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author bgruening
date Thu, 06 Feb 2014 06:40:05 -0500
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1 This package contains a collection of Galaxy workflows utilising deepTools. 1 ========================
2 Galaxy deeptools wrapper
3 ========================
2 4
3 See http://www.galaxyproject.org for information about the Galaxy Project. 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
4 26
5 27
6 Sample Data 28 ========
7 ===========
8
9 Sample data can be obtained from http://deeptools.ie-freiburg.mpg.de/library or you
10 can use aligned reads in BAM or SAM format.
11
12
13
14 Citation 29 Citation
15 ======== 30 ========
16 31
17 If you use this workflow directly, or a derivative of it, or the associated 32 deeptools are currently under review. In the meantime please refere to https://github.com/fidelram/deepTools.
18 deepTools wrappers for Galaxy, in work leading to a scientific publication,
19 please cite:
20
21 {publication under review}
22 33
23 34
24 Availability 35 =======
25 ============ 36 History
37 =======
26 38
27 This workflow is available on the main Galaxy Tool Shed: 39 - v1.0: Initial public release
28
29 http://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_workflows
30
31 Development is being done on github:
32
33 https://github.com/fidelram/deepTools
34 40
35 41
36 Dependencies 42 Licence (MIT)
37 ============ 43 =============
38 44
39 These dependencies should be resolved automatically via the Galaxy Tool Shed: 45 Permission is hereby granted, free of charge, to any person obtaining a copy
46 of this software and associated documentation files (the "Software"), to deal
47 in the Software without restriction, including without limitation the rights
48 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
49 copies of the Software, and to permit persons to whom the Software is
50 furnished to do so, subject to the following conditions:
40 51
41 * http://toolshed.g2.bx.psu.edu/view/bgruening/deeptools 52 The above copyright notice and this permission notice shall be included in
53 all copies or substantial portions of the Software.
54
55 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
56 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
57 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
58 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
59 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
60 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
61 THE SOFTWARE.