mar622 - Profile Module R programming for (meta)-genomic sequence analysis (Complete module description)

The course will provide students with a general understanding of the utility of the UNIX terminal environment and shell scripting, Python programming language and its scripting abilities, and basics of R programming. The course is designed for life scientists with mock or real-world datasets that convey typical characteristics of what researchers often encounter in data-enabled microbiology, and help them develop dry-lab skills the way they developed wet-lab skills.

Specialist skills:

The students:
- Develop an appreciation of different scripting and programming tools and recognize task-specific best practices
- Learn the basics of how to solve bioinformatics challenges in reproducible manner

Methodological competence

The students:
- Can use BASH scripting to organize datasets and implement batch work solutions
- Can use Python for quick and effective data mining and reporting
- Can use R for statistical inference and exploratory visualization needs
- Able to generate reproducible .sh, .py, and .R files, and use Jupyter notebooks
- Develop an appreciation of the basics of programming, data structures, and algorithms

- Basics of BASH, Python, and R, and how they integrate with one another.

- Description of a science question, dataset to address it, and a step-wise computational strategy.

- Goal-oriented community scripting to explore alternative solutions.

- Individual scripting to establish a student-specific solution.

Will be announced in the courses.

Will be announced

1 Examination performance:

Portfolio (max. 3 pieces of work) or minutes (approx. 15-20 pages)

Active participation in seminars and exercises.