Homework

Study Material and Exercises

Tutorial: Unix

Preliminaries

If you are a Windows user download and install Git-Bash
Please read this first: How to connect to remote accounts
Conda installation instructions

Exercises

Basic Unix operations for bioinformatics

Reading

Intro slides

Recommended Reading

The Unix Shell tutorial from the Software Carpentry Foundation
Unix commands cheat sheets:
- https://www.git-tower.com/blog/command-line-cheat-sheet/
- http://cheatsheetworld.com/programming/unix-linux-cheat-sheet/
Unix philosophy
Regular expression learning resources

Tutorial: Git

Preliminaries

Exercises

Exercise 1
Exercise 2
(Optional: Exercise 3) Suggested instead to read about uploading your repos to GitHub
GitHub Homework

Reading

Slides

Recommended Reading

Git Cheat Sheet (PDF)

Tutorial: Sequencing Technologies

Tutorial: Intro to R programming for data analysis

Self-study notebook

Reading

A selection of small chapters and sections that explain concepts we cover in the course:

R for Data Science (the whole book is great and even covers basic R)
- Section 1. Intro (if the tidyverse context or applications are not clear)
- Section 4. Workflow: basics (good tips for working with code)
- Section 5. Data Transformations
- Section 18. Pipes (about the %>% operator)
- Section 19. Functions (you can skip the last section about environments)
Advanced R
- Section 4. Subsetting (different ways to access elements in R data structures)
Misc

Recommended Reading

Tutorial: Metagenomics and Single-Cell workflows

Tutorial: Introduction to Algorithmic Thinking

Self-study notebook

Tutorial: Gene prediction/annotation

Exercise 1

Practical info for projects

How to install your own software on the server

Chalmers University of Technology