.. _api:

**************
API
**************

SCENIC+ object
================

.. automodule:: scenicplus.scenicplus_class
   :members:

Preprocessing
=============

.. automodule:: scenicplus.preprocessing.filtering
   :members:

SCENIC+ semi-automated workflow using wrapper functions
=======================================================

pycistarget wrapper
-------------------
.. automodule:: scenicplus.wrappers.run_pycistarget
   :members:

SCENIC+ wrapper
---------------
.. automodule:: scenicplus.wrappers.run_scenicplus
   :members:


Tools for non-automated workflow
================================

Cistromes
---------

.. automodule:: scenicplus.cistromes
     :members:

Enhancer-to-gene linking
------------------------

.. automodule:: scenicplus.enhancer_to_gene
   :members:

TF-to-gene linking
------------------

.. automodule:: scenicplus.TF_to_gene
   :members:

eGRN building
-------------

eRegulon Class
^^^^^^^^^^^^^^

.. automodule:: scenicplus.grn_builder.modules
   :members:

GSEA based approach
^^^^^^^^^^^^^^^^^^^

.. image:: _images/gsea.png
   :width: 800
   :align: center
   :alt: GSEA approach


.. automodule:: scenicplus.grn_builder.gsea_approach
   :members:

Downstream analysis, export and plotting
========================================

Marker genes and regions
------------------------

.. automodule:: scenicplus.diff_features
   :members:

eRegulon enrichment in cells
----------------------------

.. automodule:: scenicplus.eregulon_enrichment
   :members:

dimensionality reduction
------------------------

.. automodule:: scenicplus.dimensionality_reduction
   :members:

eRegulon specificity score (eRSS)
---------------------------------

.. automodule:: scenicplus.RSS
   :members:

Triplet score
-------------

.. automodule:: scenicplus.triplet_score
   :members:

Network
-------

.. automodule:: scenicplus.networks
   :members:

Correlation plot
----------------

.. automodule:: scenicplus.plotting.correlation_plot
   :members:

Coverage plot
-------------

.. automodule:: scenicplus.plotting.coverageplot
   :members:

dotplot
-------

.. automodule:: scenicplus.plotting.dotplot
   :members:

Export
------

Export to loom
^^^^^^^^^^^^^^

.. automodule:: scenicplus.loom
   :members:

Export to MuData
^^^^^^^^^^^^^^^^

.. automodule:: scenicplus.io.object_converted
   :members: