Bioinformatics Tutorial - Advanced
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Bioinformatics Tutorial - Advanced
Getting Startted
PART I. PROGRAMMING SKILLS
Introduction of PART I
1.Setup
2.Linux
3.Bash and Github
4.R
5.Python
6.Perl
Conclusion of PART I
PART II. MACHINE LEARNING SKILLS
1.Machine Learning
2.Feature Selection
3.Machine Learning Practice
4.Deep Learning
PART III. CASE STUDIES
Introduction of PART III
Case Study 1. exRNA-seq
Case Study 2. exSEEK
Case Study 3. DeepSHAPE
Appendix
Appendix I. Keep Learning
Appendix II. Public Data
Appendix III. Mapping Protocol of RNA-seq
Appendix IV. Useful tools for bioinformatics
SOFTWARE
I. Docker Manual
II. Local Gitbook Builder
III. Teaching Materials
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II. Local Gitbook Builder
Contributed by Xupeng Chen
Gitbook 新版不再支持pdf和其他静态导出，也不再兼容旧版command line版本，旧版command line不支持右边栏和一些hint和embed语法，需要第三方插件，

Install command line gitbook tool

先安装brew和npm两个包管理软件
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/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
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brew install node
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brew install npm
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再用npm安装gitbook
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npm install gitbook -g
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npm install gitbook-cli -g
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gitbook -V #查看版本gitbook和gitbook-cli版本
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Install packages for gitbook tool

在book.json中填入插件名称，then run gitbook install就可以自动安装依赖的插件。安装新版gitbook的一些替代插件以及一些额外的美化插件。
urlembed取代embed，效果不是很完美，tabs也没有新版gitbook的效果 插件用法
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{% urlembed %}
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https://website.org/stuff/this-is-the-path-name
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{% endurlembed %}
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{% tabs first="First Tab", second="Second Tab", third="Third Tab" %}
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​
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{% content "first" %}
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Content for first tab ...
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​
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{% content "second" %}
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Content for second tab ...
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​
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{% content "third" %}
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Content for third tab ...
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​
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{% endtabs %}
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Build gitbook (html)

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gitbook init #自动生成SUMMARY.md，但多级目录似乎无法找到，建议略过这一步用手工编辑版本
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gitbook serve #可在浏览器预览，默认在http://localhost:4000
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gitbook build #产生html
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How to build pdf/epub

    下载calibre
    ​https://calibre-ebook.com/dist/osx​
    链接到bin下
    ln -s /Applications/calibre.app/Contents/MacOS/ebook-convert /usr/local/bin
    产生pdf gitbook pdf . training_book.pdf
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III. Teaching Materials
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Contents
Install command line gitbook tool
Install packages for gitbook tool
Build gitbook (html)
How to build pdf/epub