Mercurial > repos > vipints > deseq_hts
comparison dexseq-hts_1.0/README @ 11:cec4b4fb30be draft default tip
DEXSeq version 1.6 added
author | vipints <vipin@cbio.mskcc.org> |
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date | Tue, 08 Oct 2013 08:22:45 -0400 |
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10:2fe512c7bfdf | 11:cec4b4fb30be |
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1 ----------------------------------------- | |
2 A Galaxy wrapper for DEXSeq version 1.6.0 | |
3 ----------------------------------------- | |
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: | |
9 ------------- | |
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: | |
15 --------- | |
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 | |
47 ---------- | |
48 [1] Simon Anders and Alejandro Reyes and Wolfgang Huber (2012): Detecting differential usage of exons from RNA-seq data. | |
49 | |
50 Contact: | |
51 -------- | |
52 support [at] oqtans.org |