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) (Rna 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) (Rna method) add_doublets() (Truth method), [1] add_extension() (_Assay class method) (Cnv class method) (Dna class method) (Ge class method) (Protein class method) (Rna class method) add_hrect() (LinePlot method) add_info() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) (Rna method) add_layer() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) (Rna method) add_metadata() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) (Rna method) add_row_attr() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) (Rna method) add_rows_by_fill() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) (Rna 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) (Rna 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) (Rna method) cluster_and_label() (Protein method) cluster_truth() (LikelihoodMethod method) (ProbabilityMethod method) clustered_barcodes() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) (Rna method) (Sample method) clustered_ids() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) (Rna method) Cnv (class in missionbio.mosaic.cnv) col_attrs (_Assay attribute) (Cnv attribute) (Dna attribute) (Ge attribute) (Protein attribute) (Rna 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) (Rna static method) copy() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) (Rna 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) (Rna class method) create_conditional_style() (VariantSubcloneTable static method) crosstab() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) (Rna method) crosstabmap() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) (Rna 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) (Rna 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) (Rna method) del_info() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) (Rna method) del_layer() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) (Rna method) del_metadata() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) (Rna method) del_row_attr() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) (Rna 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) (Rna 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) (Rna attribute) extract_output() (COMPASS method) F feature_scatter() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) (Rna 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) (Rna class method) G ga() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) (Rna 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) (Rna 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) (Rna method) get_labels() (_Assay method) (Cnv method) (Dna method) (Ge method) (GroupByGenotype method) (Protein method) (Rna method) get_layout() (CopyNumber method) (VariantSubcloneTable method) get_markers() (Rna method) get_normalized_reads() (LikelihoodMethod method) (ProbabilityMethod method) get_palette() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) (Rna method) get_row_ids() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) (Rna 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) (Rna method) group_by_genotype() (Dna method) group_clusters() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) (Rna 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) (Rna method) hasassay() (SampleGroup method) Heatmap (class in missionbio.plotting.heatmap) heatmap() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) (Rna method) (Sample method) hierarchical_cluster() (_Assay class method) (Cnv class method) (Dna class method) (Ge class method) (Protein class method) (Rna class method) highlight_heatmap() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) (Rna 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) (Rna method) INDEL_LENGTH (in module missionbio.mosaic.constants) index() (SPARCResult method) info (_Assay attribute) (Cnv attribute) (Dna attribute) (Ge attribute) (Protein attribute) (Rna 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) (Rna 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_pbmc() (Rna 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) (Rna 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) mean_reads_barplot() (Rna method) mean_reads_table() (Rna method) merge() (SampleGroup method) merge_assay() (SampleGroup method) merge_similar_clusters() (Dna method) metadata (_Assay attribute) (Cnv attribute) (Dna attribute) (Ge attribute) (Protein attribute) (Rna 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) (Rna attribute) (Sample attribute) name_id_by_pos() (Cnv method) NAN_L2 (_Assay attribute) (Cnv attribute) (Dna attribute) (Ge attribute) (Protein attribute) (Rna 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) (Rna method) normalize_reads() (Cnv method) (Protein method) (Rna 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) (Rna 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) (Rna method) rename_sample() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) (Rna method) reorder() (SPARCResult method) reset() (Sample method) reset_cnv_assay() (CopyNumber method) reset_ids() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) (Rna method) ridgeplot() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) (Rna method) Rna (class in missionbio.mosaic.rna) row_attrs (_Assay attribute) (Cnv attribute) (Dna attribute) (Ge attribute) (Protein attribute) (Rna attribute) run() (COMPASS method) (CopyNumber method) (VariantSubcloneTable method) run_lda() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) (Rna method) run_pca() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) (Rna method) run_umap() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) (Rna method) S Sample (class in missionbio.mosaic.sample) sample_info_map() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) (Rna method) sample_names() (Sample method) SampleGroup (class in missionbio.mosaic.samplegroup) sampleinfo (_Assay attribute) (Cnv attribute) (Dna attribute) (Ge attribute) (Protein attribute) (Rna attribute) samples() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) (Rna method) save() (in module missionbio.mosaic.io) scale_data() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) (Rna method) SCALED_LABEL (in module missionbio.mosaic.constants) scaling_factor() (NSP method) scatterplot() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) (Rna method) search_path() (SPARC method) search_path_drops() (SPARC method) select_columns() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) (Rna method) select_rows() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) (Rna method) selected_bars (_Assay attribute) (Cnv attribute) (Dna attribute) (Ge attribute) (Protein attribute) (Rna attribute) selected_ids (_Assay attribute) (Cnv attribute) (Dna attribute) (Ge attribute) (Protein attribute) (Rna 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) (Rna method) set_labels() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) (Rna method) set_layout() (LinePlot method) set_palette() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) (Rna 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) (Rna 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) (Rna attribute) signature() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) (Rna method) (Truth method) signaturemap() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) (Rna 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) (Rna method) sort_ids() (Dna method) sort_rows() (_Assay method) (Cnv method) (Dna method) (Ge method) (Protein method) (Rna 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) (Rna 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) (Rna 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) (Rna method) title (_Assay attribute) (Cnv attribute) (Dna attribute) (Ge attribute) (Protein attribute) (Rna 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) (Rna 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) (Rna method) VLINE_DATA_TRACE (Heatmap attribute) W wildtype() (SPARCResult class method)