Introduction to Programming for Bioinformatics using Python and R.
- Lecturer: Gang Chen ([email protected])
- Laptop is required for this courses
- Most softwares and packages in this courses are available on Windows, Linux and Mac OS. However, Linux and Mac OS are recommended for Bioinformatics.
- All slides of this courses are written in Markdown or LaTeX. You can check out source codes of these slides from GitHub.
Date: 10 Sept 2016
- Computer Architecture
- Computer Network
Date: 17 Sept 2016
- Overview of Python
- Setting Up Python Development Environment
- Hello Python
- Interactive and Script mode
- A IPython Notebook for Introduction to Python also can be used as a reference for 3rd week.
- Python Courses on codecademy an interactive courses of Python for people who don't have any programming experiences.
- A byte of Python
- The Hitchhiker’s Guide to Python
24 Sept 2016
- Data Type
- Variable
- List and map
- Flow Control: conditional statement and loop
- Function and module
- Computational Complexity Theory from Stanford University
- Introduction to Algorithms, 2nd
- Algorithms, 4th
8 Oct 2016
See references of Lecture 2.
15 Oct 2016
See references of Lecture 2.
22 Oct 2016
- Web Development Overview
- Overview
- LAMP: Operation System, Web Server, Database, Programming language
- LAMP: HTML, CSS, Javascript, Python, SQL
- A static website
- CGI
- Connect CGI to Database
- Web Framework: Django
- A online sequence aligner
- Django Documentations
Date: 29 Oct 2016
- NumPy, SciPy, Pandas: Scientific computing
- Scikit-Learn, NLTK: Machine Learning and natural language processing
- Matplotlib: Data visualization in Python
Exercises in Python for Andrew Ng's Machine Learning courses.
- Building Machine Learning Systems with Python
5 Nov 2016
- Bioinformatics Programming using Python
12 Nov 2016
- R in Action, 2nd
19 Nov 2016
- BioConductor
- Workflow of RNA-Seq data analysis
- Visualization of Biological Data
26 Nov 2016
- The Code Complete 2nd
3 Dec 2016
10 Dec 2016
Review slides and assignments.