Index _ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y _ __annotations__ (scranpy.aggregation.aggregate_across_cells.AggregateAcrossCellsOptions attribute) (scranpy.aggregation.downsample_by_neighbors.DownsampleByNeighborsOptions attribute) (scranpy.analyze.AnalyzeOptions.AnalyzeOptions attribute) (scranpy.analyze.AnalyzeOptions.MiscellaneousOptions attribute) (scranpy.analyze.AnalyzeResults.AnalyzeResults attribute) (scranpy.batch_correction.mnn_correct.MnnCorrectOptions attribute) (scranpy.batch_correction.mnn_correct.MnnCorrectResult attribute) (scranpy.clustering.build_snn_graph.BuildSnnGraphOptions attribute) (scranpy.dimensionality_reduction.combine_embeddings.CombineEmbeddingsOptions attribute) (scranpy.dimensionality_reduction.run_pca.RunPcaOptions attribute) (scranpy.dimensionality_reduction.run_tsne.InitializeTsneOptions attribute) (scranpy.dimensionality_reduction.run_tsne.RunTsneOptions attribute) (scranpy.dimensionality_reduction.run_umap.InitializeUmapOptions attribute) (scranpy.dimensionality_reduction.run_umap.RunUmapOptions attribute) (scranpy.feature_selection.choose_hvgs.ChooseHvgsOptions attribute) (scranpy.feature_selection.model_gene_variances.ModelGeneVariancesOptions attribute) (scranpy.feature_set_enrichment.hypergeometric_test.HypergeometricTestOptions attribute) (scranpy.feature_set_enrichment.score_feature_set.ScoreFeatureSetOptions attribute) (scranpy.marker_detection.score_markers.ScoreMarkersOptions attribute) (scranpy.nearest_neighbors.build_neighbor_index.BuildNeighborIndexOptions attribute) (scranpy.nearest_neighbors.find_nearest_neighbors.FindNearestNeighborsOptions attribute) (scranpy.normalization.center_size_factors.CenterSizeFactorsOptions attribute) (scranpy.normalization.grouped_size_factors.GroupedSizeFactorsOptions attribute) (scranpy.normalization.log_norm_counts.LogNormCountsOptions attribute) (scranpy.quality_control.create_adt_qc_filter.CreateAdtQcFilterOptions attribute) (scranpy.quality_control.create_crispr_qc_filter.CreateCrisprQcFilterOptions attribute) (scranpy.quality_control.create_rna_qc_filter.CreateRnaQcFilterOptions attribute) (scranpy.quality_control.filter_cells.FilterCellsOptions attribute) (scranpy.quality_control.per_cell_adt_qc_metrics.PerCellAdtQcMetricsOptions attribute) (scranpy.quality_control.per_cell_crispr_qc_metrics.PerCellCrisprQcMetricsOptions attribute) (scranpy.quality_control.per_cell_rna_qc_metrics.PerCellRnaQcMetricsOptions attribute) (scranpy.quality_control.suggest_adt_qc_filters.SuggestAdtQcFiltersOptions attribute) (scranpy.quality_control.suggest_crispr_qc_filters.SuggestCrisprQcFiltersOptions attribute) (scranpy.quality_control.suggest_rna_qc_filters.SuggestRnaQcFiltersOptions attribute) __dataclass_fields__ (scranpy.aggregation.aggregate_across_cells.AggregateAcrossCellsOptions attribute) (scranpy.analyze.AnalyzeOptions.AnalyzeOptions attribute) (scranpy.analyze.AnalyzeOptions.MiscellaneousOptions attribute) (scranpy.analyze.AnalyzeResults.AnalyzeResults attribute) (scranpy.batch_correction.mnn_correct.MnnCorrectOptions attribute) (scranpy.batch_correction.mnn_correct.MnnCorrectResult attribute) (scranpy.clustering.build_snn_graph.BuildSnnGraphOptions attribute) (scranpy.dimensionality_reduction.combine_embeddings.CombineEmbeddingsOptions attribute) (scranpy.dimensionality_reduction.run_pca.RunPcaOptions attribute) (scranpy.dimensionality_reduction.run_tsne.InitializeTsneOptions attribute) (scranpy.dimensionality_reduction.run_tsne.RunTsneOptions attribute) (scranpy.dimensionality_reduction.run_umap.InitializeUmapOptions attribute) (scranpy.dimensionality_reduction.run_umap.RunUmapOptions attribute) (scranpy.feature_selection.choose_hvgs.ChooseHvgsOptions attribute) (scranpy.feature_selection.model_gene_variances.ModelGeneVariancesOptions attribute) (scranpy.feature_set_enrichment.hypergeometric_test.HypergeometricTestOptions attribute) (scranpy.feature_set_enrichment.score_feature_set.ScoreFeatureSetOptions attribute) (scranpy.marker_detection.score_markers.ScoreMarkersOptions attribute) (scranpy.nearest_neighbors.build_neighbor_index.BuildNeighborIndexOptions attribute) (scranpy.nearest_neighbors.find_nearest_neighbors.FindNearestNeighborsOptions attribute) (scranpy.normalization.center_size_factors.CenterSizeFactorsOptions attribute) (scranpy.normalization.grouped_size_factors.GroupedSizeFactorsOptions attribute) (scranpy.normalization.log_norm_counts.LogNormCountsOptions attribute) (scranpy.quality_control.create_adt_qc_filter.CreateAdtQcFilterOptions attribute) (scranpy.quality_control.create_crispr_qc_filter.CreateCrisprQcFilterOptions attribute) (scranpy.quality_control.create_rna_qc_filter.CreateRnaQcFilterOptions attribute) (scranpy.quality_control.filter_cells.FilterCellsOptions attribute) (scranpy.quality_control.per_cell_adt_qc_metrics.PerCellAdtQcMetricsOptions attribute) (scranpy.quality_control.per_cell_crispr_qc_metrics.PerCellCrisprQcMetricsOptions attribute) (scranpy.quality_control.per_cell_rna_qc_metrics.PerCellRnaQcMetricsOptions attribute) (scranpy.quality_control.suggest_adt_qc_filters.SuggestAdtQcFiltersOptions attribute) (scranpy.quality_control.suggest_crispr_qc_filters.SuggestCrisprQcFiltersOptions attribute) (scranpy.quality_control.suggest_rna_qc_filters.SuggestRnaQcFiltersOptions attribute) __dataclass_params__ (scranpy.aggregation.aggregate_across_cells.AggregateAcrossCellsOptions attribute) (scranpy.analyze.AnalyzeOptions.AnalyzeOptions attribute) (scranpy.analyze.AnalyzeOptions.MiscellaneousOptions attribute) (scranpy.analyze.AnalyzeResults.AnalyzeResults attribute) (scranpy.batch_correction.mnn_correct.MnnCorrectOptions attribute) (scranpy.batch_correction.mnn_correct.MnnCorrectResult