===================================
Breast Cancer Personalized Genomics Report- RNAseq
===================================
Modules included in the RNAseq Cancer pipeline.
	
.. rst-class:: html-toggle
FASTQC
=======
.. automodule:: omics_pipe.modules.fastqc
	:members:

.. rst-class:: html-toggle	
STAR Aligner
=======	
.. automodule:: omics_pipe.modules.star
	:members:

.. rst-class:: html-toggle		
HTSEQ-count
=======	
.. automodule:: omics_pipe.modules.htseq
	:members:	

.. rst-class:: html-toggle	
RSEQC
=========
.. automodule:: omics_pipe.modules.rseqc
	:members:

.. rst-class:: html-toggle		
Fusion Catcher
==========
.. automodule:: omics_pipe.modules.fusion_catcher
	:members:	
	
.. rst-class:: html-toggle	
BWA/SNPiR
==============

BWA
-------
.. automodule:: omics_pipe.modules.bwa
	:members: bwa1, bwa2, bwa_RNA

SNPiR
-------
.. automodule:: omics_pipe.modules.snpir_variants
	:members:	

Filter Variants
-----------------
.. automodule:: omics_pipe.modules.filter_variants
	:members:	

.. rst-class:: html-toggle		
Intogen
========
.. automodule:: omics_pipe.modules.intogen
	:members:	
	
.. rst-class:: html-toggle	
OncoRep Cancer Report
================
.. automodule:: omics_pipe.modules.BreastCancer_RNA_report
	:members: