Index _ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | U | V | W _ __init__() (_Assay method) (BarGraph method) (Cnv method) (COMPASS method) (CopyNumber method) (Dna method) (DnaAssignment method) (Fishplot method) (Ge method) (GroupByGenotype method) (Heatmap method) (LikelihoodMethod method), [1] (LinePlot method) (MultiMap method) (NSP method) (PhyloTree method) (ProbabilityMethod method) (Protein method) (Sample method) (SampleGroup method) (SPARC method) (SPARCResult method) (Truth method), [1] (VariantSubcloneTable method) _Assay (class in missionbio.mosaic.assay) A add_ab() (Truth method) add_cell() (Truth method) add_col_attr() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) add_doublets() (Truth method), [1] add_extension() (_Assay class method) (Cnv class method) (Dna class method) (Ge class method) (Protein class method) add_hrect() (LinePlot method) add_info() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) add_layer() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) add_metadata() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) add_row_attr() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) add_rows_by_fill() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) ADO_PARENTS (in module missionbio.mosaic.constants) ADO_SCORE (in module missionbio.mosaic.constants) ADO_SISTERS (in module missionbio.mosaic.constants) AF_FILTERED (in module missionbio.mosaic.constants) AF_GNOMAD (VariantSubcloneTable attribute) AF_MISSING (in module missionbio.mosaic.constants) all_points_trace() (LinePlot method) allclones (Fishplot attribute) (PhyloTree attribute) AMBIGUOUS (COMPASS attribute) amp_uniformity() (Cnv method) amplicon_performance() (Cnv method) annotation() (Heatmap static method) ANNOTATIONS (in module missionbio.mosaic.constants) apply() (SampleGroup method) arcsinh() (NSP method) as_input_file() (Truth method) asaf() (Truth method) asgt() (Truth method) asindex() (Truth method) assay_color (Cnv attribute) (Dna attribute) (Ge attribute) (Protein attribute) (Sample attribute) assay_scatter() (Sample method) assays() (Sample method) assert_valid() (Truth method) assign_from_truth() (Dna method) (Protein method) assignment_logl() (LikelihoodMethod method) assignment_probabilities() (LikelihoodMethod method) (ProbabilityMethod method) B barcodes() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) BarGraph (class in missionbio.plotting.bargraph) barplot() (SampleGroup method) builtin() (Truth class method) C callback_create_figure() (CopyNumber method) (VariantSubcloneTable method) callback_filter_and_normalize() (CopyNumber method) callback_subclone_table_modifications() (VariantSubcloneTable method) callback_update_feature_options() (CopyNumber method) callback_variants_table_modifications() (VariantSubcloneTable method) CDNA (VariantSubcloneTable attribute) cell_uniformity() (Cnv method) cellnames() (Truth method) cells_per_ab() (Protein method) classify_mixed_clusters() (LikelihoodMethod method) (ProbabilityMethod method) clipped_normalized_reads() (LikelihoodMethod method) (ProbabilityMethod method) clipped_signature() (LikelihoodMethod method) (ProbabilityMethod method) clipped_values() (in module missionbio.mosaic.utils) clone() (Fishplot method) (PhyloTree method) clone_vs_analyte() (Sample method) CLUSTER (LikelihoodMethod attribute) (ProbabilityMethod attribute) cluster() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) cluster_and_label() (Protein method) cluster_truth() (LikelihoodMethod method) (ProbabilityMethod method) clustered_barcodes() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) (Sample method) clustered_ids() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) Cnv (class in missionbio.mosaic.cnv) col_attrs (_Assay attribute) (Cnv attribute) (Dna attribute) (Ge attribute) (Protein attribute) collapse_labels() (DnaAssignment class method) COLOR (Truth attribute) coloraxis() (Heatmap method) columns (Ge attribute) command_name (COMPASS attribute) common_barcodes() (Sample method) COMPASS (class in missionbio.mosaic.algorithms.compass) complete() (Truth method) compute_ploidy() (Cnv method) convolve() (_Assay static method) (Cnv static method) (Dna static method) (Ge static method) (Protein static method) copy() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) (Truth method) CopyNumber (class in missionbio.mosaic.workflows.copy_number) count() (SPARCResult method) create() (_Assay class method) (Cnv class method) (Dna class method) (Ge class method) (Protein class method) create_conditional_style() (VariantSubcloneTable static method) crosstab() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) crosstabmap() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) D DANN (VariantSubcloneTable attribute) data_lines_trace() (Heatmap