Python for downstream data analysis
25 February 2021
This course is organised over two full days. We will start with a brief recap of the basics of Python, followed by exploring libraries for data manipulation and visualization (pandas and seaborn resp.). With the help of plenty hands-on exercises, you will learn to fetch biological data and sequencing files from online databases, and be able to parse and analyze this data. There will be time to highlight specific requests of topics from participants.
The course is organized over two separate days. It is possible to follow only one day.
- Use libraries for advanced data manipulation and visualization (day 1)
- Working with biological data using Biopython (day 2)
- Being able to write scripts and functions from scratch for specific bioinformatics problems
Participants are expected to have attended an introductory Python course and/or have acquired some working knowledge of Python.
Tuur Muyldermans is a bioinformatics trainer at the VIB Bioinformatics Core and ELIXIR Belgium.
James Collier is a professional software developer with >10 years of experience working on software ranging from tiny embedded devices through to high-performance and web applications. He completed his PhD at Monash University on Australia and now works on scientific software within the VIB Bioinformatics Core.
Introduction & Python recap quiz
Data manipulation with pandas
- Exploring the pandas library
- Processing tabular data (csv-files)
- Preparing RNA-seq differentially expressed genes dataset for a heatmap
Visualization with seaborn
- Exploring seaborn library
- Basic plotting (lineplots, barplots, etc.) & multiplot grids
- Create a scatter plot & heatmap
- Introduction & fetching data
- Parsing and analyzing biological data & file formats
- BLASTing via Biopython
After a brief introduction in a specific Biopython module, the participants will have gathered enough information to tackle the exercises. Together we will discover different strategies to solve these bioinformatics related problems.
Selected topics from participants
- Answering remaining questions from participants