Index A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | U | V | W A add_dendrogram() (scanpy.pl.DotPlot method) (scanpy.pl.MatrixPlot method) (scanpy.pl.StackedViolin method) add_totals() (scanpy.pl.DotPlot method) (scanpy.pl.MatrixPlot method) (scanpy.pl.StackedViolin method) aggregate() (in module scanpy.get) autosave (scanpy._settings.ScanpyConfig property) autoshow (scanpy._settings.ScanpyConfig property) B bbknn() (in module scanpy.external.pp) biomart_annotations() (in module scanpy.queries) blobs() (in module scanpy.datasets) C cache_compression (scanpy._settings.ScanpyConfig property) cachedir (scanpy._settings.ScanpyConfig property) calculate_qc_metrics() (in module scanpy.pp) categories_to_ignore (scanpy._settings.ScanpyConfig property) cellbrowser() (in module scanpy.external.exporting) clustermap() (in module scanpy.pl) combat() (in module scanpy.pp) compute_eigen() (scanpy.Neighbors method) compute_neighbors() (scanpy.Neighbors method) compute_transitions() (scanpy.Neighbors method) confusion_matrix() (in module scanpy.metrics) connectivities (scanpy.Neighbors property) cyclone() (in module scanpy.external.tl) D datasetdir (scanpy._settings.ScanpyConfig property) dca() (in module scanpy.external.pp) DEFAULT_CATEGORY_HEIGHT (scanpy.pl.DotPlot attribute) (scanpy.pl.MatrixPlot attribute) (scanpy.pl.StackedViolin attribute) DEFAULT_CATEGORY_WIDTH (scanpy.pl.DotPlot attribute) (scanpy.pl.MatrixPlot attribute) (scanpy.pl.StackedViolin attribute) DEFAULT_COLOR_LEGEND_TITLE (scanpy.pl.DotPlot attribute) (scanpy.pl.MatrixPlot attribute) (scanpy.pl.StackedViolin attribute) DEFAULT_COLOR_ON (scanpy.pl.DotPlot attribute) DEFAULT_COLORMAP (scanpy.pl.DotPlot attribute) (scanpy.pl.MatrixPlot attribute) (scanpy.pl.StackedViolin attribute) DEFAULT_CUT (scanpy.pl.StackedViolin attribute) DEFAULT_DENSITY_NORM (scanpy.pl.StackedViolin attribute) DEFAULT_DOT_EDGECOLOR (scanpy.pl.DotPlot attribute) DEFAULT_DOT_EDGELW (scanpy.pl.DotPlot attribute) DEFAULT_DOT_MAX (scanpy.pl.DotPlot attribute) DEFAULT_DOT_MIN (scanpy.pl.DotPlot attribute) DEFAULT_EDGE_COLOR (scanpy.pl.MatrixPlot attribute) DEFAULT_EDGE_LW (scanpy.pl.MatrixPlot attribute) DEFAULT_INNER (scanpy.pl.StackedViolin attribute) DEFAULT_JITTER (scanpy.pl.StackedViolin attribute) DEFAULT_JITTER_SIZE (scanpy.pl.StackedViolin attribute) DEFAULT_LARGEST_DOT (scanpy.pl.DotPlot attribute) DEFAULT_LEGENDS_WIDTH (scanpy.pl.DotPlot attribute) (scanpy.pl.MatrixPlot attribute) (scanpy.pl.StackedViolin attribute) DEFAULT_LINE_WIDTH (scanpy.pl.StackedViolin attribute) DEFAULT_PLOT_X_PADDING (scanpy.pl.DotPlot attribute) (scanpy.pl.StackedViolin attribute) DEFAULT_PLOT_Y_PADDING (scanpy.pl.DotPlot attribute) (scanpy.pl.StackedViolin attribute) DEFAULT_PLOT_YTICKLABELS (scanpy.pl.StackedViolin attribute) DEFAULT_ROW_PALETTE (scanpy.pl.StackedViolin attribute) DEFAULT_SAVE_PREFIX (scanpy.pl.DotPlot attribute) (scanpy.pl.MatrixPlot attribute) (scanpy.pl.StackedViolin attribute) DEFAULT_SIZE_EXPONENT (scanpy.pl.DotPlot attribute) DEFAULT_SIZE_LEGEND_TITLE (scanpy.pl.DotPlot attribute) DEFAULT_SMALLEST_DOT (scanpy.pl.DotPlot attribute) DEFAULT_STRIPPLOT (scanpy.pl.StackedViolin attribute) DEFAULT_WSPACE (scanpy.pl.DotPlot attribute) (scanpy.pl.MatrixPlot attribute) (scanpy.pl.StackedViolin attribute) DEFAULT_YLIM (scanpy.pl.StackedViolin attribute) dendrogram() (in module scanpy.pl) (in module scanpy.tl) diffmap() (in module scanpy.pl) (in module scanpy.tl) distances (scanpy.Neighbors property) distances_dpt (scanpy.Neighbors property) DotPlot (class in scanpy.pl) dotplot() (in module scanpy.pl) downsample_counts() (in module scanpy.pp) dpt() (in module