Applied Bioinformatics 2025
Home
About
Source Code
Report a Bug
Version control & documentation
git pull requests
Home
Preparations
Server accounts
Visual Studio Code
Server access
Command line
screen session
Quarto
git and GitHub
Why this course?
Personal course homepage
Reproducible bioinformatics
Version control & documentation
git pull requests
Quarto blog
GitHub actions
Working with environments
Pixi
QC with Pixi
Bonus: Python in Pixi
Working with containers
Apptainer
QC with Apptainer
Workflow manager
Nextflow
Nextflow basics
Nextflow RNAseq
Pipelines
nf-core
Test nf-core
Use nf-core
Miscellaneous
ggplot
AI in bioinformatics
Version control & documentation
git pull requests
Using git collaboratively
This module will be run by Sam, and he has his own slides and content on Canvas.