comparison dexseq-hts_1.0/README @ 11:cec4b4fb30be draft default tip

DEXSeq version 1.6 added
author vipints <vipin@cbio.mskcc.org>
date Tue, 08 Oct 2013 08:22:45 -0400
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10:2fe512c7bfdf 11:cec4b4fb30be
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2 A Galaxy wrapper for DEXSeq version 1.6.0
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4
5 DEXSeq is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs.
6 DEXSeq: http://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html
7
8 Requirements:
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10 Python, HTSeq package :- Preprocessing of sequencing reads and GFF files
11 R, Bio-conductor package :- Required for DEXSeq
12 SAMTOOLS :- Sequencing read processing
13
14 Contents:
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16
17 ./bin
18 Contains a config file for running DEXSeq in different settings, setup_dexseq-hts.sh
19 will help to create the config file according to your local work station.
20
21 ./setup_dexseq-hts.sh
22 Setup script, which helps to set the right path to the config file present in the bin
23 folder.
24
25 ./README
26 Basic information about the wrapper
27
28 ./galaxy
29 Galaxy tool configuration file can be found here.
30
31 ./src
32 All relevant scripts for DEXSeq execution, Please follow the shell script to
33 understand the details.
34
35 Licenses:
36 ---------
37
38 If DEXSeq is used to obtain results for scientific publications it should be cited as [1].
39
40 This wrapper program is free software; you can redistribute it and/or modify it under the
41 terms of the GNU General Public License as published by the Free Software Foundation; either
42 version 3 of the License, or (at your option) any later version.
43
44 Copyright(C) 2013 cBio Memorial Sloan Kettering Cancer Center, New York City, USA.
45
46 References
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48 [1] Simon Anders and Alejandro Reyes and Wolfgang Huber (2012): Detecting differential usage of exons from RNA-seq data.
49
50 Contact:
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52 support [at] oqtans.org