This course was created from this GitHub template.
This course was created with Bookdown and introduces best practices and tools for neoantigen identification.
You can see the bookdown rendered course material here (GitHub pages site) or the leanpub rendered version here.
This course will introduce background concepts, tools, resources, and practical advice on designing cancer vaccines and prioritizing neoantigens with pVACtools.
This course will teach learners to:
- Understand key concepts of neoantigen identification
- Install and run pVACtools
- Demonstrate pVACview
If you are encountering any problems with this course, please file a GitHub issue or contact us at pVACtools help.
There are extensive instructions available in the OTTR documentation. Here are basic instructions/reminders:
- Clone the repo.
- Create and checkout a new branch.
- Add new chapters by copying and modifying one of the existing Rmd chapter files. Add an appropriate entry in the
_bookdown.ymlfile. - Add images to this Google Slide deck, copy the slide link, and embed in chapters following example code in existing chapters.
- Add references in BibTex format to the
book.bibfile. BibTex entries can be obtained with doi2bib.org. Cite references inline using@keywherekeyis the citation key in the first line of the BibTex entry. - Once new/revised content is ready, commit and push from the branch, and create a pull request.
- Go to pull requests and make sure all checks passing.
- Correct any reported errors. Any words incorrectly reported as spelling mistakes can be added to
resources/dictionary.txt. Commit and push to re-run PR checks. - Have someone review and approve the pull request.
- Merge the PR and delete the branch.
- Make sure all build Actions complete successfully.
- Review the bookdown build at github pages site.
- Have the leanpub course admin Preview and then Publish a new version of the course.
All materials in this course are licensed under a Creative Commons Attribution 4.0 International License unless noted otherwise.
