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Evolutionary Genetics ➜ Bioinformatics

Hate&Love (phdcomics)

  • Date: W39-W41
  • Lecturer: Jean-Claude Walser
  • Update: 27-Sep-2022

Overview

In this first module I try to explain elementary basics of bioinformatics. We will discuss different aspects of bioinformatics in relation to sequencing data and apply the newly gained knowledge. The scope will be determined by the level of knowledge and the wishes of the students. However, the command line and programming in R are important components of the course. Emphasis will also be placed on report writing in view of reproducibility.

Requirements

Have a look at the requirements. There is still enough time for you to prepare yourself and your computer for this class. It is essential that your computer is ready before we start!

Handouts

Here you can find the general handouts. The topic-related handouts can be found on the corresponding page.

Assignments

The assignment are part (⅓) of the final grade. It is important to me that you can apply what you have learned.

Deadline

▻ Sunday, 30. October 2022

Assignment - R-Function

Write your own personal R function and documentation (R-Markdown) for it. Try to implement what you have learned (e.g. comments to explain and structure the code) as well as possible. Don’t forget the title, version and author details. We saw some simple examples in the lecture and learned how to convert the R code into an R function with a few adjustments. You can find more inspiration in the Hall of Fame, a collection of original and successful R functions from former students of this course. I hope these marvellous examples give you ideas and motivation!

At the end I would like to have an R function, the corresponding images or data (if necessary), a documentation of the application as Markdown and HTML document packed in a zip archive file. 

# EvoGen_BioInf_Assignment_<Title>_<Author>.zip
# │
# ├── <Title>.Rfunction
# ├── Help_<Title>.Rmd
# ├── Help_<Title>.html
# │
# ├── Data
# │   └── table.txt  
# │
# ├── Figures
# │   └── fig1.txt
# │   └── fig2.txt
# │
# └── etc

Here is a example. Please do not use it as a template but more as an inspiration.

Best of luck and do not hesitate to ask for help. There is strength in the together!

Hall of Fame