Index

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)

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_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_SCALE (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 scanpy.datasets scanpy.experimental scanpy.experimental.pp scanpy.external 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) 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) (in module scanpy.tl)

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) 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 module scanpy.datasets module scanpy.experimental module scanpy.experimental.pp module scanpy.external 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.external.pp) scrublet_score_distribution() (in module scanpy.external.pl) scrublet_simulate_doublets() (in module scanpy.external.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) writedir (scanpy._settings.ScanpyConfig property)