attribute) (scranpy.clustering.build_snn_graph.BuildSnnGraphOptions attribute) (scranpy.dimensionality_reduction.combine_embeddings.CombineEmbeddingsOptions attribute) (scranpy.dimensionality_reduction.run_pca.RunPcaOptions attribute) (scranpy.dimensionality_reduction.run_tsne.InitializeTsneOptions attribute) (scranpy.dimensionality_reduction.run_tsne.RunTsneOptions attribute) (scranpy.dimensionality_reduction.run_umap.InitializeUmapOptions attribute) (scranpy.dimensionality_reduction.run_umap.RunUmapOptions attribute) (scranpy.feature_selection.choose_hvgs.ChooseHvgsOptions attribute) (scranpy.feature_selection.model_gene_variances.ModelGeneVariancesOptions attribute) (scranpy.feature_set_enrichment.hypergeometric_test.HypergeometricTestOptions attribute) (scranpy.feature_set_enrichment.score_feature_set.ScoreFeatureSetOptions attribute) (scranpy.marker_detection.score_markers.ScoreMarkersOptions attribute) (scranpy.nearest_neighbors.build_neighbor_index.BuildNeighborIndexOptions attribute) (scranpy.nearest_neighbors.find_nearest_neighbors.FindNearestNeighborsOptions attribute) (scranpy.normalization.center_size_factors.CenterSizeFactorsOptions attribute) (scranpy.normalization.grouped_size_factors.GroupedSizeFactorsOptions attribute) (scranpy.normalization.log_norm_counts.LogNormCountsOptions attribute) (scranpy.quality_control.create_adt_qc_filter.CreateAdtQcFilterOptions attribute) (scranpy.quality_control.create_crispr_qc_filter.CreateCrisprQcFilterOptions attribute) (scranpy.quality_control.create_rna_qc_filter.CreateRnaQcFilterOptions attribute) (scranpy.quality_control.filter_cells.FilterCellsOptions attribute) (scranpy.quality_control.per_cell_adt_qc_metrics.PerCellAdtQcMetricsOptions attribute) (scranpy.quality_control.per_cell_crispr_qc_metrics.PerCellCrisprQcMetricsOptions attribute) (scranpy.quality_control.per_cell_rna_qc_metrics.PerCellRnaQcMetricsOptions attribute) (scranpy.quality_control.suggest_adt_qc_filters.SuggestAdtQcFiltersOptions attribute) (scranpy.quality_control.suggest_crispr_qc_filters.SuggestCrisprQcFiltersOptions attribute) (scranpy.quality_control.suggest_rna_qc_filters.SuggestRnaQcFiltersOptions attribute) __deepcopy__() (scranpy.dimensionality_reduction.run_tsne.TsneStatus method) (scranpy.dimensionality_reduction.run_umap.UmapStatus method) __del__() (scranpy.dimensionality_reduction.run_tsne.TsneStatus method) (scranpy.dimensionality_reduction.run_umap.UmapStatus method) (scranpy.nearest_neighbors.build_neighbor_index.NeighborIndex method) (scranpy.nearest_neighbors.find_nearest_neighbors.NeighborResults method) __eq__() (scranpy.aggregation.aggregate_across_cells.AggregateAcrossCellsOptions method) (scranpy.analyze.AnalyzeOptions.AnalyzeOptions method) (scranpy.analyze.AnalyzeOptions.MiscellaneousOptions method) (scranpy.analyze.AnalyzeResults.AnalyzeResults method) (scranpy.batch_correction.mnn_correct.MnnCorrectOptions method) (scranpy.batch_correction.mnn_correct.MnnCorrectResult method) (scranpy.clustering.build_snn_graph.BuildSnnGraphOptions method) (scranpy.dimensionality_reduction.combine_embeddings.CombineEmbeddingsOptions method) (scranpy.dimensionality_reduction.run_pca.RunPcaOptions method) (scranpy.dimensionality_reduction.run_tsne.InitializeTsneOptions method) (scranpy.dimensionality_reduction.run_tsne.RunTsneOptions method) (scranpy.dimensionality_reduction.run_umap.InitializeUmapOptions method) (scranpy.dimensionality_reduction.run_umap.RunUmapOptions method) (scranpy.feature_selection.choose_hvgs.ChooseHvgsOptions method) (scranpy.feature_selection.model_gene_variances.ModelGeneVariancesOptions method) (scranpy.feature_set_enrichment.hypergeometric_test.HypergeometricTestOptions method) (scranpy.feature_set_enrichment.score_feature_set.ScoreFeatureSetOptions method) (scranpy.marker_detection.score_markers.ScoreMarkersOptions method) (scranpy.nearest_neighbors.build_neighbor_index.BuildNeighborIndexOptions method) (scranpy.nearest_neighbors.find_nearest_neighbors.FindNearestNeighborsOptions method) (scranpy.normalization.center_size_factors.CenterSizeFactorsOptions method) (scranpy.normalization.grouped_size_factors.GroupedSizeFactorsOptions method) (scranpy.normalization.log_norm_counts.LogNormCountsOptions method) (scranpy.quality_control.create_adt_qc_filter.CreateAdtQcFilterOptions method) (scranpy.quality_control.create_crispr_qc_filter.CreateCrisprQcFilterOptions method) (scranpy.quality_control.create_rna_qc_filter.CreateRnaQcFilterOptions method) (scranpy.quality_control.filter_cells.FilterCellsOptions method) (scranpy.quality_control.per_cell_adt_qc_metrics.PerCellAdtQcMetricsOptions method) (scranpy.quality_control.per_cell_crispr_qc_metrics.PerCellCrisprQcMetricsOptions method) (scranpy.quality_control.per_cell_rna_qc_metrics.PerCellRnaQcMetricsOptions method) (scranpy.quality_control.suggest_adt_qc_filters.SuggestAdtQcFiltersOptions method) (scranpy.quality_control.suggest_crispr_qc_filters.SuggestCrisprQcFiltersOptions method) (scranpy.quality_control.suggest_rna_qc_filters.SuggestRnaQcFiltersOptions method) __getnewargs__() (scranpy.dimensionality_reduction.run_pca.PcaResult method) (scranpy.dimensionality_reduction.run_tsne.TsneEmbedding method) (scranpy.dimensionality_reduction.run_umap.UmapEmbedding method) (scranpy.nearest_neighbors.find_nearest_neighbors.SerializedNeighborResults method) (scranpy.nearest_neighbors.find_nearest_neighbors.SingleNeighborResults method) __hash__ (scranpy.aggregation.aggregate_across_cells.AggregateAcrossCellsOptions attribute) (scranpy.analyze.AnalyzeOptions.AnalyzeOptions attribute) (scranpy.analyze.AnalyzeOptions.MiscellaneousOptions