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comparison readme.rst @ 0:7fb0a96e74c1 draft

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author bgruening
date Mon, 25 Jan 2016 20:24:44 -0500
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1 ========================
2 Galaxy deeptools wrapper
3 ========================
4
5 deepTools are user-friendly tools for the normalization and visualization of
6 deep-sequencing data.
7 They address the challenge of visualizing the large amounts of data that are now
8 routinely generated from sequencing centers in a meaningful way.
9 To do so, deepTools contain useful routines to process the mapped reads data
10 through removal of duplicates and different filtering options to create coverage
11 files in standard bedGraph and bigWig file formats. deepTools allow the creation
12 of normalized coverage files or the comparison between two files
13 (for example, treatment and control). Finally, using such normalized and
14 standardized files, multiple visualizations can be created to identify
15 enrichments with functional annotations of the genome.
16 For a gallery of images that can be produced and a description
17 of the tools see our poster_.
18
19 .. _poster: http://f1000.com/posters/browse/summary/1094053
20
21 deeptools is developed under here:
22
23 https://github.com/fidelram/deepTools
24
25 For support, questions, or feature requests contact: deeptools@googlegroups.com
26
27
28 ============
29 Installation
30 ============
31
32 Requirements: python-2.7
33
34 Galaxy should be able to automatically install all other dependencies, such as numpy or scipy.
35
36 For the best performance we recommend to install blas/lapack/atlas in your environment before
37 installing deepTools from the Tool Shed.
38
39
40 ========
41 Citation
42 ========
43
44 deeptools are currently under review. In the meantime please refere to https://github.com/fidelram/deepTools.
45
46
47 =======
48 History
49 =======
50
51 * v1.0: Initial public release
52 * v1.5.8.2: Include new citation tag, update version to 1.5.8.2 and change wrapper version
53
54
55 Licence (MIT)
56 =============
57
58 Permission is hereby granted, free of charge, to any person obtaining a copy
59 of this software and associated documentation files (the "Software"), to deal
60 in the Software without restriction, including without limitation the rights
61 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
62 copies of the Software, and to permit persons to whom the Software is
63 furnished to do so, subject to the following conditions:
64
65 The above copyright notice and this permission notice shall be included in
66 all copies or substantial portions of the Software.
67
68 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
69 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
70 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
71 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
72 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
73 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
74 THE SOFTWARE.