Index _ | A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X _ __init__() (_Assay method) (BarGraph method) (Cnv method) (COMPASS method) (CopyNumber method) (Dna method) (DnaAssignment method) (Fishplot method) (GroupByGenotype method) (Heatmap method) (LikelihoodMethod method), [1] (LinePlot method) (MultiMap method) (NSP method) (PhyloTree method) (ProbabilityMethod method) (Protein method) (Sample method) (SampleGroup method) (Truth method), [1] (VariantSubcloneTable method) _Assay (class in missionbio.mosaic.assay) A abs() (Truth method) add() (Truth method) add_ab() (Truth method) add_cell() (Truth method) add_col_attr() (_Assay method) (Cnv method) (Dna method) (Protein method) add_doublets() (Truth method), [1] add_extension() (_Assay class method) (Cnv class method) (Dna class method) (Protein class method) add_hrect() (LinePlot method) add_layer() (_Assay method) (Cnv method) (Dna method) (Protein method) add_metadata() (_Assay method) (Cnv method) (Dna method) (Protein method) add_prefix() (Truth method) add_row_attr() (_Assay method) (Cnv method) (Dna method) (Protein method) add_suffix() (Truth 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) af_to_col_index() (LikelihoodMethod method) af_to_row_index() (LikelihoodMethod class method) agg() (Truth method) aggregate() (Truth method) align() (Truth method) all() (Truth method) all_points_trace() (LinePlot method) AMBIGUOUS (COMPASS attribute) amp_uniformity() (Cnv method) amplicon_performance() (Cnv method) ANNOTATED (in module missionbio.mosaic.constants) annotation() (Heatmap static method) any() (Truth method) append() (Truth method) apply() (SampleGroup method) (Truth method) applymap() (Truth method) arcsinh() (NSP method) as_input_file() (Truth method) asfreq() (Truth method) asof() (Truth method) assay_color (Cnv attribute) (Dna attribute) (Protein attribute) (Sample attribute) assay_scatter() (Sample method) assays() (Sample method) assert_valid() (Truth method) assign() (Truth method) assign_from_truth() (Dna method) (Protein method) assignment_probabilities() (LikelihoodMethod method) (ProbabilityMethod method) astype() (Truth method) at (Truth attribute) at_time() (Truth method) AttributeType (_Assay attribute) (Cnv attribute) (Dna attribute) (Protein attribute) attrs (Truth attribute) axes (Truth attribute) B backfill() (Truth method) barcodes() (_Assay method) (Cnv method) (Dna method) (Protein method) BarGraph (class in missionbio.plotting.bargraph) barplot() (SampleGroup method) between_time() (Truth method) bfill() (Truth method) bool() (Truth method) boxplot() (Truth 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) clip() (Truth method) clipped_normalized_reads() (LikelihoodMethod method) (ProbabilityMethod method) clipped_signature() (LikelihoodMethod method) (ProbabilityMethod method) clipped_values() (in module missionbio.mosaic.utils) clone_vs_analyte() (Sample method) CLUSTER (LikelihoodMethod attribute) (ProbabilityMethod attribute) cluster() (_Assay method) (Cnv method) (Dna method) (Protein method) cluster_and_label() (Protein method) cluster_truth() (LikelihoodMethod method) (LikelihoodMethod static method) (ProbabilityMethod method) clustered_barcodes() (_Assay method) (Cnv method) (Dna method) (Protein method) (Sample method) clustered_ids() (_Assay method) (Cnv method) (Dna method) (Protein method) Cnv (class in missionbio.mosaic.cnv) col_attrs (_Assay attribute) (Cnv attribute) (Dna attribute) (Protein attribute) collapse_doublets_to_mixed() (LikelihoodMethod static method) collapse_labels() (DnaAssignment class method) COLOR (Truth attribute) coloraxis() (Heatmap method) columns (Truth attribute) combine() (Truth method) combine_first() (Truth method) command_name (COMPASS attribute) common_barcodes() (Sample method) compare() (Truth method) COMPASS (class in missionbio.mosaic.algorithms.compass) complete() (Truth method) compute_ploidy() (Cnv method) convert_dtypes() (Truth