attribute) (scranpy.analyze.AnalyzeResults.AnalyzeResults attribute) (scranpy.batch_correction.mnn_correct.MnnCorrectOptions attribute) (scranpy.batch_correction.mnn_correct.MnnCorrectResult attribute) (scranpy.clustering.build_snn_graph.BuildSnnGraphOptions attribute) (scranpy.dimensionality_reduction.combine_embeddings.CombineEmbeddingsOptions attribute) (scranpy.dimensionality_reduction.run_pca.RunPcaOptions attribute) (scranpy.dimensionality_reduction.run_tsne.InitializeTsneOptions attribute) (scranpy.dimensionality_reduction.run_tsne.RunTsneOptions attribute) (scranpy.dimensionality_reduction.run_umap.InitializeUmapOptions attribute) (scranpy.dimensionality_reduction.run_umap.RunUmapOptions attribute) (scranpy.feature_selection.choose_hvgs.ChooseHvgsOptions attribute) (scranpy.feature_selection.model_gene_variances.ModelGeneVariancesOptions attribute) (scranpy.feature_set_enrichment.hypergeometric_test.HypergeometricTestOptions attribute) (scranpy.feature_set_enrichment.score_feature_set.ScoreFeatureSetOptions attribute) (scranpy.marker_detection.score_markers.ScoreMarkersOptions attribute) (scranpy.nearest_neighbors.build_neighbor_index.BuildNeighborIndexOptions attribute) (scranpy.nearest_neighbors.find_nearest_neighbors.FindNearestNeighborsOptions attribute) (scranpy.normalization.center_size_factors.CenterSizeFactorsOptions attribute) (scranpy.normalization.grouped_size_factors.GroupedSizeFactorsOptions attribute) (scranpy.normalization.log_norm_counts.LogNormCountsOptions attribute) (scranpy.quality_control.create_adt_qc_filter.CreateAdtQcFilterOptions attribute) (scranpy.quality_control.create_crispr_qc_filter.CreateCrisprQcFilterOptions attribute) (scranpy.quality_control.create_rna_qc_filter.CreateRnaQcFilterOptions attribute) (scranpy.quality_control.filter_cells.FilterCellsOptions attribute) (scranpy.quality_control.per_cell_adt_qc_metrics.PerCellAdtQcMetricsOptions attribute) (scranpy.quality_control.per_cell_crispr_qc_metrics.PerCellCrisprQcMetricsOptions attribute) (scranpy.quality_control.per_cell_rna_qc_metrics.PerCellRnaQcMetricsOptions attribute) (scranpy.quality_control.suggest_adt_qc_filters.SuggestAdtQcFiltersOptions attribute) (scranpy.quality_control.suggest_crispr_qc_filters.SuggestCrisprQcFiltersOptions attribute) (scranpy.quality_control.suggest_rna_qc_filters.SuggestRnaQcFiltersOptions attribute) __new__() (scranpy.dimensionality_reduction.run_pca.PcaResult static method) (scranpy.dimensionality_reduction.run_tsne.TsneEmbedding static method) (scranpy.dimensionality_reduction.run_umap.UmapEmbedding static method) (scranpy.nearest_neighbors.find_nearest_neighbors.SerializedNeighborResults static method) (scranpy.nearest_neighbors.find_nearest_neighbors.SingleNeighborResults static method) __post_init__() (scranpy.clustering.build_snn_graph.BuildSnnGraphOptions method) (scranpy.dimensionality_reduction.run_pca.RunPcaOptions method) __repr__() (scranpy.aggregation.aggregate_across_cells.AggregateAcrossCellsOptions method) (scranpy.analyze.AnalyzeOptions.AnalyzeOptions method) (scranpy.analyze.AnalyzeOptions.MiscellaneousOptions method) (scranpy.analyze.AnalyzeResults.AnalyzeResults method) (scranpy.batch_correction.mnn_correct.MnnCorrectOptions method) (scranpy.batch_correction.mnn_correct.MnnCorrectResult method) (scranpy.clustering.build_snn_graph.BuildSnnGraphOptions method) (scranpy.dimensionality_reduction.combine_embeddings.CombineEmbeddingsOptions method) (scranpy.dimensionality_reduction.run_pca.PcaResult method) (scranpy.dimensionality_reduction.run_pca.RunPcaOptions method) (scranpy.dimensionality_reduction.run_tsne.InitializeTsneOptions method) (scranpy.dimensionality_reduction.run_tsne.RunTsneOptions method) (scranpy.dimensionality_reduction.run_tsne.TsneEmbedding method) (scranpy.dimensionality_reduction.run_umap.InitializeUmapOptions method) (scranpy.dimensionality_reduction.run_umap.RunUmapOptions method) (scranpy.dimensionality_reduction.run_umap.UmapEmbedding method) (scranpy.feature_selection.choose_hvgs.ChooseHvgsOptions method) (scranpy.feature_selection.model_gene_variances.ModelGeneVariancesOptions method) (scranpy.feature_set_enrichment.hypergeometric_test.HypergeometricTestOptions method) (scranpy.feature_set_enrichment.score_feature_set.ScoreFeatureSetOptions method) (scranpy.marker_detection.score_markers.ScoreMarkersOptions method) (scranpy.nearest_neighbors.build_neighbor_index.BuildNeighborIndexOptions method) (scranpy.nearest_neighbors.find_nearest_neighbors.FindNearestNeighborsOptions method) (scranpy.nearest_neighbors.find_nearest_neighbors.SerializedNeighborResults method) (scranpy.nearest_neighbors.find_nearest_neighbors.SingleNeighborResults method) (scranpy.normalization.center_size_factors.CenterSizeFactorsOptions method) (scranpy.normalization.grouped_size_factors.GroupedSizeFactorsOptions method) (scranpy.normalization.log_norm_counts.LogNormCountsOptions method) (scranpy.quality_control.create_adt_qc_filter.CreateAdtQcFilterOptions method) (scranpy.quality_control.create_crispr_qc_filter.CreateCrisprQcFilterOptions method) (scranpy.quality_control.create_rna_qc_filter.CreateRnaQcFilterOptions method) (scranpy.quality_control.filter_cells.FilterCellsOptions method) (scranpy.quality_control.per_cell_adt_qc_metrics.PerCellAdtQcMetricsOptions method) (scranpy.quality_control.per_cell_crispr_qc_metrics.PerCellCrisprQcMetricsOptions method) (scranpy.quality_control.per_cell_rna_qc_metrics.PerCellRnaQcMetricsOptions method) (scranpy.quality_control.suggest_adt_qc_filters.SuggestAdtQcFiltersOptions method) (scranpy.quality_control.suggest_crispr_qc_filters.SuggestCrisprQcFiltersOptions method) (scranpy.quality_control.suggest_rna_qc_filters.SuggestRnaQcFiltersOptions