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Installation
Tutorials
Basics
Preprocessing and clustering
Preprocessing and clustering 3k PBMCs (legacy workflow)
Integrating data using ingest and BBKNN
Plotting
Core plotting functions
Customizing Scanpy plots
Trajectories
Trajectory inference for hematopoiesis in mouse
Experimental
How to preprocess UMI count data with analytic Pearson residuals
Using
dask
with Scanpy
Usage Principles
How to
Cell-Cycle Scoring and Regression
Using other kNN libraries in Scanpy
Plotting with Marsilea
API
Preprocessing:
pp
scanpy.pp.calculate_qc_metrics
scanpy.pp.filter_cells
scanpy.pp.filter_genes
scanpy.pp.highly_variable_genes
scanpy.pp.log1p
scanpy.pp.pca
scanpy.pp.normalize_total
scanpy.pp.regress_out
scanpy.pp.scale
scanpy.pp.sample
scanpy.pp.downsample_counts
scanpy.pp.recipe_zheng17
scanpy.pp.recipe_weinreb17
scanpy.pp.recipe_seurat
scanpy.pp.combat
scanpy.pp.scrublet
scanpy.pp.scrublet_simulate_doublets
scanpy.pp.neighbors
Tools:
tl
scanpy.pp.pca
scanpy.tl.tsne
scanpy.tl.umap
scanpy.tl.draw_graph
scanpy.tl.diffmap
scanpy.tl.embedding_density
scanpy.tl.leiden
scanpy.tl.dendrogram
scanpy.tl.dpt
scanpy.tl.paga
scanpy.tl.ingest
scanpy.tl.rank_genes_groups
scanpy.tl.filter_rank_genes_groups
scanpy.tl.marker_gene_overlap
scanpy.tl.score_genes
scanpy.tl.score_genes_cell_cycle
scanpy.tl.sim
Plotting:
pl
scanpy.pl.scatter
scanpy.pl.heatmap
scanpy.pl.dotplot
scanpy.pl.tracksplot
scanpy.pl.violin
scanpy.pl.stacked_violin
scanpy.pl.matrixplot
scanpy.pl.clustermap
scanpy.pl.ranking
scanpy.pl.dendrogram
scanpy.pl.DotPlot
scanpy.pl.DotPlot.DEFAULT_COLORMAP
scanpy.pl.DotPlot.DEFAULT_COLOR_LEGEND_TITLE
scanpy.pl.DotPlot.DEFAULT_COLOR_ON
scanpy.pl.DotPlot.DEFAULT_DOT_EDGECOLOR
scanpy.pl.DotPlot.DEFAULT_DOT_EDGELW
scanpy.pl.DotPlot.DEFAULT_DOT_MAX
scanpy.pl.DotPlot.DEFAULT_DOT_MIN
scanpy.pl.DotPlot.DEFAULT_LARGEST_DOT
scanpy.pl.DotPlot.DEFAULT_LEGENDS_WIDTH
scanpy.pl.DotPlot.DEFAULT_PLOT_X_PADDING
scanpy.pl.DotPlot.DEFAULT_PLOT_Y_PADDING
scanpy.pl.DotPlot.DEFAULT_SAVE_PREFIX
scanpy.pl.DotPlot.DEFAULT_SIZE_EXPONENT
scanpy.pl.DotPlot.DEFAULT_SIZE_LEGEND_TITLE
scanpy.pl.DotPlot.DEFAULT_SMALLEST_DOT
scanpy.pl.DotPlot.legend
scanpy.pl.DotPlot.style
scanpy.pl.MatrixPlot
scanpy.pl.MatrixPlot.DEFAULT_COLORMAP
scanpy.pl.MatrixPlot.DEFAULT_COLOR_LEGEND_TITLE
scanpy.pl.MatrixPlot.DEFAULT_EDGE_COLOR
scanpy.pl.MatrixPlot.DEFAULT_EDGE_LW
scanpy.pl.MatrixPlot.DEFAULT_SAVE_PREFIX
scanpy.pl.MatrixPlot.style
scanpy.pl.StackedViolin
scanpy.pl.StackedViolin.DEFAULT_COLORMAP
scanpy.pl.StackedViolin.DEFAULT_COLOR_LEGEND_TITLE
scanpy.pl.StackedViolin.DEFAULT_CUT
scanpy.pl.StackedViolin.DEFAULT_DENSITY_NORM
scanpy.pl.StackedViolin.DEFAULT_INNER
scanpy.pl.StackedViolin.DEFAULT_JITTER
scanpy.pl.StackedViolin.DEFAULT_JITTER_SIZE
scanpy.pl.StackedViolin.DEFAULT_LINE_WIDTH
scanpy.pl.StackedViolin.DEFAULT_PLOT_X_PADDING
scanpy.pl.StackedViolin.DEFAULT_PLOT_YTICKLABELS
scanpy.pl.StackedViolin.DEFAULT_PLOT_Y_PADDING
scanpy.pl.StackedViolin.DEFAULT_ROW_PALETTE
scanpy.pl.StackedViolin.DEFAULT_SAVE_PREFIX
scanpy.pl.StackedViolin.DEFAULT_STRIPPLOT
scanpy.pl.StackedViolin.DEFAULT_YLIM
scanpy.pl.StackedViolin.style
scanpy.pl.highest_expr_genes
scanpy.pl.highly_variable_genes
scanpy.pl.scrublet_score_distribution
scanpy.pl.pca
scanpy.pl.pca_loadings
scanpy.pl.pca_variance_ratio
scanpy.pl.pca_overview
scanpy.pl.tsne
scanpy.pl.umap
scanpy.pl.diffmap
scanpy.pl.draw_graph
scanpy.pl.spatial
scanpy.pl.embedding
scanpy.pl.embedding_density
scanpy.pl.dpt_groups_pseudotime
scanpy.pl.dpt_timeseries
scanpy.pl.paga
scanpy.pl.paga_path
scanpy.pl.paga_compare
scanpy.pl.correlation_matrix
scanpy.pl.rank_genes_groups
scanpy.pl.rank_genes_groups_violin
