-
Notifications
You must be signed in to change notification settings - Fork 5
/
Copy pathdoc.html
113 lines (111 loc) · 4.7 KB
/
doc.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8">
<title>Genotet - Help Document</title>
<link rel="shortcut icon" href="favicon.ico" type="image/x-icon">
<script type="text/javascript" src="bower_components/jquery/dist/jquery.min.js"></script>
<script type="text/javascript" src="bower_components/jquery-ui/jquery-ui.min.js"></script>
<script type="text/javascript" src="bower_components/bootstrap/dist/js/bootstrap.min.js"></script>
<link rel="stylesheet" href="bower_components/jquery-ui/themes/smoothness/jquery-ui.min.css"/>
<link rel="stylesheet" href="bower_components/jquery-ui/themes/smoothness/theme.css"/>
<link rel="stylesheet" href="bower_components/bootstrap/dist/css/bootstrap.min.css"/>
<link rel="stylesheet" href="bower_components/bootstrap/dist/css/bootstrap-theme.min.css"/>
</head>
<body>
<div class="container">
<h2> Genotet - Help Document </h2>
<p>For more information, contact <a href="mailto:[email protected]">Bowen</a>, <a href="mailto:[email protected]">Jiaming</a> or <a href="mailto:[email protected]">Liana</a>. </p>
<p>Note: This document is currently only for data format of data uploading.</p>
<h3>Network</h3>
<ul>
<li>Currently, we accept *.tsv file for network uploading.</li>
<li>The first line contains N + 2 space seperated strings, containing 2 table head of "regulator", "target" and N names of values.</li>
<li>Following M lines, containing M edges from regulators to targets, each line contains N + 2 elements. They are 1 regulator, 1 target and N float values.</li>
<li>It is like
<pre>
regulator target value_name1 ... value_nameN
regulator_name[1] target_name[1] value[1][1] ... value[1][N]
...
regulator_name[M] target_name[M] value[M][1] ... value[M][N]</pre>
</li>
<li>Sample Data:
<pre>
regular target alpha beta
Batf Maf 0.1 3.2
IRF4 Batf3 1.9 5.3</pre>
</li>
</ul>
<h3>Binding</h3>
<ul>
<li>Currently, we only accept *.bw files to be uploaded.</li>
<li>You can get more information <a href="http://genome.ucsc.edu/goldenpath/help/bigWig.html" target="_blank">here</a>.</li>
</ul>
<h3>Expression Matrix</h3>
<ul>
<li>Expression Matices are simple matrices.</li>
<li>The first line contains N + 1 space seperated strings, including one table head of "GENE", and N condition names.</li>
<li>For the next M lines, each line contains N + 1 space seperated elements, including 1 gene name and N float values.</li>
<li>It is like:
<pre>
GENE condition[1] ... condition[N]
gene[1] value[1][1] ... value[1][N]
...
gene[M] value[M][1] ... value[M][N]</pre>
</li>
<li>Sample Data:
<pre>
GENE SigH1_1_FG SigH1_2_FG
SigA -0.8 1.5
SigB -0.9 3.9</pre>
</li>
</ul>
<h3>Bed</h3>
<ul>
<li>We accept *.bed data. It contains several lines, and we only use the first 4 columns for now.</li>
<li>The first 4 elements of each line are the chromosome, start position, end position and name.</li>
<li>It is like
<pre>
chromosome[1] start[1] end[1] name[1]
...
chromosome[N] start[N] end[N] name[N]</pre>
</li>
<li>Sample Data:
<pre>
chr13 49344650 49344667 unknown_BatfIrf4Th17f_1_mm9
chr5 101662494 101662511 unknown_BatfIrf4Th17f_1_mm9
chr8 26382888 26382905 unknown_BatfIrf4Th17f_1_mm9</pre>
</li>
</ul>
<h3>Mapping</h3>
<ul>
<li>The mapping data maps genes to binding files.</li>
<li>It contains several lines, each line contains a gene and a binding file name.</li>
<li>Sample Data:
<pre>
BATF SL3037_SL3036
IRF4 SL2872_SL2876
RORC SL2870_SL2871</pre>
</li>
</ul>
<h3>Batch Upload</h3>
<ul>
<li>We provide a python batch upload script uploadBatch.py, you can find it in Github. You can use is to upload several data files at once.</li>
<li>You should use is properly. First, you may modify the server path at line #14.</li>
<pre>
url = 'http://genotetserver'</pre>
<li>Then, define a proper .tsv file, each line shoud be [tab] separated parameters.</li>
<pre>
file_path data_name data_type description</pre>
<li>Note that file_path should be full path or the path relevant to the uploadBatch.py.</li>
<li>The data name is specified to the data, like the gene name and so on.</li>
<li>The data type should be one of binding, network, expression, bed and mapping.</li>
<li>Description can contain whitespaces.</li>
<li>Then, you should use the following command to upload data.</li>
<pre>
python uploadBatch.py username example.tsv</pre>
<li>Note that you should replace the username with your username, and example.tsv as the tsv file you defined.</li>
</ul>
</div>
</body>
</html>