method) __slots__ (scranpy.dimensionality_reduction.run_pca.PcaResult attribute) (scranpy.dimensionality_reduction.run_tsne.TsneEmbedding attribute) (scranpy.dimensionality_reduction.run_umap.UmapEmbedding attribute) (scranpy.nearest_neighbors.find_nearest_neighbors.SerializedNeighborResults attribute) (scranpy.nearest_neighbors.find_nearest_neighbors.SingleNeighborResults attribute) A adt_feature_names (scranpy.analyze.AnalyzeOptions.MiscellaneousOptions attribute), [1] adt_log_norm_counts_options (scranpy.analyze.AnalyzeOptions.AnalyzeOptions attribute), [1] adt_markers (scranpy.analyze.AnalyzeResults.AnalyzeResults attribute), [1] adt_pca (scranpy.analyze.AnalyzeResults.AnalyzeResults attribute), [1] adt_quality_control_filter (scranpy.analyze.AnalyzeResults.AnalyzeResults attribute), [1] adt_quality_control_metrics (scranpy.analyze.AnalyzeResults.AnalyzeResults attribute), [1] adt_quality_control_thresholds (scranpy.analyze.AnalyzeResults.AnalyzeResults attribute), [1] adt_run_pca_options (scranpy.analyze.AnalyzeOptions.AnalyzeOptions attribute), [1] adt_score_markers_options (scranpy.analyze.AnalyzeOptions.AnalyzeOptions attribute), [1] adt_size_factors (scranpy.analyze.AnalyzeResults.AnalyzeResults attribute), [1] aggregate_across_cells() (in module scranpy.aggregation.aggregate_across_cells) AggregateAcrossCellsOptions (class in scranpy.aggregation.aggregate_across_cells) allow_non_finite (scranpy.normalization.center_size_factors.CenterSizeFactorsOptions attribute), [1] allow_zeros (scranpy.normalization.center_size_factors.CenterSizeFactorsOptions attribute), [1] analyze() (in module scranpy.analyze.analyze) analyze_sce() (in module scranpy.analyze.analyze) analyze_se() (in module scranpy.analyze.analyze) AnalyzeOptions (class in scranpy.analyze.AnalyzeOptions) AnalyzeResults (class in scranpy.analyze.AnalyzeResults) approximate (scranpy.batch_correction.mnn_correct.MnnCorrectOptions attribute), [1] (scranpy.dimensionality_reduction.combine_embeddings.CombineEmbeddingsOptions attribute), [1] (scranpy.nearest_neighbors.build_neighbor_index.BuildNeighborIndexOptions attribute), [1] assay_type (scranpy.aggregation.aggregate_across_cells.AggregateAcrossCellsOptions attribute), [1] (scranpy.dimensionality_reduction.run_pca.RunPcaOptions attribute), [1] (scranpy.feature_selection.model_gene_variances.ModelGeneVariancesOptions attribute), [1] (scranpy.feature_set_enrichment.score_feature_set.ScoreFeatureSetOptions attribute), [1] (scranpy.marker_detection.score_markers.ScoreMarkersOptions attribute), [1] (scranpy.normalization.grouped_size_factors.GroupedSizeFactorsOptions attribute), [1] (scranpy.normalization.log_norm_counts.LogNormCountsOptions attribute), [1] (scranpy.quality_control.per_cell_adt_qc_metrics.PerCellAdtQcMetricsOptions attribute), [1] (scranpy.quality_control.per_cell_crispr_qc_metrics.PerCellCrisprQcMetricsOptions attribute), [1] (scranpy.quality_control.per_cell_rna_qc_metrics.PerCellRnaQcMetricsOptions attribute), [1] B block (scranpy.analyze.AnalyzeOptions.MiscellaneousOptions attribute), [1] (scranpy.dimensionality_reduction.run_pca.RunPcaOptions attribute), [1] (scranpy.feature_selection.model_gene_variances.ModelGeneVariancesOptions attribute), [1] (scranpy.feature_set_enrichment.score_feature_set.ScoreFeatureSetOptions attribute), [1] (scranpy.marker_detection.score_markers.ScoreMarkersOptions attribute), [1] (scranpy.normalization.center_size_factors.CenterSizeFactorsOptions attribute), [1] (scranpy.normalization.grouped_size_factors.GroupedSizeFactorsOptions attribute), [1] (scranpy.normalization.log_norm_counts.LogNormCountsOptions attribute) (scranpy.quality_control.create_adt_qc_filter.CreateAdtQcFilterOptions attribute), [1] (scranpy.quality_control.create_crispr_qc_filter.CreateCrisprQcFilterOptions attribute), [1] (scranpy.quality_control.create_rna_qc_filter.CreateRnaQcFilterOptions attribute), [1] (scranpy.quality_control.suggest_adt_qc_filters.SuggestAdtQcFiltersOptions attribute), [1] (scranpy.quality_control.suggest_crispr_qc_filters.SuggestCrisprQcFiltersOptions attribute), [1] (scranpy.quality_control.suggest_rna_qc_filters.SuggestRnaQcFiltersOptions attribute), [1] block_method (scranpy.dimensionality_reduction.run_pca.RunPcaOptions attribute), [1] block_weights (scranpy.dimensionality_reduction.run_pca.RunPcaOptions attribute), [1] build_neighbor_index() (in module scranpy.nearest_neighbors.build_neighbor_index) build_neighbor_index_options (scranpy.analyze.AnalyzeOptions.AnalyzeOptions attribute), [1] (scranpy.clustering.build_snn_graph.BuildSnnGraphOptions attribute), [1] build_snn_graph() (in module scranpy.clustering.build_snn_graph) build_snn_graph_options (scranpy.analyze.AnalyzeOptions.AnalyzeOptions attribute), [1] BuildNeighborIndexOptions (class in scranpy.nearest_neighbors.build_neighbor_index) BuildSnnGraphOptions (class in scranpy.clustering.build_snn_graph) C cell_names (scranpy.analyze.AnalyzeOptions.MiscellaneousOptions attribute), [1] (scranpy.quality_control.per_cell_adt_qc_metrics.PerCellAdtQcMetricsOptions attribute), [1] (scranpy.quality_control.per_cell_crispr_qc_metrics.PerCellCrisprQcMetricsOptions attribute), [1] (scranpy.quality_control.per_cell_rna_qc_metrics.PerCellRnaQcMetricsOptions attribute), [1] center (scranpy.normalization.log_norm_counts.LogNormCountsOptions attribute), [1] center_size_factors() (in module scranpy.normalization.center_size_factors) center_size_factors_options (scranpy.normalization.log_norm_counts.LogNormCountsOptions attribute), [1] CenterSizeFactorsOptions (class in scranpy.normalization.center_size_factors) choose_hvgs() (in module