view README.rst @ 1:4419c2f77b60

Add script to run Python unit tests

riboseqr_wrapper
----------------
`riboSeqR <http://bioconductor.org/packages/3.0/bioc/html/riboSeqR.html>`_
integration for `Galaxy <http://galaxyproject.org/>`_ and
`RiboGalaxy <http://ribogalaxy.ucc.ie/>`_.

Included tools
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In the order they are run

1. Prepare riboSeqR Input - Prepare riboSeqR format input files from SAM format alignment files.
   The SAM format files should be obtained by aligning Ribo-Seq and RNA-Seq data to the transcriptome.
   (RNA-Seq data is optional but required for Differential translation analysis).

2. Triplet Periodicity - Plot triplet periodicity for different read lengths.

3. Metagene Analysis

4. Plot Ribosome Profile

   [OR]

   Differential Translation Analysis - Get Ribo and RNA-Seq counts with riboSeqR. Perform differential
   translation analysis with baySeq.

Dependencies
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Tested on Ubuntu Linux 14.04 LTS, 64-bit. Dependencies should install automatically on Linux x86_64.

**R** ``3.1.2``

**riboSeqR** ``1.0.5``

**baySeq** ``2.0.50``

**rpy2** ``2.3.10``