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author Vimalkumar Velayudhan <vimal@biotechcoder.com>
date Tue, 21 Jul 2015 14:48:39 +0100
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1 riboseqr_wrapper
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2 ----------------
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3 `riboSeqR <http://bioconductor.org/packages/3.0/bioc/html/riboSeqR.html>`_
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4 integration for `Galaxy <http://galaxyproject.org/>`_ and
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5 `RiboGalaxy <http://ribogalaxy.ucc.ie/>`_.
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6
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7 Included tools
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8 ..............
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9 In the order they are run
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11 1. Prepare riboSeqR Input - Prepare riboSeqR format input files from SAM format alignment files.
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12 The SAM format files should be obtained by aligning Ribo-Seq and RNA-Seq data to the transcriptome.
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13 (RNA-Seq data is optional but required for Differential translation analysis).
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14
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15 2. Triplet Periodicity - Plot triplet periodicity for different read lengths.
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17 3. Metagene Analysis
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18
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19 4. Plot Ribosome Profile
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20
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21 [OR]
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22
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23 Differential Translation Analysis - Get Ribo and RNA-Seq counts with riboSeqR. Perform differential
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24 translation analysis with baySeq.
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25
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26 Dependencies
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27 ............
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28 Tested on Ubuntu Linux 14.04 LTS, 64-bit. Dependencies should install automatically on Linux x86_64.
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29
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30 **R** ``3.1.2``
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31
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32 **riboSeqR** ``1.0.5``
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33
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34 **baySeq** ``2.0.50``
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35
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36 **rpy2** ``2.3.10``