method) convolve() (_Assay static method) (Cnv static method) (Dna static method) (Protein static method) copy() (_Assay method) (Cnv method) (Dna method) (Protein method) (Truth method), [1] CopyNumber (class in missionbio.mosaic.workflows.copy_number) corr() (Truth method) corrwith() (Truth method) count() (Truth method) cov() (Truth method) create() (_Assay class method) (Cnv class method) (Dna class method) (Protein class method) create_conditional_style() (VariantSubcloneTable static method) crosstab() (_Assay method) (Cnv method) (Dna method) (Protein method) crosstabmap() (_Assay method) (Cnv method) (Dna method) (Protein method) cummax() (Truth method) cummin() (Truth method) cumprod() (Truth method) cumsum() (Truth method) D DANN (VariantSubcloneTable attribute) data_lines_trace() (Heatmap method) DATA_TRACE (Heatmap attribute) data_trace() (Heatmap method) DBSNP (VariantSubcloneTable attribute) del_ab() (Truth method) del_cell() (Truth method) del_col_attr() (_Assay method) (Cnv method) (Dna method) (Protein method) del_layer() (_Assay method) (Cnv method) (Dna method) (Protein method) del_metadata() (_Assay method) (Cnv method) (Dna method) (Protein method) del_row_attr() (_Assay method) (Cnv method) (Dna method) (Protein method) describe() (Truth method) diff() (Truth method) disable_logging() (in module missionbio.mosaic.utils) div() (Truth method) divide() (Truth method) Dna (class in missionbio.mosaic.dna) dna_modified() (CopyNumber method) DnaAssignment (class in missionbio.mosaic.algorithms.dna_assignment) dot() (Truth method) draw() (BarGraph method) (Fishplot method) (Heatmap method) (LinePlot method) (MultiMap method) (PhyloTree method) drop() (_Assay method) (Cnv method) (Dna method) (Protein method) (Truth method) drop_duplicates() (Truth method) droplevel() (Truth method) dropna() (Truth method) dtypes (Truth attribute) duplicated() (Truth method) E empty (Truth attribute) eq() (Truth method) equals() (Truth method) eval() (Truth method) ewm() (Truth method) expanding() (Truth method) expected_fig_size() (PhyloTree method) explode() (Truth method) EXPRESSION (Truth attribute) extend_docs() (in module missionbio.mosaic.utils) extensions (Cnv attribute) (Dna attribute) (Protein attribute) extract_output() (COMPASS method) F feature_scatter() (_Assay method) (Cnv method) (Dna method) (Protein method) ffill() (Truth method) fillna() (Truth method) filter() (Truth method) filter_amplicons() (Cnv method) filter_barcodes() (Dna method) filter_options (CopyNumber attribute) filter_somatic_variants() (Dna method) filter_variants() (Dna method) (Truth method) filter_variants_consecutive() (Dna method) filter_variants_table() (VariantSubcloneTable method) find_clones() (Dna method) find_relevant_variants() (Dna method) first() (Truth method) first_valid_index() (Truth method) Fishplot (class in missionbio.plotting.fishplot) fishplot() (SampleGroup method) flags (Truth attribute) floordiv() (Truth method) FONT_ASPECT (PhyloTree attribute) FONT_LINESPACE (PhyloTree attribute) format_subclone_df() (VariantSubcloneTable method) from_dict() (Truth class method) from_records() (Truth class method) G ga() (_Assay method) (Cnv method) (Dna method) (Protein method) ge() (Truth method) GENE (VariantSubcloneTable attribute) GENE_NAME (in module missionbio.mosaic.constants) GENOTYPED_CELLS (VariantSubcloneTable attribute) get() (Truth method), [1] get_ado_scores() (GroupByGenotype method) get_annotations() (Dna method) get_attribute() (_Assay method) (Cnv method) (Dna method) (Protein method) get_clones() (VariantSubcloneTable method) get_fraction_match() (LikelihoodMethod method) get_gene_and_gt_names() (VariantSubcloneTable method) get_gene_names() (Cnv method) get_indexes() (in module missionbio.mosaic.utils) get_labels() (_Assay method) (Cnv method) (Dna 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) (Protein method) get_row_ids() (_Assay method) (Cnv method) (Dna