method) DATA_TRACE (Heatmap attribute) data_trace() (Heatmap method) DBSNP (VariantSubcloneTable attribute) deduplicate_barcodes() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) del_ab() (Truth method) del_cell() (Truth method) del_clone() (Fishplot method) (PhyloTree method) del_col_attr() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) del_info() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) del_layer() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) del_metadata() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) del_row_attr() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) disable_logging() (in module missionbio.mosaic.utils) Dna (class in missionbio.mosaic.dna) dna_modified() (CopyNumber method) DnaAssignment (class in missionbio.mosaic.algorithms.dna_assignment) draw() (BarGraph method) (Fishplot method) (Heatmap method) (LinePlot method) (MultiMap method) (PhyloTree method) (SPARCResult method) drop() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) dropped_variants_ (SPARC attribute) E events (SPARCResult attribute) expected_fig_size() (PhyloTree method) EXPRESSION (Truth attribute) extend_docs() (in module missionbio.mosaic.utils) extensions (Cnv attribute) (Dna attribute) (Ge attribute) (Protein attribute) extract_output() (COMPASS method) F feature_scatter() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) file (Sample attribute) filter_amplicons() (Cnv method) filter_barcodes() (Dna method) filter_options (CopyNumber attribute) filter_somatic_variants() (Dna method) filter_variants() (Dna method) (Ge method) (Truth method) filter_variants_consecutive() (Dna method) filter_variants_table() (VariantSubcloneTable method) find_clones() (Dna method) find_relevant_variants() (Dna method) Fishplot (class in missionbio.plotting.fishplot) fishplot() (SampleGroup method) format_subclone_df() (VariantSubcloneTable method) from_assay() (_Assay class method) (Cnv class method) (Dna class method) (Ge class method) (Protein class method) G ga() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) Ge (class in missionbio.mosaic.ge) GENE (VariantSubcloneTable attribute) GENE_NAME (in module missionbio.mosaic.constants) genome (Cnv attribute) (Dna attribute) (Ge attribute) GENOTYPED_CELLS (VariantSubcloneTable attribute) get() (Truth method) get_ado_scores() (GroupByGenotype method) get_all_variants_table() (Ge method) get_annotated_ids() (Dna method) get_annotations() (Dna method) get_attribute() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) get_clones() (VariantSubcloneTable method) get_final_edit_status() (Ge method) get_gene_and_gt_names() (VariantSubcloneTable method) get_gene_names() (Cnv method) get_indexes() (in module missionbio.mosaic.utils) get_info() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) get_labels() (_Assay method) (Cnv method) (Dna method) (Ge method) (GroupByGenotype method) (Protein method) get_layout() (CopyNumber method) (VariantSubcloneTable method) get_normalized_reads() (LikelihoodMethod method) (ProbabilityMethod method) get_palette() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) get_row_ids() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) get_target_modifications() (Ge method) get_variant_bulk_metrics() (Dna method) get_variants() (in module missionbio.mosaic.io) get_variants_df() (VariantSubcloneTable method) getassays() (SampleGroup method) gi() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) group_by_genotype() (Dna method) group_clusters() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) GroupByGenotype (class in missionbio.mosaic.algorithms.group_by_genotype) groups_median_trace() (LinePlot method) H has_cell() (Truth method) has_info() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) hasassay() (SampleGroup method) Heatmap (class in missionbio.plotting.heatmap) heatmap() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) (Sample method) hierarchical_cluster() (_Assay class method) (Cnv class method) (Dna class method) (Ge class method) (Protein class method) highlight_heatmap() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) HLINE_DATA_TRACE (Heatmap attribute) HLINE_LABEL_TRACE (Heatmap attribute) HORIZONTAL (PhyloTree attribute) I ids() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) INDEL_LENGTH (in module missionbio.mosaic.constants) index() (SPARCResult method) info (_Assay attribute) (Cnv attribute) (Dna attribute) (Ge attribute) (Protein attribute) is_contiguous() (Heatmap static method) is_panel_compatible() (Truth class method) is_port_in_use() (CopyNumber static method) (VariantSubcloneTable static method) isolate() (Truth method) iter_slices() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) K keep_diff_variants() (Truth method) L