-
Notifications
You must be signed in to change notification settings - Fork 2
/
feed.xml
171 lines (124 loc) · 8.9 KB
/
feed.xml
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
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
<?xml version="1.0" encoding="utf-8" standalone="yes" ?>
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
<channel>
<title>CJchen's Blog</title>
<link>http://CJ-Chen.github.io/</link>
<description>Recent content on CJchen's Blog</description>
<generator>Hugo -- gohugo.io</generator>
<language>en-us</language>
<lastBuildDate>Mon, 18 Jul 2016 08:50:28 +0800</lastBuildDate>
<atom:link href="http://CJ-Chen.github.io/feed/index.xml" rel="self" type="application/rss+xml" />
<item>
<title>TBtools seminar</title>
<link>http://cj-chen.github.io/tbtools/TBtools-seminar/</link>
<pubDate>Mon, 18 Jul 2016 08:50:28 +0800</pubDate>
<guid>http://cj-chen.github.io/tbtools/TBtools-seminar/</guid>
<description><p>Hello, there.
I have shared <strong><em>TBtools</em></strong> with friends from bioinformatics*中国(QQ group num: 276151571) last night.<br />
The video that has recorded all things during the seminar time has been uploaded on YouKu.</p>
<p><embed src="http://player.youku.com/player.php/sid/XMTY0Nzg0NjU5Mg==/v.swf" allowFullScreen="true" quality="high" width="480" height="400" align="middle" allowScriptAccess="always" type="application/x-shockwave-flash"></embed></p>
<p>If the video is not clear enough, you may also <a href="http://v.youku.com/v_show/id_XMTY0Nzg0NjU5Mg==.html#paction">Click Me</a> to watch it.
Hope that it will be useful if it knew about TBtools and use it.</p>
<p>CJ
20160718</p>
</description>
</item>
<item>
<title>Extracting_Fasta_Records</title>
<link>http://cj-chen.github.io/tbtools/Extracting_Fasta_Records/</link>
<pubDate>Fri, 06 May 2016 19:30:21 +0800</pubDate>
<guid>http://cj-chen.github.io/tbtools/Extracting_Fasta_Records/</guid>
<description>
<h1 id="extracting-fasta-records:a8080c3e60ba11a758f8217788b94420">Extracting Fasta Records</h1>
<p>Multiple fasta records extraction is the most frequently needs in daily molecular data analysis.<br />
To skillful programmer or bioinformatisian, a small scripts or one command is the only need to achieve it.<br />
However, to others, precious time may be wasted on ID searching and text copying.<br />
With TBtools, user just need to drag a file containing sequences in fasta format, like transcriptome assembly result and a target id list (or manual enter id list) into the software and then get all sequences of need in a short time.<br />
Besides,if ID with start base position and end base position were given, regions of corresponding sequences could be extracted, which is very useful to extract up-stream and down-stream of gene position from big genome sequences.</p>
<h1 id="example:a8080c3e60ba11a758f8217788b94420">Example</h1>
<p><img src="http://CJ-Chen.github.io/tbtools/images/FastaExtracter.gif" alt="Extractingfastarecords" title="FastaExtracter" /></p>
<h1 id="download-current-version:a8080c3e60ba11a758f8217788b94420">Download Current Version</h1>
<p><a href="https://github.com/CJ-Chen/TBtools/archive/master.zip">Click To Download</a></p>
</description>
</item>
<item>
<title>About TBtools</title>
<link>http://cj-chen.github.io/tbtools/Introduction/</link>
<pubDate>Thu, 28 Apr 2016 16:17:18 +0800</pubDate>
<guid>http://cj-chen.github.io/tbtools/Introduction/</guid>
<description>
<h1 id="a-breif-introduction-of-tbtools:eb3a74b7ffe83afb3fea66e45dd8e260">A Breif Introduction of TBtools</h1>
<p><a href="https://github.com/CJ-Chen/TBtools/releases">TBtool</a> is a Toolset that was written by CJ-Chen for wet-lab biologists.<br />
It can run in all Operating system including Mac, Linux, Windows, which have <a href="http://www.oracle.com/technetwork/java/javase/downloads/jre8-downloads-2133155.html">Java 1.8 run time environment</a>.<br />
