preprocessing.md

Preprocessing: PP

.. module:: scanpy.external.pp
.. currentmodule:: scanpy.external

Previously found here, but now part of scanpy’s main API:

• {func}scanpy.pp.harmony_integrate
• {func}scanpy.pp.scrublet
• {func}scanpy.pp.scrublet_simulate_doublets

(external-data-integration)=

Data integration

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

   pp.bbknn
   pp.mnn_correct
   pp.scanorama_integrate

Sample demultiplexing

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

   pp.hashsolo

Imputation

Note that the fundamental limitations of imputation are still under debate.

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

   pp.magic