LABEL (in module missionbio.mosaic.constants) label_cells() (DnaAssignment method) (LikelihoodMethod method), [1] (ProbabilityMethod method) label_lines_trace() (Heatmap method) label_sticky_cells() (LikelihoodMethod method) (ProbabilityMethod method) (Protein method) label_trace() (Heatmap method) labels (SPARCResult attribute) labels_ (COMPASS attribute) LABELS_TRACE (Heatmap attribute) labels_valid (SPARCResult attribute) layers (_Assay attribute) (Cnv attribute) (Dna attribute) (Ge attribute) (Protein attribute) LikelihoodMethod (class in missionbio.demultiplex.dna.likelihood) (class in missionbio.demultiplex.protein.pace.likelihood) likelihoods() (LikelihoodMethod static method) (ProbabilityMethod static method) LinePlot (class in missionbio.plotting.lineplot) lines_trace() (LinePlot method) load() (in module missionbio.mosaic.io) load_example_dataset() (in module missionbio.mosaic.io) log_likelihood() (LikelihoodMethod method) (ProbabilityMethod method) M MARKER_TEXTSPACE (PhyloTree attribute) MAX_CELLS_TO_SHOW_POINTS (VariantSubcloneTable attribute) MAX_NAME_LENGTH (VariantSubcloneTable attribute) merge() (SampleGroup method) merge_assay() (SampleGroup method) merge_similar_clusters() (Dna method) metadata (_Assay attribute) (Cnv attribute) (Dna attribute) (Ge attribute) (Protein attribute) missionbio.mosaic.constants module missionbio.mosaic.io module missionbio.mosaic.utils module MIXED (COMPASS attribute) model_amplicons() (Cnv method) model_cnv() (SPARC method) module missionbio.mosaic.constants missionbio.mosaic.io missionbio.mosaic.utils MultiMap (class in missionbio.plotting.multimap) MUTATED_CELLS (VariantSubcloneTable attribute) mutated_cells() (Dna method) N name (_Assay attribute) (Cnv attribute) (Dna attribute) (Ge attribute) (Protein attribute) (Sample attribute) name_id_by_pos() (Cnv method) NAN_L2 (_Assay attribute) (Cnv attribute) (Dna attribute) (Ge attribute) (Protein attribute) NGT_FILTERED (in module missionbio.mosaic.constants) node_descriptions() (COMPASS method) node_fractions() (COMPASS method) node_genotypes_ (COMPASS attribute) nodes_ (COMPASS attribute) normalize_barcodes() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) normalize_reads() (Cnv method) (Protein method) NORMALIZED_READS (in module missionbio.mosaic.constants) NSP (class in missionbio.demultiplex.protein.nsp) O ORIGINAL_ID (in module missionbio.mosaic.constants) P PALETTE (in module missionbio.mosaic.constants) palette() (LikelihoodMethod method) (ProbabilityMethod method) (Truth method) panel (Ge attribute) panel_uniformity() (Cnv method) PARENT (Truth attribute) parse_var_id() (COMPASS static method) pathscale() (Dna method) PCA_LABEL (in module missionbio.mosaic.constants) PhyloTree (class in missionbio.plotting.phylotree) PLOIDY (in module missionbio.mosaic.constants) plot() (GroupByGenotype method) (NSP method) (Truth method) plot_options() (CopyNumber method) plot_ploidy() (Cnv method) plot_profiles() (NSP method) plot_tree() (COMPASS method) plot_variant_correlation() (Dna method) POS_DEL_OFFSET (in module missionbio.mosaic.constants) positions() (Cnv method) predict() (SPARC method) prep_amplicon_reads() (COMPASS method) prep_variants() (COMPASS method) prepare_input() (COMPASS method) probability_ (COMPASS attribute) ProbabilityMethod (class in missionbio.demultiplex.protein.pace.probability) profile (SPARCResult attribute) profile_init (SPARCResult attribute) profile_valid (SPARCResult attribute) PROFILES (Truth attribute) Protein (class in missionbio.mosaic.protein) R raw_counts() (Sample method) raw_heatmaps() (Sample method) read_csv() (Truth static method) read_data() (Sample method) read_depth_dependence() (Protein method) read_distribution() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) read_panel() (Truth class method) read_yaml() (Truth class method) READS (in module missionbio.mosaic.constants) reads_to_ab() (Protein method) recolor_labels() (DnaAssignment class method) REFSEQ_ID (VariantSubcloneTable attribute) relabel() (COMPASS method) remove_correlated_variants() (Truth method) remove_filtered_variants() (Truth method) remove_non_snp_variants() (Truth method) rename() (Sample method) rename_clones() (VariantSubcloneTable method) rename_labels() (_Assay method) (Cnv method) (Dna method) (Ge method) (GroupByGenotype method) (Protein method) rename_sample() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) reorder() (SPARCResult method) reset() (Sample method) reset_cnv_assay() (CopyNumber method) reset_ids() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) ridgeplot() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) row_attrs (_Assay attribute) (Cnv attribute) (Dna attribute) (Ge attribute) (Protein attribute) run() (COMPASS method) (CopyNumber