API Reference
=============

Top-level functions
-------------------

.. automodule:: ncountr
   :members:
   :undoc-members:

Data container
--------------

.. autoclass:: ncountr.experiment.NanostringExperiment
   :members:
   :undoc-members:

I/O
---

.. automodule:: ncountr.io.rcc
   :members:

.. automodule:: ncountr.io.export
   :members:

.. automodule:: ncountr.io.geo
   :members:

Core analysis
-------------

.. automodule:: ncountr.core.qc
   :members:

.. automodule:: ncountr.core.normalize
   :members:

.. automodule:: ncountr.core.de
   :members:

.. automodule:: ncountr.core.pathway
   :members:

Datasets
--------

.. automodule:: ncountr.datasets
   :members:

Plotting
--------

.. automodule:: ncountr.plotting.qc_plots
   :members:

.. automodule:: ncountr.plotting.de_plots
   :members:

.. automodule:: ncountr.plotting.pathway_plots
   :members:

.. automodule:: ncountr.plotting.heatmaps
   :members:

Cross-platform validation
-------------------------

.. automodule:: ncountr.crossplatform.correlation
   :members:

.. automodule:: ncountr.crossplatform.concordance
   :members:

.. automodule:: ncountr.crossplatform.composition
   :members: