Index A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | U | V | W A aggregate() (in module scanpy.get) autosave (scanpy.settings property) autoshow (scanpy.settings property) B bbknn() (in module scanpy.external.pp) biomart_annotations() (in module scanpy.queries) blobs() (in module scanpy.datasets) C cache_compression (scanpy.settings property) cachedir (scanpy.settings property) calculate_qc_metrics() (in module scanpy.pp) categories_to_ignore (scanpy.settings 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 property) dca() (in module scanpy.external.pp) debug (scanpy.Verbosity 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) 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_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) error (scanpy.Verbosity attribute) F figdir (scanpy.settings property) file_format_data (scanpy.settings property) file_format_figs (scanpy.settings 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) 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) hint (scanpy.Verbosity attribute) I info (scanpy.Verbosity attribute) ingest() (in module scanpy.tl) K krumsiek11() (in module scanpy.datasets) L legend() (scanpy.pl.DotPlot method) leiden() (in module scanpy.tl) level (scanpy.Verbosity property) log1p() (in module scanpy.pp) logfile (scanpy.settings property) logpath (scanpy.settings property) louvain() (in module scanpy.tl) M magic() (in module scanpy.external.pp) marker_gene_overlap() (in module scanpy.tl) MatrixPlot (class in scanpy.pl) matrixplot() (in module scanpy.pl) max_memory (scanpy.settings property) 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 property) N_PCS (scanpy.settings property) 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) override() (scanpy.Verbosity method) 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 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) 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 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) settings (class in scanpy) 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) 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 (class in scanpy) verbosity (scanpy.settings property) violin() (in module scanpy.pl) visium_sge() (in module scanpy.datasets) W warning (scanpy.Verbosity attribute) wishbone() (in module scanpy.external.tl) wishbone_marker_trajectory() (in module scanpy.external.pl) write() (in module scanpy) writedir (scanpy.settings property)
