Bioinformatics Tutorial - Basic
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Bioinformatics Tutorial - Basic
Getting Started
Part I. Basic Skills
1.Setup
2.Linux
2.1.Basic Command
2.2.Practice Guide
2.3.Linux Bash
3.R
4.Python
PART II. BASIC ANALYSES
1.Blast
2.Conservation Analysis
3.Function Analysis
4.Clinical Analyses
Part III. NGS DATA ANALYSES
1.Mapping
2.RNA-seq
3.ChIP-seq
4.Motif
5.Network
6.RNA Regulation Analyses
Part IV. MACHINE LEARNING
1.Machine Learning Basics
2.Machine Learning with R
3.Machine Learning with Python
Part V. Quiz
1.Precision Medicine - exSEEK
2.RNA Regulation - RiboShape
Appendix
Appendix I. Keep Learning
Appendix II. Databases & Servers
Appendix III. How to Backup
Appendix IV. Teaching Materials
Appendix V. Software and Tools
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2.Linux

1) Table of Contents

我们从一些 Linux 的基本操作开始我们的学习。本节包括两个部分
    ​Basic Command: 一些基本命令的介绍和相关阅读推荐,供大家课前预习了解。
    ​Practice Guide: 一个简单的上机指南供大家练习。
    ​Linux Bash: 一个快速入门bash的教程和相关阅读推荐。

2) Files Needed

Method 1: use docker

docker images的下载链接如附表所示，加载完我们提供的image后，文件都已经准备好了，可以这样查看：
1
cd /home/test/linux
2
ls
Copied!
本教程docker使用方式：
    1) 运行容器: docker exec -it bioinfo_tsinghua bash
    2) 进行Linux系统的相关操作
    3) 退出容器：exit

Method 2: directly download files needed

    如果不使用docker，也可以直接从该链接中Files needed by this Tutorial中的清华云Bioinformatics Tutorial / Files路径下的相应文件夹中下载所需要的文件。

3) Recommended Videos (link)

    Part I: 2.1 How to use Linux - ZJL
    Part I: 2.1 How to use Vim
    Part I: 2.2 Programming in Linux - LXF
    Part I: 2.3 bash - Shell脚本编程案例 (20min)
    Part I: 2.3 bash - Shell脚本编程基础 (1hr)
对零基础的同学可以先学习一下以下两个视频：
    2.1 Linux小白Shell入门
    2.1 Linux Editor - nano
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Contents
1) Table of Contents
2) Files Needed
Method 1: use docker
Method 2: directly download files needed
3) Recommended Videos (link)