/agisPracticalBioinformatics2021

Primary LanguagePython

Welcome to Practical Bioinformatics course

A graduate course covering critical computational skills and practical bioinformatic packages.

AGIS, CAAS

A graduate course covering critical computational skills for working with biological data

Instructors: Yuwen Liu, Li Wang

Time/Location: Wednesday evenings 6.30--9:10pm; D104

Web View: Practical Bioinfomatics 2020 Autumn

Reading Material

Course Schedule

Week 1

Week 2

Week 3

Week 4

Week 5

Week 6

Week 7

Week 8

Week 9

Week 10

Week 11

Week 12

Week 13

Week 14

Week 15

Week 16

Final Group Project

The group projects will be due at the end of the semester during the last two class meetings, where each group will give a presentation on their work.

Questions： 我们是否需要教一些Unix/R/Python Basics,还是suppose这些大家就会呢？

Brainstorm ideas:

  1. 建立微信群进行交流
  2. 测评：1)每部分内容有一些作业 30% 2) 考试：group project and presentations 70%
  3. 一共48课时，大概20周时间，20-2=18周，一周是三个课时？16*3=48

Basic Bioinformatic tools:

  • Basic Unix
  • Regular Expression
  • Markdown files
  • access to HPC clusters
  • version control using Git
  • Advanced Shell Pipelines
  • Jupyter Notebook
  • Make Snake/SOS?

Programming

  • R: 这部分可以结合统计学知识一起讲.

    1. 安装软件包
    2. 读取和存储数据
    3. 基本的统计分析（chi-square，t.test, permutation, hypergeometric test）
    4. Visualization (box plot, point plot, linear regression etc)

  • Python:

    1. loops
    2. reading and writing files
    3. modules and libraries
    4. introduction to "pandas"

实用生信软件介绍:

  1. 序列比对：Bowtie, BWA
  2. 基因表达分析：EdgeR, DeSeq2, GO enrichment
  3. ChIP-Seq Peak分析:贝叶斯模型; 软件应用 Macs2
  4. 关联图谱分析：GWAS 线性模型 混合线性模型 软件应用 GEMMA
  5. 群体遗传结构的分析： STRUCTURE, PCA, ADMIXTURE
  6. 基因功能区域划分: 马可夫链; 软件应用 ChroHMM， Phastcons
  7. 新生突变: 混合泊松模型; 软件应用 TADA-Annotation
  8. 机器学习: CNN 模型; 软件应用 DeepSEA