A graduate course covering critical computational skills and practical bioinformatic packages.
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
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:
- 建立微信群进行交流
- 测评:1)每部分内容有一些作业 30% 2) 考试:group project and presentations 70%
- 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.
- 安装软件包
- 读取和存储数据
- 基本的统计分析(chi-square,t.test, permutation, hypergeometric test)
- Visualization (box plot, point plot, linear regression etc)
-
Python:
- loops
- reading and writing files
- modules and libraries
- introduction to "pandas"
实用生信软件介绍:
- 序列比对:Bowtie, BWA
- 基因表达分析:EdgeR, DeSeq2, GO enrichment
- ChIP-Seq Peak分析:贝叶斯模型; 软件应用 Macs2
- 关联图谱分析:GWAS 线性模型 混合线性模型 软件应用 GEMMA
- 群体遗传结构的分析: STRUCTURE, PCA, ADMIXTURE
- 基因功能区域划分: 马可夫链; 软件应用 ChroHMM, Phastcons
- 新生突变: 混合泊松模型; 软件应用 TADA-Annotation
- 机器学习: CNN 模型; 软件应用 DeepSEA