Mercurial > repos > greg > gregs
comparison readme.rst @ 6:5742b322f956 draft default tip
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| author | greg |
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| date | Tue, 10 Dec 2013 10:09:39 -0500 |
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| 5:a80606f72321 | 6:5742b322f956 |
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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 Citation | |
| 30 ======== | |
| 31 | |
| 32 deeptools are currently under review. In the meantime please refere to https://github.com/fidelram/deepTools. | |
| 33 | |
| 34 | |
| 35 ======= | |
| 36 History | |
| 37 ======= | |
| 38 | |
| 39 - v1.0: Initial public release | |
| 40 | |
| 41 | |
| 42 Licence (MIT) | |
| 43 ============= | |
| 44 | |
| 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: | |
| 51 | |
| 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. |