scranpy.feature_selection.choose_hvgs) choose_hvgs_options (scranpy.analyze.AnalyzeOptions.AnalyzeOptions attribute), [1] ChooseHvgsOptions (class in scranpy.feature_selection.choose_hvgs) clone() (scranpy.dimensionality_reduction.run_tsne.TsneStatus method) (scranpy.dimensionality_reduction.run_umap.UmapStatus method) clusters (scranpy.analyze.AnalyzeResults.AnalyzeResults attribute), [1] combine_embeddings() (in module scranpy.dimensionality_reduction.combine_embeddings) combine_embeddings_options (scranpy.analyze.AnalyzeOptions.AnalyzeOptions attribute) combined_pcs (scranpy.analyze.AnalyzeResults.AnalyzeResults attribute), [1] CombineEmbeddingsOptions (class in scranpy.dimensionality_reduction.combine_embeddings) compute_auc (scranpy.marker_detection.score_markers.ScoreMarkersOptions attribute), [1] compute_detected (scranpy.aggregation.aggregate_across_cells.AggregateAcrossCellsOptions attribute), [1] compute_sums (scranpy.aggregation.aggregate_across_cells.AggregateAcrossCellsOptions attribute), [1] corrected (scranpy.batch_correction.mnn_correct.MnnCorrectResult attribute), [1] create_adt_qc_filter() (in module scranpy.quality_control.create_adt_qc_filter) create_adt_qc_filter_options (scranpy.analyze.AnalyzeOptions.AnalyzeOptions attribute), [1] create_crispr_qc_filter() (in module scranpy.quality_control.create_crispr_qc_filter) create_crispr_qc_filter_options (scranpy.analyze.AnalyzeOptions.AnalyzeOptions attribute), [1] create_rna_qc_filter() (in module scranpy.quality_control.create_rna_qc_filter) create_rna_qc_filter_options (scranpy.analyze.AnalyzeOptions.AnalyzeOptions attribute), [1] CreateAdtQcFilterOptions (class in scranpy.quality_control.create_adt_qc_filter) CreateCrisprQcFilterOptions (class in scranpy.quality_control.create_crispr_qc_filter) CreateRnaQcFilterOptions (class in scranpy.quality_control.create_rna_qc_filter) crispr_feature_names (scranpy.analyze.AnalyzeOptions.MiscellaneousOptions attribute), [1] crispr_log_norm_counts_options (scranpy.analyze.AnalyzeOptions.AnalyzeOptions attribute), [1] crispr_markers (scranpy.analyze.AnalyzeResults.AnalyzeResults attribute), [1] crispr_pca (scranpy.analyze.AnalyzeResults.AnalyzeResults attribute), [1] crispr_quality_control_filter (scranpy.analyze.AnalyzeResults.AnalyzeResults attribute), [1] crispr_quality_control_metrics (scranpy.analyze.AnalyzeResults.AnalyzeResults attribute), [1] crispr_quality_control_thresholds (scranpy.analyze.AnalyzeResults.AnalyzeResults attribute), [1] crispr_run_pca_options (scranpy.analyze.AnalyzeOptions.AnalyzeOptions attribute), [1] crispr_score_markers_options (scranpy.analyze.AnalyzeOptions.AnalyzeOptions attribute), [1] crispr_size_factors (scranpy.analyze.AnalyzeResults.AnalyzeResults attribute), [1] custom_thresholds (scranpy.quality_control.suggest_adt_qc_filters.SuggestAdtQcFiltersOptions attribute), [1] (scranpy.quality_control.suggest_crispr_qc_filters.SuggestCrisprQcFiltersOptions attribute), [1] (scranpy.quality_control.suggest_rna_qc_filters.SuggestRnaQcFiltersOptions attribute), [1] D delayed (scranpy.normalization.log_norm_counts.LogNormCountsOptions attribute), [1] (scranpy.quality_control.filter_cells.FilterCellsOptions attribute), [1] discard (scranpy.quality_control.filter_cells.FilterCellsOptions attribute), [1] distance (scranpy.nearest_neighbors.find_nearest_neighbors.SerializedNeighborResults attribute) (scranpy.nearest_neighbors.find_nearest_neighbors.SingleNeighborResults attribute) downsample_by_neighbors() (in module scranpy.aggregation.downsample_by_neighbors) DownsampleByNeighborsOptions (class in scranpy.aggregation.downsample_by_neighbors) dry_analyze() (in module scranpy.analyze.dry_analyze) E epoch() (scranpy.dimensionality_reduction.run_umap.UmapStatus method) extract() (scranpy.dimensionality_reduction.run_tsne.TsneStatus method) (scranpy.dimensionality_reduction.run_umap.UmapStatus method) F feature_names (scranpy.feature_selection.model_gene_variances.ModelGeneVariancesOptions attribute), [1] (scranpy.marker_detection.score_markers.ScoreMarkersOptions attribute), [1] filter_cells() (in module scranpy.quality_control.filter_cells) filter_cells_options (scranpy.analyze.AnalyzeOptions.AnalyzeOptions attribute), [1] filter_on_adt_qc (scranpy.analyze.AnalyzeOptions.MiscellaneousOptions attribute), [1] filter_on_crispr_qc (scranpy.analyze.AnalyzeOptions.MiscellaneousOptions attribute), [1] filter_on_rna_qc (scranpy.analyze.AnalyzeOptions.MiscellaneousOptions attribute), [1] FilterCellsOptions (class in scranpy.quality_control.filter_cells) find_nearest_neighbors() (in module scranpy.nearest_neighbors.find_nearest_neighbors) find_nearest_neighbors_options (scranpy.analyze.AnalyzeOptions.AnalyzeOptions attribute), [1] FindNearestNeighborsOptions (class in scranpy.nearest_neighbors.find_nearest_neighbors) G gene_variances (scranpy.analyze.AnalyzeResults.AnalyzeResults attribute), [1] get() (scranpy.nearest_neighbors.find_nearest_neighbors.NeighborResults method) grouped_size_factors() (in module scranpy.normalization.grouped_size_factors) grouped_size_factors_options (scranpy.analyze.AnalyzeOptions.AnalyzeOptions attribute), [1] GroupedSizeFactorsOptions (class in scranpy.normalization.grouped_size_factors) groups (scranpy.normalization.grouped_size_factors.GroupedSizeFactorsOptions attribute), [1] guess_mito_from_symbols() (in module scranpy.quality_control.guess_mito_from_symbols) H hvgs (scranpy.analyze.AnalyzeResults.AnalyzeResults attribute), [1] hypergeometric_test() (in module scranpy.feature_set_enrichment.hypergeometric_test) HypergeometricTestOptions (class in scranpy.feature_set_enrichment.hypergeometric_test) I in_place (scranpy.normalization.center_size_factors.CenterSizeFactorsOptions attribute), [1] index (scranpy.nearest_neighbors.find_nearest_neighbors.SerializedNeighborResults attribute) (scranpy.nearest_neighbors.find_nearest_neighbors.SingleNeighborResults attribute) initial_factors (scranpy.normalization.grouped_size_factors.GroupedSizeFactorsOptions attribute), [1] initialize_tsne (scranpy.dimensionality_reduction.run_tsne.RunTsneOptions attribute), [1] initialize_tsne() (in module scranpy.dimensionality_reduction.run_tsne) initialize_umap (scranpy.dimensionality_reduction.run_umap.RunUmapOptions attribute), [1] initialize_umap() (in module scranpy.dimensionality_reduction.run_umap) InitializeTsneOptions (class in scranpy.dimensionality_reduction.run_tsne) InitializeUmapOptions (class in scranpy.dimensionality_reduction.run_umap) intersect (scranpy.quality_control.filter_cells.FilterCellsOptions attribute), [1] iteration() (scranpy.dimensionality_reduction.run_tsne.TsneStatus method) K k (scranpy.batch_correction.mnn_correct.MnnCorrectOptions attribute), [1] L live_analyze() (in module scranpy.analyze.live_analyze) log (scranpy.feature_set_enrichment.hypergeometric_test.HypergeometricTestOptions attribute), [1] log_norm_counts() (in module scranpy.normalization.log_norm_counts) LogNormCountsOptions (class in scranpy.normalization.log_norm_counts) M mass_cap (scranpy.batch_correction.mnn_correct.MnnCorrectOptions attribute), [1] max_iterations (scranpy.dimensionality_reduction.run_tsne.RunTsneOptions attribute), [1] merge_order (scranpy.batch_correction.mnn_correct.MnnCorrectResult attribute), [1] min_dist (scranpy.dimensionality_reduction.run_umap.InitializeUmapOptions attribute) miscellaneous_options (scranpy.analyze.AnalyzeOptions.AnalyzeOptions attribute), [1] MiscellaneousOptions (class in scranpy.analyze.AnalyzeOptions) mnn (scranpy.analyze.AnalyzeResults.AnalyzeResults attribute), [1] mnn_correct() (in module scranpy.batch_correction.mnn_correct) mnn_correct_options (scranpy.analyze.AnalyzeOptions.AnalyzeOptions attribute), [1] MnnCorrectOptions (class in scranpy.batch_correction.mnn_correct) MnnCorrectResult (class in scranpy.batch_correction.mnn_correct) model_gene_variances() (in module scranpy.feature_selection.model_gene_variances) model_gene_variances_options (scranpy.analyze.AnalyzeOptions.AnalyzeOptions attribute), [1] ModelGeneVariancesOptions (class in scranpy.feature_selection.model_gene_variances) module scranpy scranpy.aggregation scranpy.aggregation.aggregate_across_cells scranpy.aggregation.downsample_by_neighbors scranpy.analyze scranpy.analyze.analyze scranpy.analyze.AnalyzeOptions scranpy.analyze.AnalyzeResults scranpy.analyze.dry_analyze scranpy.analyze.live_analyze scranpy.analyze.run_neighbor_suite scranpy.analyze.update scranpy.batch_correction scranpy.batch_correction.mnn_correct scranpy.clustering scranpy.clustering.build_snn_graph scranpy.dimensionality_reduction scranpy.dimensionality_reduction.combine_embeddings scranpy.dimensionality_reduction.run_pca scranpy.dimensionality_reduction.run_tsne scranpy.dimensionality_reduction.run_umap scranpy.feature_selection scranpy.feature_selection.choose_hvgs scranpy.feature_selection.model_gene_variances scranpy.feature_set_enrichment scranpy.feature_set_enrichment.hypergeometric_test scranpy.feature_set_enrichment.score_feature_set scranpy.marker_detection scranpy.marker_detection.score_markers scranpy.nearest_neighbors scranpy.nearest_neighbors.build_neighbor_index scranpy.nearest_neighbors.find_nearest_neighbors scranpy.normalization scranpy.normalization.center_size_factors scranpy.normalization.grouped_size_factors scranpy.normalization.log_norm_counts scranpy.quality_control scranpy.quality_control.create_adt_qc_filter scranpy.quality_control.create_crispr_qc_filter scranpy.quality_control.create_rna_qc_filter scranpy.quality_control.filter_cells scranpy.quality_control.guess_mito_from_symbols scranpy.quality_control.per_cell_adt_qc_metrics scranpy.quality_control.per_cell_crispr_qc_metrics scranpy.quality_control.per_cell_rna_qc_metrics scranpy.quality_control.suggest_adt_qc_filters scranpy.quality_control.suggest_crispr_qc_filters scranpy.quality_control.suggest_rna_qc_filters N NeighborIndex (class in scranpy.nearest_neighbors.build_neighbor_index) NeighborResults (class in scranpy.nearest_neighbors.find_nearest_neighbors) neighbors (scranpy.dimensionality_reduction.combine_embeddings.CombineEmbeddingsOptions attribute), [1] num_cells() (scranpy.dimensionality_reduction.run_tsne.TsneStatus method) (scranpy.dimensionality_reduction.run_umap.UmapStatus method) (scranpy.nearest_neighbors.build_neighbor_index.NeighborIndex method) (scranpy.nearest_neighbors.find_nearest_neighbors.NeighborResults method) num_dimensions() (scranpy.nearest_neighbors.build_neighbor_index.NeighborIndex method) num_epochs (scranpy.dimensionality_reduction.run_umap.InitializeUmapOptions attribute) num_epochs() (scranpy.dimensionality_reduction.run_umap.UmapStatus method) num_mads (scranpy.batch_correction.mnn_correct.MnnCorrectOptions attribute), [1] (scranpy.quality_control.suggest_adt_qc_filters.SuggestAdtQcFiltersOptions attribute), [1] (scranpy.quality_control.suggest_crispr_qc_filters.SuggestCrisprQcFiltersOptions attribute), [1] (scranpy.quality_control.suggest_rna_qc_filters.SuggestRnaQcFiltersOptions attribute), [1] num_neighbors (scranpy.clustering.build_snn_graph.BuildSnnGraphOptions attribute), [1] (scranpy.dimensionality_reduction.run_umap.InitializeUmapOptions attribute) num_neighbors() (scranpy.nearest_neighbors.find_nearest_neighbors.NeighborResults method) num_pairs (scranpy.batch_correction.mnn_correct.MnnCorrectResult attribute), [1] num_threads (scranpy.aggregation.aggregate_across_cells.AggregateAcrossCellsOptions attribute), [1] (scranpy.aggregation.downsample_by_neighbors.DownsampleByNeighborsOptions attribute), [1] (scranpy.batch_correction.mnn_correct.MnnCorrectOptions attribute), [1] (scranpy.clustering.build_snn_graph.BuildSnnGraphOptions attribute), [1] (scranpy.dimensionality_reduction.combine_embeddings.CombineEmbeddingsOptions attribute), [1] (scranpy.dimensionality_reduction.run_pca.RunPcaOptions attribute), [1] (scranpy.dimensionality_reduction.run_tsne.InitializeTsneOptions attribute), [1] (scranpy.dimensionality_reduction.run_umap.InitializeUmapOptions attribute) (scranpy.feature_selection.model_gene_variances.ModelGeneVariancesOptions attribute), [1] (scranpy.feature_set_enrichment.hypergeometric_test.HypergeometricTestOptions attribute), [1] (scranpy.feature_set_enrichment.score_feature_set.ScoreFeatureSetOptions attribute), [1] (scranpy.marker_detection.score_markers.ScoreMarkersOptions attribute), [1] (scranpy.nearest_neighbors.find_nearest_neighbors.FindNearestNeighborsOptions attribute), [1] (scranpy.normalization.grouped_size_factors.GroupedSizeFactorsOptions attribute), [1] (scranpy.normalization.log_norm_counts.LogNormCountsOptions attribute), [1] (scranpy.quality_control.per_cell_adt_qc_metrics.PerCellAdtQcMetricsOptions attribute), [1] (scranpy.quality_control.per_cell_crispr_qc_metrics.PerCellCrisprQcMetricsOptions attribute), [1] (scranpy.quality_control.per_cell_rna_qc_metrics.PerCellRnaQcMetricsOptions attribute), [1] number (scranpy.feature_selection.choose_hvgs.ChooseHvgsOptions attribute), [1] O order (scranpy.batch_correction.mnn_correct.MnnCorrectOptions attribute), [1] P PcaResult (class in scranpy.dimensionality_reduction.run_pca) per_cell_adt_qc_metrics() (in module scranpy.quality_control.per_cell_adt_qc_metrics) per_cell_adt_qc_metrics_options (scranpy.analyze.AnalyzeOptions.AnalyzeOptions attribute), [1] per_cell_crispr_qc_metrics() (in module scranpy.quality_control.per_cell_crispr_qc_metrics) per_cell_crispr_qc_metrics_options (scranpy.analyze.AnalyzeOptions.AnalyzeOptions attribute), [1] per_cell_rna_qc_metrics() (in module scranpy.quality_control.per_cell_rna_qc_metrics) per_cell_rna_qc_metrics_options (scranpy.analyze.AnalyzeOptions.AnalyzeOptions attribute), [1] PerCellAdtQcMetricsOptions (class in scranpy.quality_control.per_cell_adt_qc_metrics) PerCellCrisprQcMetricsOptions (class in scranpy.quality_control.per_cell_crispr_qc_metrics) PerCellRnaQcMetricsOptions (class in scranpy.quality_control.per_cell_rna_qc_metrics) perplexity (scranpy.dimensionality_reduction.run_tsne.InitializeTsneOptions attribute), [1] principal_components (scranpy.dimensionality_reduction.run_pca.PcaResult attribute) ptr (scranpy.nearest_neighbors.build_neighbor_index.NeighborIndex property) (scranpy.nearest_neighbors.find_nearest_neighbors.NeighborResults property) Q quality_control_retained (scranpy.analyze.AnalyzeResults.AnalyzeResults attribute), [1] R rank (scranpy.dimensionality_reduction.run_pca.RunPcaOptions attribute), [1] (scranpy.normalization.grouped_size_factors.GroupedSizeFactorsOptions attribute), [1] reference_policy (scranpy.batch_correction.mnn_correct.MnnCorrectOptions attribute), [1] rna_feature_names (scranpy.analyze.AnalyzeOptions.MiscellaneousOptions attribute), [1] rna_log_norm_counts_options (scranpy.analyze.AnalyzeOptions.AnalyzeOptions attribute), [1] rna_markers (scranpy.analyze.AnalyzeResults.AnalyzeResults attribute), [1] rna_pca (scranpy.analyze.AnalyzeResults.AnalyzeResults attribute), [1] rna_quality_control_filter (scranpy.analyze.AnalyzeResults.AnalyzeResults attribute), [1] rna_quality_control_metrics (scranpy.analyze.AnalyzeResults.AnalyzeResults attribute), [1] rna_quality_control_thresholds (scranpy.analyze.AnalyzeResults.AnalyzeResults attribute), [1] rna_run_pca_options (scranpy.analyze.AnalyzeOptions.AnalyzeOptions attribute), [1] rna_score_markers_options (scranpy.analyze.AnalyzeOptions.AnalyzeOptions attribute), [1] rna_size_factors (scranpy.analyze.AnalyzeResults.AnalyzeResults attribute), [1] run() (scranpy.dimensionality_reduction.run_tsne.TsneStatus method) (scranpy.dimensionality_reduction.run_umap.UmapStatus method) run_neighbor_suite() (in module scranpy.analyze.run_neighbor_suite) run_pca() (in module scranpy.dimensionality_reduction.run_pca) run_tsne() (in module scranpy.dimensionality_reduction.run_tsne) run_tsne_options (scranpy.analyze.AnalyzeOptions.AnalyzeOptions attribute), [1] run_umap() (in module scranpy.dimensionality_reduction.run_umap) run_umap_options (scranpy.analyze.AnalyzeOptions.AnalyzeOptions attribute), [1] RunPcaOptions (class in scranpy.dimensionality_reduction.run_pca) RunTsneOptions (class in scranpy.dimensionality_reduction.run_tsne) RunUmapOptions (class in scranpy.dimensionality_reduction.run_umap) S scale (scranpy.dimensionality_reduction.run_pca.RunPcaOptions attribute), [1] (scranpy.feature_set_enrichment.score_feature_set.ScoreFeatureSetOptions attribute), [1] score_feature_set() (in module scranpy.feature_set_enrichment.score_feature_set) score_markers() (in module scranpy.marker_detection.score_markers) ScoreFeatureSetOptions (class in scranpy.feature_set_enrichment.score_feature_set) ScoreMarkersOptions (class in scranpy.marker_detection.score_markers) scranpy module scranpy.aggregation module scranpy.aggregation.aggregate_across_cells module scranpy.aggregation.downsample_by_neighbors module scranpy.analyze module scranpy.analyze.analyze module scranpy.analyze.AnalyzeOptions module scranpy.analyze.AnalyzeResults module scranpy.analyze.dry_analyze module scranpy.analyze.live_analyze module scranpy.analyze.run_neighbor_suite