tools.md

Tools: tl

.. module:: scanpy.tl

.. currentmodule:: scanpy

Any transformation of the data matrix that is not preprocessing. In contrast to a preprocessing function, a tool usually adds an easily interpretable annotation to the data matrix, which can then be visualized with a corresponding plotting function.

Embeddings

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

   pp.pca
   tl.tsne
   tl.umap
   tl.draw_graph
   tl.diffmap

Compute densities on embeddings.

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

   tl.embedding_density

Clustering and trajectory inference

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

   tl.leiden
   tl.dendrogram
   tl.dpt
   tl.paga

(data-integration)=

Data integration

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

   tl.ingest

Marker genes

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

   tl.rank_genes_groups
   tl.filter_rank_genes_groups
   tl.marker_gene_overlap

Gene scores, Cell cycle

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

   tl.score_genes
   tl.score_genes_cell_cycle

Simulations

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

   tl.sim