scanpy.tl) dpt_groups_pseudotime() (in module scanpy.pl) dpt_timeseries() (in module scanpy.pl) draw_graph() (in module scanpy.pl) (in module scanpy.tl) E ebi_expression_atlas() (in module scanpy.datasets) eigen_basis (scanpy.Neighbors property) eigen_values (scanpy.Neighbors property) embedding() (in module scanpy.pl) embedding_density() (in module scanpy.pl) (in module scanpy.tl) enrich() (in module scanpy.queries) F figdir (scanpy._settings.ScanpyConfig property) file_format_data (scanpy._settings.ScanpyConfig property) file_format_figs (scanpy._settings.ScanpyConfig property) filter_cells() (in module scanpy.pp) filter_genes() (in module scanpy.pp) filter_genes_dispersion() (in module scanpy.pl) (in module scanpy.pp) filter_rank_genes_groups() (in module scanpy.tl) G gearys_c() (in module scanpy.metrics) gene_coordinates() (in module scanpy.queries) get_axes() (scanpy.pl.DotPlot method) (scanpy.pl.MatrixPlot method) (scanpy.pl.StackedViolin method) getdoc() (scanpy.Neighbors method) (scanpy.pl.DotPlot method) (scanpy.pl.MatrixPlot method) (scanpy.pl.StackedViolin method) H harmony_integrate() (in module scanpy.external.pp) harmony_timeseries() (in module scanpy.external.tl) hashsolo() (in module scanpy.external.pp) heatmap() (in module scanpy.pl) highest_expr_genes() (in module scanpy.pl) highly_variable_genes() (in module scanpy.experimental.pp) (in module scanpy.pl) (in module scanpy.pp) I ingest() (in module scanpy.tl) K krumsiek11() (in module scanpy.datasets) L legend() (scanpy.pl.DotPlot method) (scanpy.pl.MatrixPlot method) (scanpy.pl.StackedViolin method) leiden() (in module scanpy.tl) log1p() (in module scanpy.pp) logfile (scanpy._settings.ScanpyConfig property) logpath (scanpy._settings.ScanpyConfig property) louvain() (in module scanpy.tl) M magic() (in module scanpy.external.pp) make_figure() (scanpy.pl.DotPlot method) (scanpy.pl.MatrixPlot method) (scanpy.pl.StackedViolin method) marker_gene_overlap() (in module scanpy.tl) MatrixPlot (class in scanpy.pl) matrixplot() (in module scanpy.pl) max_memory (scanpy._settings.ScanpyConfig property) MAX_NUM_CATEGORIES (scanpy.pl.DotPlot attribute) (scanpy.pl.MatrixPlot attribute) (scanpy.pl.StackedViolin attribute) MIN_FIGURE_HEIGHT (scanpy.pl.DotPlot attribute) (scanpy.pl.MatrixPlot attribute) (scanpy.pl.StackedViolin attribute) mitochondrial_genes() (in module scanpy.queries) mnn_correct() (in module scanpy.external.pp) module scanpy.datasets scanpy.experimental scanpy.experimental.pp scanpy.external scanpy.external.exporting scanpy.external.pl scanpy.external.pp scanpy.external.tl scanpy.get scanpy.metrics scanpy.pl scanpy.pp scanpy.queries scanpy.tl moignard15() (in module scanpy.datasets) morans_i() (in module scanpy.metrics) N n_jobs (scanpy._settings.ScanpyConfig property) N_PCS (scanpy._settings.ScanpyConfig attribute) Neighbors (class in scanpy) neighbors() (in module scanpy.pp) normalize_pearson_residuals() (in module scanpy.experimental.pp) normalize_pearson_residuals_pca() (in module scanpy.experimental.pp) normalize_per_cell() (in module scanpy.pp) normalize_total() (in module scanpy.pp) O obs_df() (in module scanpy.get) P paga() (in module scanpy.pl) (in module scanpy.tl) paga_compare() (in module scanpy.pl) paga_path() (in module scanpy.pl) palantir() (in module scanpy.external.tl) palantir_results() (in module scanpy.external.tl) paul15() (in module scanpy.datasets) pbmc3k() (in module scanpy.datasets) pbmc3k_processed() (in module scanpy.datasets) pbmc68k_reduced() (in module scanpy.datasets) pca() (in module scanpy.pl) (in module scanpy.pp) pca_loadings() (in module scanpy.pl) pca_overview() (in module scanpy.pl) pca_variance_ratio() (in module scanpy.pl) phate() (in module scanpy.external.pl) (in module scanpy.external.tl) phenograph() (in module scanpy.external.tl) plot_suffix (scanpy._settings.ScanpyConfig property) print_header() (in module scanpy.logging) print_versions() (in module scanpy.logging) R rank_genes_groups() (in module scanpy.pl) (in module scanpy.tl) rank_genes_groups_df() (in module scanpy.get) rank_genes_groups_dotplot() (in module scanpy.pl) rank_genes_groups_heatmap() (in module scanpy.pl) rank_genes_groups_matrixplot() (in module scanpy.pl) rank_genes_groups_stacked_violin() (in module scanpy.pl) rank_genes_groups_tracksplot() (in module scanpy.pl) rank_genes_groups_violin() (in module scanpy.pl) ranking() (in module scanpy.pl) read() (in module scanpy) read_10x_h5() (in module scanpy) read_10x_mtx() (in module scanpy) read_csv() (in module scanpy) read_excel() (in module scanpy) read_h5ad() (in module scanpy) read_hdf() (in module scanpy) read_loom() (in module scanpy) read_mtx() (in module scanpy) read_text() (in module scanpy) read_umi_tools() (in module scanpy) read_visium() (in module scanpy) recipe_pearson_residuals() (in module scanpy.experimental.pp) recipe_seurat() (in module scanpy.pp) recipe_weinreb17() (in module scanpy.pp) recipe_zheng17() (in module scanpy.pp) regress_out() (in module scanpy.pp) rp_forest (scanpy.Neighbors property) S sam() (in module scanpy.external.pl) (in module scanpy.external.tl) sample() (in module scanpy.pp) sandbag() (in module scanpy.external.tl) savefig() (scanpy.pl.DotPlot method) (scanpy.pl.MatrixPlot method) (scanpy.pl.StackedViolin method) scale() (in module scanpy.pp) scanorama_integrate() (in module scanpy.external.pp) scanpy.datasets module scanpy.experimental module scanpy.experimental.pp module scanpy.external module scanpy.external.exporting module scanpy.external.pl module scanpy.external.pp module scanpy.external.tl module scanpy.get module scanpy.metrics module scanpy.pl module scanpy.pp module scanpy.queries module scanpy.tl module ScanpyConfig (class in scanpy._settings) scatter() (in module scanpy.pl) score_genes() (in module scanpy.tl) score_genes_cell_cycle() (in module scanpy.tl) scrublet() (in module scanpy.pp) scrublet_score_distribution() (in module scanpy.pl) scrublet_simulate_doublets() (in module scanpy.pp) set_figure_params() (in module scanpy) (scanpy._settings.ScanpyConfig method) show() (scanpy.pl.DotPlot method) (scanpy.pl.MatrixPlot method) (scanpy.pl.StackedViolin method) sim() (in module scanpy.pl) (in module scanpy.tl) spatial() (in module scanpy.pl) spring_project() (in module scanpy.external.exporting) stacked_violin() (in module scanpy.pl) StackedViolin (class in scanpy.pl) style() (scanpy.pl.DotPlot method) (scanpy.pl.MatrixPlot method) (scanpy.pl.StackedViolin method) subsample() (in module scanpy.pp) swap_axes() (scanpy.pl.DotPlot method) (scanpy.pl.MatrixPlot method) (scanpy.pl.StackedViolin method) T to_igraph() (scanpy.Neighbors method) toggleswitch() (in module scanpy.datasets) tracksplot() (in module scanpy.pl) transitions (scanpy.Neighbors property) transitions_sym (scanpy.Neighbors property) trimap() (in module scanpy.external.pl) (in module scanpy.external.tl) tsne() (in module scanpy.pl) (in module scanpy.tl) U umap() (in module scanpy.pl) (in module scanpy.tl) V var_df() (in module scanpy.get) verbosity (scanpy._settings.ScanpyConfig property) violin() (in module scanpy.pl) visium_sge() (in module scanpy.datasets) W wishbone() (in module scanpy.external.tl) wishbone_marker_trajectory() (in module scanpy.external.pl) write() (in module scanpy) writedir (scanpy._settings.ScanpyConfig property)
