Mercurial > repos > iuc > macs2
comparison readme.rst @ 0:fe62ba547975 draft
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| author | iuc |
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| date | Wed, 11 Feb 2015 10:18:02 -0500 |
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| -1:000000000000 | 0:fe62ba547975 |
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| 1 ======================== | |
| 2 Galaxy wrapper for MACS2 | |
| 3 ======================== | |
| 4 | |
| 5 With the improvement of sequencing techniques, chromatin immunoprecipitation | |
| 6 followed by high throughput sequencing (ChIP-Seq) is getting popular to study | |
| 7 genome-wide protein-DNA interactions. To address the lack of powerful ChIP-Seq | |
| 8 analysis method, we present a novel algorithm, named Model-based Analysis of | |
| 9 ChIP-Seq (MACS), for identifying transcript factor binding sites. MACS captures | |
| 10 the influence of genome complexity to evaluate the significance of enriched ChIP | |
| 11 regions, and MACS improves the spatial resolution of binding sites through | |
| 12 combining the information of both sequencing tag position and orientation. | |
| 13 MACS can be easily used for ChIP-Seq data alone, or with control sample with the increase of specificity. | |
| 14 | |
| 15 | |
| 16 ============ | |
| 17 Installation | |
| 18 ============ | |
| 19 | |
| 20 It is recommended to install this wrapper via the `Galaxy Tool Shed`. | |
| 21 | |
| 22 .. _`Galaxy Tool Shed`: http://toolshed.g2.bx.psu.edu/view/modencode-dcc/macs2 | |
| 23 | |
| 24 | |
| 25 ======= | |
| 26 History | |
| 27 ======= | |
| 28 - v2.0.10.1: Initial public release | |
| 29 - v2.0.10.3: add "broad peaks" options | |
| 30 | |
| 31 | |
| 32 ==================== | |
| 33 Detailed description | |
| 34 ==================== | |
| 35 | |
| 36 View the original MACS2 documentation: https://github.com/taoliu/MACS/blob/master/README.rst | |
| 37 | |
| 38 | |
| 39 =============================== | |
| 40 Wrapper Licence (MIT/BSD style) | |
| 41 =============================== | |
| 42 | |
| 43 Permission to use, copy, modify, and distribute this software and its | |
| 44 documentation with or without modifications and for any purpose and | |
| 45 without fee is hereby granted, provided that any copyright notices | |
| 46 appear in all copies and that both those copyright notices and this | |
| 47 permission notice appear in supporting documentation, and that the | |
| 48 names of the contributors or copyright holders not be used in | |
| 49 advertising or publicity pertaining to distribution of the software | |
| 50 without specific prior permission. | |
| 51 | |
| 52 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL | |
| 53 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED | |
| 54 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE | |
| 55 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT | |
| 56 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS | |
| 57 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE | |
| 58 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE | |
| 59 OR PERFORMANCE OF THIS SOFTWARE. | |
| 60 |