comparison readme.rst @ 0:fe62ba547975 draft

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author iuc
date Wed, 11 Feb 2015 10:18:02 -0500
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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