Both command line usages and GUI manipulation have been implemented.<br />
U can use it and distribute it freely, for researches or for commecial purpose.<br />
Well, if u found it useful to u, I will be very graceful that u cite TBtool in u paper&hellip;</p>
<h1 id="download-current-version:eb3a74b7ffe83afb3fea66e45dd8e260">Download Current Version</h1>
<p><a href="https://github.com/CJ-Chen/TBtools/archive/master.zip">Click To Download the lastest version</a></p>
<h1 id="see-the-manual-of-gui-part-of-tbtools:eb3a74b7ffe83afb3fea66e45dd8e260">See the <strong><em>Manual</em></strong> of GUI part of TBtools</h1>
<p><a href="http://cjchen.name/html5/TBtoolsGuiManual.pdf">Click To Download the manual</a></p>
<h1 id="aims:eb3a74b7ffe83afb3fea66e45dd8e260">Aims</h1>
<p>Facilate some common and elaborate but simple molecular analysis tasks such as <strong><em>sequences extract, gene set funtional enrichment</em></strong><br />
Be a useful toolkit for biologists to better untilizate upstream analysis results of high-throughput data</p>
<h1 id="part-of-functions:eb3a74b7ffe83afb3fea66e45dd8e260">Part of Functions</h1>
<ol>
<li>Comparise ID lists Using Venn Diagrams</li>
<li>Check Expression Trends of Interesting Genes</li>
<li>Get Annotation Information from tables</li>
<li>Extract Fasta Records</li>
<li>Compare Two sequences(set) leveraging blast automately</li>
<li>Visualize Blast Results</li>
<li>GO Analysis (Counts On Levels/Parser GO term/GO enrichmen/GO term Compare&hellip;)</li>
<li>Label Newick Tree (partial functions of EasyCodeML.jar)
&hellip;<br /></li>
</ol>
<h1 id="gui-usages-entry:eb3a74b7ffe83afb3fea66e45dd8e260">GUI usages entry</h1>
<p>In default mode, if running in working in a environment graphical, the GUI of TBtools will be showed.<br />
Genrally, what u need to do is <strong><em>double clicking</em></strong> the icon of TBtool_v0.X.jar<br />
!if it doesn&rsquo;t work in this way, u may need to open the GUI of TBtools from command line.<br />
example command is:</p>
<pre><code>java -jar PATH/TBtools_0.X.jar
</code></pre>
<p>Then, TBtools GUI will pop out, as followed:
<img src="http://CJ-Chen.github.io/tbtools/images/MainWindows.png" alt="TBtools GUI MainWindows" title="MainWindows" /></p>
<h1 id="command-line-usages-entry:eb3a74b7ffe83afb3fea66e45dd8e260">Command line usages entry</h1>
<p>If working environment doesn&rsquo;t contain graphical mode, the command line usage will defaultly showed, when u type</p>
<pre><code>java -jar PATH/TBtools_v0.X.jar
</code></pre>
<p>However, if u want to use command line functions of TBtools in a graphical working environment, a little modification of the command shoud be made.<br />
example command is:</p>
<pre><code>java -jar PATH/TBtools_v0.X.jar anythings
</code></pre>
</description>
</item>
<item>
<title>First Post</title>
<link>http://cj-chen.github.io/post/FirstPost/</link>
<pubDate>Wed, 27 Apr 2016 16:17:18 +0800</pubDate>
<guid>http://cj-chen.github.io/post/FirstPost/</guid>
<description>
<h2 id="hello-there-again:da240d7e5080f14f53a771c9b2113a34">Hello,there&hellip;.again</h2>
<p>really busy recently</p>
<p>Some friends from QQ group asks me about the progress of &lsquo;building&rsquo; this blog</p>
<p>So tonight.I make some effort on it.</p>
<p>The new site just finished.</p>
<p>Some post will be updated.</p>
</description>
</item>
<item>
<title>about</title>
<link>http://cj-chen.github.io/about/</link>
<pubDate>Fri, 08 Apr 2016 16:17:18 +0800</pubDate>
<guid>http://cj-chen.github.io/about/</guid>
<description>
<h3 id="hello-there:6083a88ee3411b0d17ce02d738f69d47">Hello, there.</h3>
<p>Things were not going good recently.<br />
My old blog was closed because I was too busy to manage it.<br />
WordPress+mySQL always fail.suck~~~
I want to write in Chinese.<br />
However, worry about the compatiblity.
So, what will be showed here limmited English is my limited English.</p>
</description>
</item>
</channel>
</rss>