RNA-seq lesson

This repository generates the RNA-seq lesson materials based on the website template from The Carpentries Foundation.

Table of contents

• Preview changes to the lesson locally
• Contributing
  • How to contribute
  • Writing math symbols and formulas
• Credits
  • Maintainer(s)
  • Authors
  • Citation
  • Source of inspiration

Preview changes to the lesson locally

The lesson website is built through Github and Jekyll.

Option 1: follow the Carpentries setup: http://carpentries.github.io/lesson-example/setup.html The detailed instructions are listed in the "Jekyll Setup for Lesson Development" section.

Option 2: use a Docker container 1. Open a Shell window. 2. Navigate to the rna-seq-lesson/ folder using the cd command. 3. Since the lesson relies Jekyll 3.8.5, type within the Shell export JEKYLL_VERSION=3.8.5. 4. Make sure you have Docker for Windows or Mac installed: https://docs.docker.com/install/ 5. With the Docker Desktop application running (you should see a little whale with containers at the top of your screen), type docker run --rm --volume="$PWD:/srv/jekyll" -p 4000:4000 -it jekyll/jekyll:$JEKYLL_VERSION jekyll serve
6. Open a web browser and type http://0.0.0.0:4000/ in the navigation bar. You should see the lesson website. Your changes should be automatically reflected online.

Contributing

How to contribute

We welcome all contributions to improve the lesson! Maintainers will do their best to help you if you have any questions, concerns, or experience any difficulties along the way.

We'd like to ask you to familiarize yourself with our Contribution Guide and have a look at the [more detailed guidelines][lesson-example] on proper formatting, ways to render the lesson locally, and even how to write new episodes.

Please see the current list of [issues][FIXME] for ideas for contributing to this repository. For making your contribution, we use the GitHub flow, which is nicely explained in the chapter Contributing to a Project in Pro Git by Scott Chacon. Look for the tag . This indicates that the mantainers will welcome a pull request fixing this issue.

Writing math symbols and formulas

Sometimes, you need to render mathematical formula etc. GitHub pages which is using Jekyll to render html pages makes use of MathJax.

Visit the official website and consult this thread for quick ways to render math symbols.

Credits

Maintainer(s)

Current maintainers of this lesson are

• Marc Galland, Data analyst and manager (University of Amsterdam, SILS, Plant Physiology Department).
• Tijs Bliek, research technician (University of Amsterdam, SILS, Plant Development and Epigenetics).

Authors

A list of contributors to the lesson can be found in AUTHORS

Citation

To cite this lesson, please consult with CITATION

Source of inspiration

This lesson is heavily based on teaching materials from the Harvard Chan Bioinformatics Core (HBC) in-depth NGS data analysis course. Materials have been adapted and some exercises created to comply with the Carpentries Foundation teaching requirements.