Introduction
================
.. automodule:: pyseqrna
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Quality Submodules
=====================

pyseqrna.quality\_check module
------------------------------

.. automodule:: pyseqrna.quality_check
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pyseqrna.quality\_trimming module
---------------------------------

.. automodule:: pyseqrna.quality_trimming
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pyseqrna.ribosomal module
-------------------------

.. automodule:: pyseqrna.ribosomal
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Alignment Submodules
=====================

pyseqrna.aligners module
------------------------

.. automodule:: pyseqrna.aligners
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pyseqrna.pyseqrna\_stats module
-------------------------------

.. automodule:: pyseqrna.pyseqrna_stats
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Quantification Submodules
==========================

pyseqrna.quantification module
------------------------------

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pyseqrna.multimapped\_groups module
-----------------------------------

.. automodule:: pyseqrna.multimapped_groups
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pyseqrna.normalize\_counts module
---------------------------------

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pyseqrna.clustering module
--------------------------

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Differential Genes Submodules
=============================

pyseqrna.differential\_expression module
----------------------------------------

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Functional Annotation Submodules
================================

pyseqrna.gene\_ontology module
------------------------------

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pyseqrna.pathway module
-----------------------

.. automodule:: pyseqrna.pathway
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Utility Submodules
==================

pyseqrna.arg\_parser module
---------------------------

.. automodule:: pyseqrna.arg_parser
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pyseqrna.pyseqrna\_utils module
-------------------------------

.. automodule:: pyseqrna.pyseqrna_utils
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pyseqrna.version module
-----------------------

.. automodule:: pyseqrna.version
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pyseqrna.pyseqrna\_plots module
-------------------------------

.. automodule:: pyseqrna.pyseqrna_plots
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