module scranpy.analyze.update module scranpy.batch_correction module scranpy.batch_correction.mnn_correct module scranpy.clustering module scranpy.clustering.build_snn_graph module scranpy.dimensionality_reduction module scranpy.dimensionality_reduction.combine_embeddings module scranpy.dimensionality_reduction.run_pca module scranpy.dimensionality_reduction.run_tsne module scranpy.dimensionality_reduction.run_umap module scranpy.feature_selection module scranpy.feature_selection.choose_hvgs module scranpy.feature_selection.model_gene_variances module scranpy.feature_set_enrichment module scranpy.feature_set_enrichment.hypergeometric_test module scranpy.feature_set_enrichment.score_feature_set module scranpy.marker_detection module scranpy.marker_detection.score_markers module scranpy.nearest_neighbors module scranpy.nearest_neighbors.build_neighbor_index module scranpy.nearest_neighbors.find_nearest_neighbors module scranpy.normalization module scranpy.normalization.center_size_factors module scranpy.normalization.grouped_size_factors module scranpy.normalization.log_norm_counts module scranpy.quality_control module scranpy.quality_control.create_adt_qc_filter module scranpy.quality_control.create_crispr_qc_filter module scranpy.quality_control.create_rna_qc_filter module scranpy.quality_control.filter_cells module scranpy.quality_control.guess_mito_from_symbols module scranpy.quality_control.per_cell_adt_qc_metrics module scranpy.quality_control.per_cell_crispr_qc_metrics module scranpy.quality_control.per_cell_rna_qc_metrics module scranpy.quality_control.suggest_adt_qc_filters module scranpy.quality_control.suggest_crispr_qc_filters module scranpy.quality_control.suggest_rna_qc_filters module seed (scranpy.dimensionality_reduction.run_tsne.InitializeTsneOptions attribute), [1] (scranpy.dimensionality_reduction.run_umap.InitializeUmapOptions attribute) serialize() (scranpy.nearest_neighbors.find_nearest_neighbors.NeighborResults method) SerializedNeighborResults (class in scranpy.nearest_neighbors.find_nearest_neighbors) set_seed() (scranpy.analyze.AnalyzeOptions.AnalyzeOptions method) set_threads() (scranpy.analyze.AnalyzeOptions.AnalyzeOptions method) (scranpy.clustering.build_snn_graph.BuildSnnGraphOptions method) (scranpy.dimensionality_reduction.run_tsne.InitializeTsneOptions method) (scranpy.dimensionality_reduction.run_tsne.RunTsneOptions method) (scranpy.dimensionality_reduction.run_umap.InitializeUmapOptions method) (scranpy.dimensionality_reduction.run_umap.RunUmapOptions method) SingleNeighborResults (class in scranpy.nearest_neighbors.find_nearest_neighbors) size_factors (scranpy.normalization.log_norm_counts.LogNormCountsOptions attribute), [1] snn_graph (scranpy.analyze.AnalyzeResults.AnalyzeResults attribute), [1] snn_graph_multilevel_resolution (scranpy.analyze.AnalyzeOptions.MiscellaneousOptions attribute), [1] span (scranpy.feature_selection.model_gene_variances.ModelGeneVariancesOptions attribute), [1] subset (scranpy.dimensionality_reduction.run_pca.RunPcaOptions attribute), [1] subsets (scranpy.quality_control.per_cell_adt_qc_metrics.PerCellAdtQcMetricsOptions attribute), [1] (scranpy.quality_control.per_cell_rna_qc_metrics.PerCellRnaQcMetricsOptions attribute), [1] suggest_adt_qc_filters() (in module scranpy.quality_control.suggest_adt_qc_filters) suggest_adt_qc_filters_options (scranpy.analyze.AnalyzeOptions.AnalyzeOptions attribute), [1] suggest_crispr_qc_filters() (in module scranpy.quality_control.suggest_crispr_qc_filters) suggest_crispr_qc_filters_options (scranpy.analyze.AnalyzeOptions.AnalyzeOptions attribute), [1] suggest_rna_qc_filters() (in module scranpy.quality_control.suggest_rna_qc_filters) suggest_rna_qc_filters_options (scranpy.analyze.AnalyzeOptions.AnalyzeOptions attribute), [1] SuggestAdtQcFiltersOptions (class in scranpy.quality_control.suggest_adt_qc_filters) SuggestCrisprQcFiltersOptions (class in scranpy.quality_control.suggest_crispr_qc_filters) SuggestRnaQcFiltersOptions (class in scranpy.quality_control.suggest_rna_qc_filters) T threshold (scranpy.marker_detection.score_markers.ScoreMarkersOptions attribute), [1] to_sce() (scranpy.analyze.AnalyzeResults.AnalyzeResults method) tsne (scranpy.analyze.AnalyzeResults.AnalyzeResults attribute), [1] tsne_perplexity_to_neighbors() (in module scranpy.dimensionality_reduction.run_tsne) TsneEmbedding (class in scranpy.dimensionality_reduction.run_tsne) TsneStatus (class in scranpy.dimensionality_reduction.run_tsne) U umap (scranpy.analyze.AnalyzeResults.AnalyzeResults attribute), [1] UmapEmbedding (class in scranpy.dimensionality_reduction.run_umap) UmapStatus (class in scranpy.dimensionality_reduction.run_umap) unserialize() (scranpy.nearest_neighbors.find_nearest_neighbors.NeighborResults class method) update() (in module scranpy.analyze.update) upper_tail (scranpy.feature_set_enrichment.hypergeometric_test.HypergeometricTestOptions attribute), [1] V variance_explained (scranpy.dimensionality_reduction.run_pca.PcaResult attribute) W weight_scheme (scranpy.clustering.build_snn_graph.BuildSnnGraphOptions attribute), [1] weights (scranpy.dimensionality_reduction.combine_embeddings.CombineEmbeddingsOptions attribute), [1] with_retain_vector (scranpy.quality_control.filter_cells.FilterCellsOptions attribute), [1] with_size_factors (scranpy.normalization.log_norm_counts.LogNormCountsOptions attribute), [1] X x (scranpy.dimensionality_reduction.run_tsne.TsneEmbedding attribute) (scranpy.dimensionality_reduction.run_umap.UmapEmbedding attribute) Y y (scranpy.dimensionality_reduction.run_tsne.TsneEmbedding attribute) (scranpy.dimensionality_reduction.run_umap.UmapEmbedding attribute)