The material available on these pages is produced and maintained for a course on how to make your data analyses reproducible. In particular, it covers:

  • Data management
  • Conda
  • Snakemake
  • Git
  • Jupyter
  • R Markdown
  • Docker
  • Singularity


Source code

The source code for this documentation and all resources used in the course are available as a GitHub repo.


Links to slides from lectures covering the topics above are available in HTML format here. The source code used to create the lectures is available under the lecture/ directory.

Project template

A template directory and file structure consistent with the material described in the course is available as a GitHub repo that you can use to initialize a new project.

The authors

Leif Wigge, Rasmus Ă…gren, John Sundh, Verena Kutschera, Erik Fasterius, Tomas Larsson

SciLifeLab, National Bioinformatics Infrastructure Sweden (NBIS)


MIT (see LICENCE.txt in the GitHub repo).