method) (Protein method) get_variant_bulk_metrics() (Dna method) get_variants() (in module missionbio.mosaic.io) get_variants_df() (VariantSubcloneTable method) getassays() (SampleGroup method) group_by_genotype() (Dna method) group_clusters() (_Assay method) (Cnv method) (Dna method) (Protein method) groupby() (Truth method) GroupByGenotype (class in missionbio.mosaic.algorithms.group_by_genotype) groups_median_trace() (LinePlot method) gt() (Truth method) H has_cell() (Truth method) hasassay() (SampleGroup method) head() (Truth method) Heatmap (class in missionbio.plotting.heatmap) heatmap() (_Assay method) (Cnv method) (Dna method) (Protein method) (Sample method) hierarchical_cluster() (_Assay class method) (Cnv class method) (Dna class method) (Protein class method) highlight_heatmap() (_Assay method) (Cnv method) (Dna method) (Protein method) hist() (Truth method) HLINE_DATA_TRACE (Heatmap attribute) HLINE_LABEL_TRACE (Heatmap attribute) human_readable_variant_name() (COMPASS static method) I iat (Truth attribute) ids() (_Assay method) (Cnv method) (Dna method) (Protein method) idxmax() (Truth method) idxmin() (Truth method) iloc (Truth attribute) index (Truth attribute) infer_objects() (Truth method) info() (Truth method) insert() (Truth method) interpolate() (Truth method) is_contiguous() (Heatmap static method) is_panel_compatible() (Truth class method) is_port_in_use() (CopyNumber static method) (VariantSubcloneTable static method) isetitem() (Truth method) isin() (Truth method) isna() (Truth method) isnull() (Truth method) isolate() (Truth method) items() (Truth method) iter_slices() (_Assay method) (Cnv method) (Dna method) (Protein method) iteritems() (Truth method) iterrows() (Truth method) itertuples() (Truth method) J join() (Truth method) K keep_diff_variants() (Truth method) keys() (Truth method) kurt() (Truth method) kurtosis() (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_ (COMPASS attribute) LABELS_TRACE (Heatmap attribute) last() (Truth method) last_valid_index() (Truth method) layers (_Assay attribute) (Cnv attribute) (Dna attribute) (Protein attribute) le() (Truth method) LikelihoodMethod (class in missionbio.demultiplex.dna.likelihood) (class in missionbio.demultiplex.protein.pace.likelihood) likelihoods() (LikelihoodMethod method) (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) loc (Truth attribute) log_likelihood() (LikelihoodMethod method) (ProbabilityMethod method) lookup() (Truth method) lt() (Truth method) M mad() (Truth method) MARKER_TEXTSPACE (PhyloTree attribute) mask() (Truth method) max() (Truth method) MAX_CELLS_TO_SHOW_POINTS (VariantSubcloneTable attribute) MAX_NAME_LENGTH (VariantSubcloneTable attribute) mean() (Truth method) median() (Truth method) melt() (Truth method) memory_usage() (Truth method) merge() (SampleGroup method) (Truth method) merge_assay() (SampleGroup method) merge_similar_clusters() (Dna method) metadata (_Assay attribute) (Cnv attribute) (Dna attribute) (Protein attribute) min() (Truth method) missionbio.mosaic.constants module missionbio.mosaic.io module missionbio.mosaic.utils module MIXED (COMPASS attribute) mod() (Truth method) mode() (Truth method) module missionbio.mosaic.constants missionbio.mosaic.io missionbio.mosaic.utils mul() (Truth method) MultiMap (class in missionbio.plotting.multimap) multiply() (Truth method) MUTATED_CELLS (VariantSubcloneTable attribute) mutated_cells() (Dna method) N name (_Assay attribute) (Cnv attribute) (Dna attribute) (Protein attribute) (Sample attribute) name_id_by_pos() (Cnv method) NAN_L2 (_Assay attribute) (Cnv attribute) (Dna attribute) (Protein attribute) ndim (Truth attribute) ne() (Truth method) NGT_FILTERED (in module missionbio.mosaic.constants) nlargest() (Truth method) NO_ADO_HET_DISTRIBUTION (LikelihoodMethod attribute) node_descriptions() (COMPASS method) node_genotypes_ (COMPASS attribute) nodes_ (COMPASS attribute) normalize_barcodes() (_Assay method) (Cnv