Mercurial > repos > vimalkumarvelayudhan > riboseqr_wrapper

comparison README.rst @ 0:c34c364ce75d

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
First commit
author Vimalkumar Velayudhan <vimal@biotechcoder.com>
date Tue, 21 Jul 2015 14:48:39 +0100
parents
children d7ce95ccf54f 423ad61697c4
comparison
equal deleted inserted replaced
-1:000000000000 0:c34c364ce75d
1 riboseqr_wrapper
2 ----------------
3 `riboSeqR <http://bioconductor.org/packages/3.0/bioc/html/riboSeqR.html>`_
4 integration for `Galaxy <http://galaxyproject.org/>`_ and
5 `RiboGalaxy <http://ribogalaxy.ucc.ie/>`_.
6
7 Included tools
8 ..............
9 In the order they are run
10
11 1. Prepare riboSeqR Input - Prepare riboSeqR format input files from SAM format alignment files.
12 The SAM format files should be obtained by aligning Ribo-Seq and RNA-Seq data to the transcriptome.
13 (RNA-Seq data is optional but required for Differential translation analysis).
14
15 2. Triplet Periodicity - Plot triplet periodicity for different read lengths.
16
17 3. Metagene Analysis
18
19 4. Plot Ribosome Profile
20
21 [OR]
22
23 Differential Translation Analysis - Get Ribo and RNA-Seq counts with riboSeqR. Perform differential
24 translation analysis with baySeq.
25
26 Dependencies
27 ............
28 Tested on Ubuntu Linux 14.04 LTS, 64-bit. Dependencies should install automatically on Linux x86_64.
29
30 **R** ``3.1.2``
31
32 **riboSeqR** ``1.0.5``
33
34 **baySeq** ``2.0.50``
35
36 **rpy2** ``2.3.10``