scanpy.pl.rank_genes_groups_stacked_violin
scanpy.pl.rank_genes_groups_heatmap
scanpy.pl.rank_genes_groups_dotplot
scanpy.pl.rank_genes_groups_matrixplot
scanpy.pl.rank_genes_groups_tracksplot
scanpy.pl.sim
Reading and Writing
scanpy.write
scanpy.read
scanpy.read_10x_h5
scanpy.read_10x_mtx
scanpy.read_visium
scanpy.read_h5ad
scanpy.read_csv
scanpy.read_excel
scanpy.read_hdf
scanpy.read_loom
scanpy.read_mtx
scanpy.read_text
scanpy.read_umi_tools
Get object from
AnnData
:
get
scanpy.get.obs_df
scanpy.get.var_df
scanpy.get.rank_genes_groups_df
scanpy.get.aggregate
Queries
scanpy.queries.biomart_annotations
scanpy.queries.gene_coordinates
scanpy.queries.mitochondrial_genes
scanpy.queries.enrich
Metrics
scanpy.metrics.confusion_matrix
scanpy.metrics.gearys_c
scanpy.metrics.morans_i
Experimental
scanpy.experimental.pp.normalize_pearson_residuals
scanpy.experimental.pp.normalize_pearson_residuals_pca
scanpy.experimental.pp.highly_variable_genes
scanpy.experimental.pp.recipe_pearson_residuals
Classes
scanpy.Neighbors
scanpy.Neighbors.connectivities
scanpy.Neighbors.distances
scanpy.Neighbors.distances_dpt
scanpy.Neighbors.eigen_basis
scanpy.Neighbors.eigen_values
scanpy.Neighbors.rp_forest
scanpy.Neighbors.transitions
scanpy.Neighbors.transitions_sym
scanpy.Neighbors.compute_eigen
scanpy.Neighbors.compute_neighbors
scanpy.Neighbors.compute_transitions
scanpy.Neighbors.to_igraph
Settings
scanpy.set_figure_params
scanpy.settings
scanpy.settings.N_PCS
scanpy.settings.autosave
scanpy.settings.autoshow
scanpy.settings.cache_compression
scanpy.settings.cachedir
scanpy.settings.categories_to_ignore
scanpy.settings.datasetdir
scanpy.settings.figdir
scanpy.settings.file_format_data
scanpy.settings.file_format_figs
scanpy.settings.logfile
scanpy.settings.logpath
scanpy.settings.max_memory
scanpy.settings.n_jobs
scanpy.settings.plot_suffix
scanpy.settings.verbosity
scanpy.settings.writedir
scanpy.Verbosity
scanpy.Verbosity.level
scanpy.Verbosity.error
scanpy.Verbosity.warning
scanpy.Verbosity.info
scanpy.Verbosity.hint
scanpy.Verbosity.debug
scanpy.Verbosity.override
scanpy.logging.print_header
Datasets
scanpy.datasets.blobs
scanpy.datasets.ebi_expression_atlas
scanpy.datasets.krumsiek11
scanpy.datasets.moignard15
scanpy.datasets.pbmc3k
scanpy.datasets.pbmc3k_processed
scanpy.datasets.pbmc68k_reduced
scanpy.datasets.paul15
scanpy.datasets.toggleswitch
scanpy.datasets.visium_sge
Deprecated functions
scanpy.pp.filter_genes_dispersion
scanpy.pp.normalize_per_cell
scanpy.pp.subsample
scanpy.pl.filter_genes_dispersion
scanpy.tl.louvain
scanpy.logging.print_versions
External API
Preprocessing: PP
scanpy.external.pp.bbknn
scanpy.external.pp.harmony_integrate
scanpy.external.pp.mnn_correct
scanpy.external.pp.scanorama_integrate
scanpy.external.pp.hashsolo
scanpy.external.pp.dca
scanpy.external.pp.magic
Tools: TL
scanpy.external.tl.phate
scanpy.external.tl.palantir
scanpy.external.tl.trimap
scanpy.external.tl.sam
scanpy.external.tl.phenograph
scanpy.external.tl.harmony_timeseries
scanpy.external.tl.wishbone
scanpy.external.tl.palantir
scanpy.external.tl.palantir_results
scanpy.external.tl.sandbag
scanpy.external.tl.cyclone
Plotting: PL
scanpy.external.pl.phate
scanpy.external.pl.trimap
scanpy.external.pl.sam
scanpy.external.pl.wishbone_marker_trajectory
Exporting
scanpy.external.exporting.spring_project
scanpy.external.exporting.cellbrowser
Ecosystem
Release notes
Community
News
Contributing
Contributing code
Getting set up
Tests
Documentation
CI
Versioning
Making a release
Contributors
References
.rst
.pdf
scanpy.settings.file_format_data
Contents
settings.file_format_data
scanpy.settings.file_format_data
#
settings.
file_format_data
=
'h5ad'
[source]
#
Contents
settings.file_format_data
