pyviper package
=================

pyviper\.aREA
--------------------

.. autoclass:: pyviper.aREA
   :noindex:

pyviper\.NaRnEA
--------------------

.. autoclass:: pyviper.NaRnEA
   :noindex:

pyviper\.config
--------------------

.. automodule:: pyviper.config
   :members:
   :undoc-members:
   :show-inheritance:
.. autofunction:: pyviper.config.set_regulators_filepath
.. autofunction:: pyviper.config.set_regulators_species_to_use

pyviper.Interactome
-------------------------

.. autoclass:: pyviper.Interactome
   :members:
   :undoc-members:
   :show-inheritance:


pyviper\.load
----------------

.. automodule:: pyviper.load
   :members:
   :undoc-members:
   :show-inheritance:
.. autofunction:: pyviper.load.TFs
.. autofunction:: pyviper.load.coTFs
.. autofunction:: pyviper.load.human2mouse
.. autofunction:: pyviper.load.msigdb_regulon
.. autofunction:: pyviper.load.sig
.. autofunction:: pyviper.load.surf


pyviper\.pl
----------------

.. automodule:: pyviper.pl
   :members:
   :undoc-members:
   :show-inheritance:
.. autofunction:: pyviper.pl.__get_stored_uns_data_and_prep_to_plot
.. autofunction:: pyviper.pl.pca
.. autofunction:: pyviper.pl.umap
.. autofunction:: pyviper.pl.tsne
.. autofunction:: pyviper.pl.diffmap
.. autofunction:: pyviper.pl.draw_graph
.. autofunction:: pyviper.pl.spatial
.. autofunction:: pyviper.pl.embedding
.. autofunction:: pyviper.pl.embedding_density
.. autofunction:: pyviper.pl.heatmap
.. autofunction:: pyviper.pl.dotplot
.. autofunction:: pyviper.pl.tracksplot
.. autofunction:: pyviper.pl.violin
.. autofunction:: pyviper.pl.stacked_violin
.. autofunction:: pyviper.pl.matrixplot
.. autofunction:: pyviper.pl.clustermap
.. autofunction:: pyviper.pl.ranking
.. autofunction:: pyviper.pl.dendrogram

pyviper\.pp
----------------

.. automodule:: pyviper.pp
   :members:
   :undoc-members:
   :show-inheritance:
.. autofunction:: pyviper.pp.rank_norm
.. autofunction:: pyviper.pp.stouffer
.. autofunction:: pyviper.pp.mwu
.. autofunction:: pyviper.pp.spearman
.. autofunction:: pyviper.pp.viper_similarity
.. autofunction:: pyviper.pp.aracne3_to_regulon
.. autofunction:: pyviper.pp.nes_to_pval
.. autofunction:: pyviper.pp.repr_subsample
.. autofunction:: pyviper.pp.repr_metacells

pyviper\.tl
----------------

.. automodule:: pyviper.tl
   :members:
   :undoc-members:
   :show-inheritance:
.. autofunction:: pyviper.tl.pca
.. autofunction:: pyviper.tl.dendrogram
.. autofunction:: pyviper.tl.oncomatch
.. autofunction:: pyviper.tl.find_top_mrs
.. autofunction:: pyviper.tl.path_enr

pyviper.viper
--------------------

.. autofunction:: pyviper.viper
   :noindex: