preprocessing.md

Preprocessing: pp

.. module:: scanpy.pp

.. currentmodule:: scanpy

Filtering of highly-variable genes, batch-effect correction, per-cell normalization, preprocessing recipes.

Any transformation of the data matrix that is not a tool. Other than tools, preprocessing steps usually don't return an easily interpretable annotation, but perform a basic transformation on the data matrix.

Basic Preprocessing

For visual quality control, see {func}~scanpy.pl.highest_expr_genes and {func}~scanpy.pl.highly_variable_genes in {mod}scanpy.pl.

.. autosummary::
   :nosignatures:
   :toctree: ../generated/

   pp.calculate_qc_metrics
   pp.filter_cells
   pp.filter_genes
   pp.highly_variable_genes
   pp.log1p
   pp.pca
   pp.normalize_total
   pp.regress_out
   pp.scale
   pp.sample
   pp.downsample_counts

Recipes

.. autosummary::
   :nosignatures:
   :toctree: generated/

   pp.recipe_zheng17
   pp.recipe_weinreb17
   pp.recipe_seurat

(pp-data-integration)=

Data integration

Batch effect correction and other data integration. Note that a simple batch correction method is available via {func}pp.regress_out.

.. autosummary::
   :nosignatures:
   :toctree: generated/

   pp.combat
   pp.harmony_integrate

Also see {ref}data integration tools <data-integration> and external {ref}external data integration <external-data-integration>.

Doublet detection

.. autosummary::
   :nosignatures:
   :toctree: generated/

   pp.scrublet
   pp.scrublet_simulate_doublets

Neighbors

.. autosummary::
   :nosignatures:
   :toctree: generated/

   pp.neighbors