method) (VariantSubcloneTable method) run_lda() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) run_pca() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) run_umap() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) S Sample (class in missionbio.mosaic.sample) sample_info_map() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) sample_names() (Sample method) SampleGroup (class in missionbio.mosaic.samplegroup) sampleinfo (_Assay attribute) (Cnv attribute) (Dna attribute) (Ge attribute) (Protein attribute) samples() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) save() (in module missionbio.mosaic.io) scale_data() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) SCALED_LABEL (in module missionbio.mosaic.constants) scaling_factor() (NSP method) scatterplot() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) search_path() (SPARC method) search_path_drops() (SPARC method) select_columns() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) select_rows() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) selected_bars (_Assay attribute) (Cnv attribute) (Dna attribute) (Ge attribute) (Protein attribute) selected_ids (_Assay attribute) (Cnv attribute) (Dna attribute) (Ge attribute) (Protein attribute) selected_variants (VariantSubcloneTable attribute) serialize_clones() (SPARCResult method) set_annotated_ids() (Dna method) set_color() (Truth method) set_ids_from_cols() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) set_labels() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) set_layout() (LinePlot method) set_palette() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) set_port() (CopyNumber class method) (VariantSubcloneTable class method) set_random_seed() (in module missionbio.mosaic.utils) set_selected_labels() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) set_ticks() (Heatmap static method) (LinePlot static method) set_xticks() (Heatmap method) (LinePlot method) set_yticks() (Heatmap method) setup_callbacks() (CopyNumber method) (VariantSubcloneTable method) shape (_Assay attribute) (Cnv attribute) (Dna attribute) (Ge attribute) (Protein attribute) signature() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) (Truth method) signaturemap() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) (Sample method) SLASH (in module missionbio.mosaic.constants) snps() (Dna method) somatic_variants (COMPASS attribute) sort_columns() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) sort_ids() (Dna method) sort_rows() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) sort_variants_table() (VariantSubcloneTable method) SOURCE (Truth attribute) SPARC (class in missionbio.demultiplex.phylogeny.sparc) sparc() (Sample method) SPARCResult (class in missionbio.demultiplex.phylogeny.state) split() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) (Sample method) split_filter_part() (VariantSubcloneTable static method) static_fig() (in module missionbio.mosaic.utils) stop() (CopyNumber method) (VariantSubcloneTable method) stripplot() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) subclone_options_layout (VariantSubcloneTable attribute) subclone_table() (GroupByGenotype method) subclone_table_component (VariantSubcloneTable attribute) T test_signature() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) title (_Assay attribute) (Cnv attribute) (Dna attribute) (Ge attribute) (Protein attribute) to_yaml() (Truth method) to_zip() (in module missionbio.mosaic.io) toaf() (Truth method) tongt() (Truth method) trace() (BarGraph method) transform() (NSP method) tree (SPARCResult attribute) tree_ (COMPASS attribute) tree_valid (SPARCResult attribute) trim() (Truth method) Truth (class in missionbio.demultiplex.dna.truth) (class in missionbio.demultiplex.protein.truth) truth() (Dna method) (DnaAssignment class method) (Protein method) U UMAP_LABEL (in module missionbio.mosaic.constants) umaps() (Sample method) update_coloraxis() (_Assay static method) (Cnv static method) (Dna static method) (Ge static method) (Protein static method) V VAF_HET_CELLS (VariantSubcloneTable attribute) VAF_HOM_CELLS (VariantSubcloneTable attribute) VAF_WT_CELLS (VariantSubcloneTable attribute) valid_ngts (SPARCResult attribute) VARIANT (VariantSubcloneTable attribute) VARIANT_CLONE_ERROR_RATE (COMPASS attribute) variant_params_ (SPARC attribute) VARIANT_TYPE (VariantSubcloneTable attribute) variants_table_component (VariantSubcloneTable attribute) VariantSubcloneTable (class in missionbio.mosaic.workflows.variant_subclone_table) VERSION (Truth attribute) VERTICAL (PhyloTree attribute) violin_options_layout (VariantSubcloneTable attribute) violinplot() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) VLINE_DATA_TRACE (Heatmap attribute) W wildtype() (SPARCResult class method)