current-topics-bioinformatics-lecture

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# Current methods and concepts in Bioinformatics

*Lecture at the Medical University of Innsbruck, winter term 2021*

In this course students will learn about current bioinformatic tools, state of the art software development and data analysis frameworks, and code writing concepts which are fundamental for conducting scalable and reproducible data analyses.
Attendees should have basic skills and knowledge in Linux and command line usage.

## News

* **Due to the core-lecture, the first three lectures (2021-10-07, 2021-10-14, and 2021-10-21) have been postponed to 10:15)**.

## Logistics

* The lecture takes place every Thursday from 09:00 to 09:45 in the seminar room, CCB 4th floor (I80/8204M.04.383). 
 * There will be exercises for each lectures. We will discuss the solutions in the next lecture. Where applicable, exercises need to be handed in via GitHub or GitLab
 * You can pose questions in the [issue tracker](https://github.com/icbi-lab/current-topics-bioinformatics-lecture/issues). 
 
## Lecture material

* Is organized in this repository
 * Slides are available from the [course website](https://icbi-lab.github.io/current-topics-bioinformatics-lecture/)
 * If you find a mistake, feel free to send a [pull request](https://github.com/icbi-lab/current-topics-bioinformatics-lecture/pulls) or open an [issue](https://github.com/icbi-lab/current-topics-bioinformatics-lecture/issues).

## Lecture overview

1. Advanced Linux command line use - Part I ([[material](01_bash_tricks)], [[slides](https://icbi-lab.github.io/current-topics-bioinformatics-lecture/01_bash_tricks.html#1)])
   - bash tricks
1. Advanced Linux command line use - Part II ([[material](02_bash_tricks)], [[slides](https://icbi-lab.github.io/current-topics-bioinformatics-lecture/02_bash_tricks.html#1)])
   - more bash tricks
1. Advanced Linux command line use - Part III ([[material](03_bash_tricks)], [[slides](https://icbi-lab.github.io/current-topics-bioinformatics-lecture/03_bash_tricks.html#1)])
   - combining commands with pipes
   - terminal multiplexing with tmux
1. Software version control and collaboration - Part I  ([[material](04_git_basics)], [[slides](https://icbi-lab.github.io/current-topics-bioinformatics-lecture/04_git_basics.html#1)])
   - git basics
1. Nextflow - Part I ([[material](05_nextflow_basics)], [[slides](https://icbi-lab.github.io/current-topics-bioinformatics-lecture/05_nextflow_basics.html)])
   - benefits of workflow managers
   - nextflow features 
   - basic nextflow scripting
1. Software version control and collaboration - Part II ([[material](06_git_collaboration)], [[slides](https://icbi-lab.github.io/current-topics-bioinformatics-lecture/06_git_collaboration.html)])
   - working with git remotes (GitHub/GitLab)
   - issues and pull requests
   - code review
   - continuous integration
1. Nextflow - Part II ([[material](07_nextflow_dsl2)], [[slides](https://icbi-lab.github.io/current-topics-bioinformatics-lecture/07_nextflow_dsl2.html)])
   - Modular workflows with DSL2
1. Tidy data and `dplyr` ([[material](08_dplyr_tidy_data)], [[slides](https://icbi-lab.github.io/current-topics-bioinformatics-lecture/08_dplyr_tidy_data.html)])
1. Data formats and their use-cases ([[material](09_data_formats_python)], [[slides](https://icbi-lab.github.io/current-topics-bioinformatics-lecture/09_data_formats_python.html)])
1. Fundamentals of data visualization

The slides are not be available online for copyright reasons. However, the book [Fundamentals of data visualization](https://clauswilke.com/dataviz/) is freely available online. 
   
1. Virtual environments
   - conda
   - docker
   - singularity

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