external.md

External API

.. module:: scanpy.external

.. currentmodule:: scanpy.external

More tools that integrate well with scanpy and anndata can be found on the {doc}`ecosystem page <../ecosystem>`.

Import Scanpy's wrappers to external tools as:

import scanpy.external as sce

If you'd like to include a tool here, consider making a pull request ({doc}instructions <../dev/external-tools>). If the tool already uses scanpy or anndata, it may fit better in the {doc}ecosystem page <../ecosystem>.

Preprocessing: PP

Data integration

.. autosummary::
   :toctree: generated/

   pp.bbknn
   pp.harmony_integrate
   pp.mnn_correct
   pp.scanorama_integrate

Sample demultiplexing, Doublet detection

.. autosummary::
   :toctree: generated/

   pp.scrublet
   pp.scrublet_simulate_doublets
   pl.scrublet_score_distribution
   pp.hashsolo

Imputation

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

.. autosummary::
   :toctree: generated/

   pp.dca
   pp.magic

Tools: TL

Embeddings

.. autosummary::
   :toctree: generated/

   tl.phate
   tl.palantir
   tl.trimap
   tl.sam

Clustering and trajectory inference

.. autosummary::
   :toctree: generated/

   tl.phenograph
   tl.harmony_timeseries
   tl.wishbone
   tl.palantir
   tl.palantir_results

Gene scores, Cell cycle

.. autosummary::
   :toctree: generated/

   tl.sandbag
   tl.cyclone

Plotting: PL

.. autosummary::
   :toctree: generated/

   pl.phate
   pl.trimap
   pl.sam
   pl.wishbone_marker_trajectory

Exporting

.. autosummary::
   :toctree: generated/

   exporting.spring_project
   exporting.cellbrowser