scikit-genome package
=====================

Module ``skgenome`` contents
----------------------------

.. automodule:: skgenome
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.. _api_tabio:

Tabular file I/O (tabio)
------------------------

``tabio``
~~~~~~~~~

.. automodule:: skgenome.tabio
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.. _api_sk_gary:

Base class: GenomicArray
------------------------

The base class of the core objects used throughout CNVkit and scikit-genome is
GenomicArray. It wraps a `pandas <http://pandas.pydata.org/>`_ DataFrame
instance, which is accessible through the ``.data`` attribute and can be used
for any manipulations that aren't already provided by methods in the wrapper
class.

``gary``
~~~~~~~~

.. automodule:: skgenome.gary
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.. _api_sk_interval:

Genomic interval arithmetic
---------------------------

``intersect``
~~~~~~~~~~~~~

.. automodule:: skgenome.intersect
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``merge``
~~~~~~~~~

.. automodule:: skgenome.merge
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``subdivide``
~~~~~~~~~~~~~

.. automodule:: skgenome.subdivide
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``subtract``
~~~~~~~~~~~~

.. automodule:: skgenome.subtract
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.. _api_sk_helpers:

Helper modules
--------------

``chromsort``
~~~~~~~~~~~~~

.. automodule:: skgenome.chromsort
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``combiners``
~~~~~~~~~~~~~

.. automodule:: skgenome.combiners
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``rangelabel``
~~~~~~~~~~~~~~

.. automodule:: skgenome.rangelabel
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