API

Import Scanpy as:

import scanpy as sc

Note

Additional functionality is available in the broader ecosystem, with some tools being wrapped in the scanpy.external module.

• Preprocessing: pp
  • Basic Preprocessing
  • Recipes
  • Batch effect correction
  • Doublet detection
  • Neighbors
• Tools: tl
  • Embeddings
  • Clustering and trajectory inference
  • Data integration
  • Marker genes
  • Gene scores, Cell cycle
  • Simulations
• Plotting: pl
  • Generic
  • Classes
  • Preprocessing
  • Tools
• Reading
  • 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
• Settings
  • scanpy.set_figure_params
  • scanpy._settings.ScanpyConfig
  • scanpy.logging.print_header
  • scanpy.logging.print_versions
• 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