Mercurial > repos > bgruening > deeptools
comparison readme.rst @ 0:d957e25e18a3 draft
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| author | bgruening |
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| date | Thu, 14 Nov 2013 16:39:18 -0500 |
| parents | |
| children | c54d31467be4 |
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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 | |
| 33 | |
| 34 | |
| 35 ======= | |
| 36 History | |
| 37 ======= | |
| 38 | |
| 39 - v1.0: Initial public release | |
| 40 | |
| 41 | |
| 42 =============================== | |
| 43 Wrapper Licence (MIT/BSD style) | |
| 44 =============================== | |
| 45 | |
| 46 Permission to use, copy, modify, and distribute this software and its | |
| 47 documentation with or without modifications and for any purpose and | |
| 48 without fee is hereby granted, provided that any copyright notices | |
| 49 appear in all copies and that both those copyright notices and this | |
| 50 permission notice appear in supporting documentation, and that the | |
| 51 names of the contributors or copyright holders not be used in | |
| 52 advertising or publicity pertaining to distribution of the software | |
| 53 without specific prior permission. | |
| 54 | |
| 55 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL | |
| 56 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED | |
| 57 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE | |
| 58 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT | |
| 59 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS | |
| 60 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE | |
| 61 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE | |
| 62 OR PERFORMANCE OF THIS SOFTWARE. | |
| 63 |