method) (Dna method) (Protein method) normalize_reads() (Cnv method) (Protein method) NORMALIZED_READS (in module missionbio.mosaic.constants) notna() (Truth method) notnull() (Truth method) nsmallest() (Truth method) NSP (class in missionbio.demultiplex.protein.nsp) nunique() (Truth method) O ORG_BARCODE (in module missionbio.mosaic.constants) ORIGINAL_ID (in module missionbio.mosaic.constants) P pad() (Truth method) PALETTE (in module missionbio.mosaic.constants) palette() (LikelihoodMethod method) (ProbabilityMethod method) (Truth method) panel_uniformity() (Cnv method) PARENT (Truth attribute) parse_var_id() (COMPASS static method) pathscale() (Dna method) PCA_LABEL (in module missionbio.mosaic.constants) pct_change() (Truth method) PhyloTree (class in missionbio.plotting.phylotree) pipe() (Truth method) pivot() (Truth method) pivot_table() (Truth method) 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) pop() (Truth method) positions() (Cnv method) pow() (Truth 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) prod() (Truth method) product() (Truth method) PROFILES (Truth attribute) Protein (class in missionbio.mosaic.protein) Q quantile() (Truth method) query() (Truth method) R radd() (Truth method) rank() (Truth method) raw_counts() (Sample method) raw_heatmaps() (Sample method) rdiv() (Truth method) read_csv() (Truth static method) read_data() (Sample method) read_depth_dependence() (Protein method) read_distribution() (_Assay method) (Cnv method) (Dna 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) reindex() (Truth method) reindex_like() (Truth method) remove_correlated_variants() (Truth method) remove_filtered_variants() (Truth method) remove_non_snp_variants() (Truth method) rename() (Sample method) (Truth method) rename_axis() (Truth method) rename_clones() (VariantSubcloneTable method) rename_labels() (_Assay method) (Cnv method) (Dna method) (GroupByGenotype method) (Protein method) rename_sample() (_Assay method) (Cnv method) (Dna method) (Protein method) reorder_levels() (Truth method) replace() (Truth method) resample() (Truth method) reset() (Sample method) reset_cnv_assay() (CopyNumber method) reset_ids() (_Assay method) (Cnv method) (Dna method) (Protein method) reset_index() (Truth method) rfloordiv() (Truth method) ridgeplot() (_Assay method) (Cnv method) (Dna method) (Protein method) rmod() (Truth method) rmul() (Truth method) rolling() (Truth method) round() (Truth method) row_attrs (_Assay attribute) (Cnv attribute) (Dna attribute) (Protein attribute) rpow() (Truth method) rsub() (Truth method) rtruediv() (Truth method) run() (COMPASS method) (CopyNumber method) (VariantSubcloneTable method) run_lda() (_Assay method) (Cnv method) (Dna method) (Protein method) run_pca() (_Assay method) (Cnv method) (Dna method) (Protein method) run_umap() (_Assay method) (Cnv method) (Dna method) (Protein method) S Sample (class in missionbio.mosaic.sample) sample() (Truth method) sample_names() (Sample method) SampleGroup (class in missionbio.mosaic.samplegroup) samples() (_Assay method) (Cnv method) (Dna method) (Protein method) save() (in module missionbio.mosaic.io) scale_data() (_Assay method) (Cnv method) (Dna method) (Protein method) SCALED_LABEL (in module missionbio.mosaic.constants) scaling_factor() (NSP method) scatterplot() (_Assay method) (Cnv method) (Dna method) (Protein method) select_columns() (_Assay method) (Cnv method) (Dna method) (Protein method) select_dtypes() (Truth method) select_rows() (_Assay method) (Cnv method) (Dna method) (Protein method) selected_bars (_Assay attribute) (Cnv attribute) (Dna attribute) (Protein attribute) selected_ids (_Assay attribute) (Cnv attribute) (Dna attribute) (Protein attribute) selected_variants (VariantSubcloneTable attribute) sem() (Truth method) set_axis() (Truth method) set_color() (Truth method) set_flags() (Truth method) set_ids_from_cols() (_Assay method) (Cnv method) (Dna method) (Protein