset method) plot_methylation_trace() (in module modality.analysis) (modality.ContigDataset method) plot_pca_scatter() (in module modality.analysis) plot_pca_scree() (in module modality.analysis) plot_pearson_matrix() (in module modality.analysis) (modality.ContigDataset method) plot_six_base_ternary() (in module modality.analysis) (modality.ContigDataset method) plot_volcano() (modality.analysis.DMRResult method) pop() (modality.ContigDataset method) R reduce_bybins() (modality.ContigDataset method) reduce_byranges() (modality.ContigDataset method) ref_genome (modality.ContigDataset property) relplot() (in module modality.analysis) remove() (modality.ContigDataset method) remove_slice_attributes() (modality.ContigDataset method) rename_samples() (modality.ContigDataset method) reverse() (modality.ContigDataset method) run() (modality.analysis.DMRBatchWorkflow method) (modality.analysis.DMRWorkflow method) run_pca() (in module modality.analysis) S sample_ids (modality.ContigDataset property) sample_ix (modality.ContigDataset property) select_samples() (modality.ContigDataset method) set_compress_dmr_file() (modality.analysis.DMRBatchWorkflow method) set_condition_order() (modality.analysis.DMRWorkflow method) set_covariates() (modality.analysis.DMRWorkflow method) set_include_headers_in_dmr_file() (modality.analysis.DMRBatchWorkflow method) set_regions() (modality.analysis.DMRWorkflow method) slices (modality.ContigDataset property) subset_bycontigs() (modality.ContigDataset method) subset_bycoverage() (modality.ContigDataset method) subset_byranges() (modality.ContigDataset method) summary_cpg_coverage() (modality.ContigDataset method) T to_bedgraph() (modality.ContigDataset method) to_bedmethyl() (modality.ContigDataset method) to_bismark_cov_report() (modality.ContigDataset method) to_cxreport() (modality.ContigDataset method) to_quant() (modality.ContigDataset method) to_zarrz() (modality.ContigDataset method) V validate_methylation_contexts() (modality.ContigDataset method) vstack() (modality.ContigDataset method) W where() (modality.ContigDataset method)