annotate readme.rst @ 29:3a2aab18a217 draft

Uploaded
author bgruening
date Tue, 16 Sep 2014 13:46:05 -0400
parents f7712a057440
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
26
2ad3b027dfcd Uploaded
bgruening
parents: 25
diff changeset
1 ========================
2ad3b027dfcd Uploaded
bgruening
parents: 25
diff changeset
2 Galaxy deeptools wrapper
2ad3b027dfcd Uploaded
bgruening
parents: 25
diff changeset
3 ========================
0
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
4
26
2ad3b027dfcd Uploaded
bgruening
parents: 25
diff changeset
5 deepTools are user-friendly tools for the normalization and visualization of
2ad3b027dfcd Uploaded
bgruening
parents: 25
diff changeset
6 deep-sequencing data.
2ad3b027dfcd Uploaded
bgruening
parents: 25
diff changeset
7 They address the challenge of visualizing the large amounts of data that are now
2ad3b027dfcd Uploaded
bgruening
parents: 25
diff changeset
8 routinely generated from sequencing centers in a meaningful way.
2ad3b027dfcd Uploaded
bgruening
parents: 25
diff changeset
9 To do so, deepTools contain useful routines to process the mapped reads data
2ad3b027dfcd Uploaded
bgruening
parents: 25
diff changeset
10 through removal of duplicates and different filtering options to create coverage
2ad3b027dfcd Uploaded
bgruening
parents: 25
diff changeset
11 files in standard bedGraph and bigWig file formats. deepTools allow the creation
2ad3b027dfcd Uploaded
bgruening
parents: 25
diff changeset
12 of normalized coverage files or the comparison between two files
2ad3b027dfcd Uploaded
bgruening
parents: 25
diff changeset
13 (for example, treatment and control). Finally, using such normalized and
2ad3b027dfcd Uploaded
bgruening
parents: 25
diff changeset
14 standardized files, multiple visualizations can be created to identify
2ad3b027dfcd Uploaded
bgruening
parents: 25
diff changeset
15 enrichments with functional annotations of the genome.
2ad3b027dfcd Uploaded
bgruening
parents: 25
diff changeset
16 For a gallery of images that can be produced and a description
2ad3b027dfcd Uploaded
bgruening
parents: 25
diff changeset
17 of the tools see our poster_.
2ad3b027dfcd Uploaded
bgruening
parents: 25
diff changeset
18
2ad3b027dfcd Uploaded
bgruening
parents: 25
diff changeset
19 .. _poster: http://f1000.com/posters/browse/summary/1094053
2ad3b027dfcd Uploaded
bgruening
parents: 25
diff changeset
20
2ad3b027dfcd Uploaded
bgruening
parents: 25
diff changeset
21 deeptools is developed under here:
2ad3b027dfcd Uploaded
bgruening
parents: 25
diff changeset
22
2ad3b027dfcd Uploaded
bgruening
parents: 25
diff changeset
23 https://github.com/fidelram/deepTools
2ad3b027dfcd Uploaded
bgruening
parents: 25
diff changeset
24
2ad3b027dfcd Uploaded
bgruening
parents: 25
diff changeset
25 For support, questions, or feature requests contact: deeptools@googlegroups.com
0
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
26
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
27
28
f7712a057440 new bugfix release
bgruening
parents: 26
diff changeset
28 ============
f7712a057440 new bugfix release
bgruening
parents: 26
diff changeset
29 Installation
f7712a057440 new bugfix release
bgruening
parents: 26
diff changeset
30 ============
f7712a057440 new bugfix release
bgruening
parents: 26
diff changeset
31
f7712a057440 new bugfix release
bgruening
parents: 26
diff changeset
32 Requirements: python-2.7
f7712a057440 new bugfix release
bgruening
parents: 26
diff changeset
33
f7712a057440 new bugfix release
bgruening
parents: 26
diff changeset
34 Galaxy should be able to automatically install all other dependencies, such as numpy or scipy.
f7712a057440 new bugfix release
bgruening
parents: 26
diff changeset
35
f7712a057440 new bugfix release
bgruening
parents: 26
diff changeset
36 For the best performance we recommend to install blas/lapack/atlas in your environment before
f7712a057440 new bugfix release
bgruening
parents: 26
diff changeset
37 installing deepTools from the Tool Shed.
f7712a057440 new bugfix release
bgruening
parents: 26
diff changeset
38
f7712a057440 new bugfix release
bgruening
parents: 26
diff changeset
39
26
2ad3b027dfcd Uploaded
bgruening
parents: 25
diff changeset
40 ========
0
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
41 Citation
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
42 ========
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
43
26
2ad3b027dfcd Uploaded
bgruening
parents: 25
diff changeset
44 deeptools are currently under review. In the meantime please refere to https://github.com/fidelram/deepTools.
2ad3b027dfcd Uploaded
bgruening
parents: 25
diff changeset
45
0
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
46
26
2ad3b027dfcd Uploaded
bgruening
parents: 25
diff changeset
47 =======
2ad3b027dfcd Uploaded
bgruening
parents: 25
diff changeset
48 History
2ad3b027dfcd Uploaded
bgruening
parents: 25
diff changeset
49 =======
2ad3b027dfcd Uploaded
bgruening
parents: 25
diff changeset
50
29
3a2aab18a217 Uploaded
bgruening
parents: 28
diff changeset
51 * v1.0: Initial public release
3a2aab18a217 Uploaded
bgruening
parents: 28
diff changeset
52 * v1.5.8.2: Include new citation tag, update version to 1.5.8.2 and change wrapper version
0
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
53
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
54
26
2ad3b027dfcd Uploaded
bgruening
parents: 25
diff changeset
55 Licence (MIT)
2ad3b027dfcd Uploaded
bgruening
parents: 25
diff changeset
56 =============
5
c54d31467be4 Uploaded
bgruening
parents: 0
diff changeset
57
26
2ad3b027dfcd Uploaded
bgruening
parents: 25
diff changeset
58 Permission is hereby granted, free of charge, to any person obtaining a copy
2ad3b027dfcd Uploaded
bgruening
parents: 25
diff changeset
59 of this software and associated documentation files (the "Software"), to deal
2ad3b027dfcd Uploaded
bgruening
parents: 25
diff changeset
60 in the Software without restriction, including without limitation the rights
2ad3b027dfcd Uploaded
bgruening
parents: 25
diff changeset
61 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
2ad3b027dfcd Uploaded
bgruening
parents: 25
diff changeset
62 copies of the Software, and to permit persons to whom the Software is
2ad3b027dfcd Uploaded
bgruening
parents: 25
diff changeset
63 furnished to do so, subject to the following conditions:
0
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
64
26
2ad3b027dfcd Uploaded
bgruening
parents: 25
diff changeset
65 The above copyright notice and this permission notice shall be included in
2ad3b027dfcd Uploaded
bgruening
parents: 25
diff changeset
66 all copies or substantial portions of the Software.
0
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
67
26
2ad3b027dfcd Uploaded
bgruening
parents: 25
diff changeset
68 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
2ad3b027dfcd Uploaded
bgruening
parents: 25
diff changeset
69 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
2ad3b027dfcd Uploaded
bgruening
parents: 25
diff changeset
70 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
2ad3b027dfcd Uploaded
bgruening
parents: 25
diff changeset
71 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
2ad3b027dfcd Uploaded
bgruening
parents: 25
diff changeset
72 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
2ad3b027dfcd Uploaded
bgruening
parents: 25
diff changeset
73 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
2ad3b027dfcd Uploaded
bgruening
parents: 25
diff changeset
74 THE SOFTWARE.