method) set_index() (Truth method) set_labels() (_Assay method) (Cnv method) (Dna method) (Protein method) set_layout() (LinePlot method) set_palette() (_Assay method) (Cnv method) (Dna 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) (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) (Protein attribute) (Truth attribute) shift() (Truth method) signature() (_Assay method) (Cnv method) (Dna method) (Protein method) (Truth method) signaturemap() (_Assay method) (Cnv method) (Dna method) (Protein method) (Sample method) sim_af() (LikelihoodMethod method) size (Truth attribute) skew() (Truth method) slice_shift() (Truth method) somatic_variants (COMPASS attribute) sort_columns() (_Assay method) (Cnv method) (Dna method) (Protein method) sort_ids() (Dna method) sort_index() (Truth method) sort_rows() (_Assay method) (Cnv method) (Dna method) (Protein method) sort_values() (Truth method) sort_variants_table() (VariantSubcloneTable method) SOURCE (Truth attribute) split() (_Assay method) (Cnv method) (Dna method) (Protein method) (Sample method) split_filter_part() (VariantSubcloneTable static method) squeeze() (Truth method) stack() (Truth method) static_fig() (in module missionbio.mosaic.utils) std() (Truth method) stop() (CopyNumber method) (VariantSubcloneTable method) stripplot() (_Assay method) (Cnv method) (Dna method) (Protein method) style (Truth attribute) sub() (Truth method) subclone_options_layout (VariantSubcloneTable attribute) subclone_table() (GroupByGenotype method) subclone_table_component (VariantSubcloneTable attribute) subtract() (Truth method) sum() (Truth method) swapaxes() (Truth method) swaplevel() (Truth method) T T (Truth attribute) tail() (Truth method) take() (Truth method) test_signature() (_Assay method) (Cnv method) (Dna method) (Protein method) title (_Assay attribute) (Cnv attribute) (Dna attribute) (Protein attribute) to_clipboard() (Truth method) to_csv() (Truth method) to_dict() (Truth method) to_excel() (Truth method) to_feather() (Truth method) to_gbq() (Truth method) to_hdf() (Truth method) to_html() (Truth method) to_json() (Truth method) to_latex() (Truth method) to_markdown() (Truth method) to_numpy() (Truth method) to_orc() (Truth method) to_parquet() (Truth method) to_period() (Truth method) to_pickle() (Truth method) to_records() (Truth method) to_sql() (Truth method) to_stata() (Truth method) to_string() (Truth method) to_timestamp() (Truth method) to_xarray() (Truth method) to_xml() (Truth method) to_yaml() (Truth method) to_zip() (in module missionbio.mosaic.io) trace() (BarGraph method) transform() (NSP method) (Truth method) transpose() (Truth method) tree_ (COMPASS attribute) trim() (Truth method) truediv() (Truth method) truncate() (Truth method) Truth (class in missionbio.demultiplex.dna.truth) (class in missionbio.demultiplex.protein.truth) truth() (Dna method) (DnaAssignment class method) (Protein method) tshift() (Truth method) tz_convert() (Truth method) tz_localize() (Truth method) U UMAP_LABEL (in module missionbio.mosaic.constants) umaps() (Sample method) unstack() (Truth method) update() (Truth method) update_coloraxis() (_Assay static method) (Cnv static method) (Dna static method) (Protein static method) V VAF_HET_CELLS (VariantSubcloneTable attribute) VAF_HOM_CELLS (VariantSubcloneTable attribute) VAF_WT_CELLS (VariantSubcloneTable attribute) value_counts() (Truth method) values (Truth attribute) var() (Truth method) VARIANT (VariantSubcloneTable attribute) VARIANT_CLONE_ERROR_RATE (COMPASS attribute) VARIANT_TYPE (VariantSubcloneTable attribute) variants_table_component (VariantSubcloneTable attribute) VariantSubcloneTable (class in missionbio.mosaic.workflows.variant_subclone_table) VERSION (Truth attribute) violin_options_layout (VariantSubcloneTable attribute) violinplot() (_Assay method) (Cnv method) (Dna method) (Protein method) VLINE_DATA_TRACE (Heatmap attribute) W where() (Truth method) X xs() (Truth method)