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https://github.com/griffithlab/civic_svi_course
A hands on course explaining how to complete somatic cancer variant interpretation using CIViC and current guidelines
https://github.com/griffithlab/civic_svi_course
Last synced: 2 days ago
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A hands on course explaining how to complete somatic cancer variant interpretation using CIViC and current guidelines
- Host: GitHub
- URL: https://github.com/griffithlab/civic_svi_course
- Owner: griffithlab
- License: cc-by-4.0
- Created: 2023-04-24T15:42:11.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2024-09-17T20:01:36.000Z (about 2 months ago)
- Last Synced: 2024-09-18T01:42:15.871Z (about 2 months ago)
- Language: CSS
- Size: 69.2 MB
- Stars: 0
- Watchers: 15
- Forks: 2
- Open Issues: 1
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Metadata Files:
- Readme: README.md
- License: LICENSE.md
- Code of conduct: code_of_conduct.md
Awesome Lists containing this project
README
# Introduction to Clinical Interpretation of Somatic Cancer Variants
This course was created from [this GitHub template](https://github.com/jhudsl/OTTR_Template).
This course was created with Bookdown and introduces best practices and tools for clinical interpretation of somatic cancer variants.
You can see the [bookdown rendered course material here (GitHub pages site)](https://course.civicdb.org/) or the [leanpub course here](https://leanpub.com/c/introcivic).
## About this course
This course will introduce background concepts, tools, resources, and relevant standard operating procedures and guidelines for the clinical interpretation of somatic cancer variants.
## Learning Objectives
This course will teach learners to:
- Understand key concepts of somatic cancer variant interpretation
- Introduce ClinGen Somatic Cancer efforts
- Introduce key SOPs and guidelines for classifying the clinical relevance and oncogenicity of somatic cancer variants
- Introduce CIViC as a curation platform for somatic variant interpretation
## Encountering problems?
If you are encountering any problems with this course, please file a GitHub issue or [contact us at CIViC help](mailto:[email protected]).
## How to contribute to this course
There are extensive instructions available in the [OTTR documentation](https://www.ottrproject.org/index.html). Here are basic instructions/reminders:
1. Clone the repo.
2. Create and checkout a new branch.
3. Add new chapters by copying and modifying one of the existing Rmd chapter files. Add an appropriate entry in the `_bookdown.yml` file.
4. Add images to this [Google Slide deck](https://docs.google.com/presentation/d/1zwvAVLWpN2mKrJLgo5ZcAuSKQrHZ8zunIYHLe-w6bBo/edit?usp=sharing), copy the slide link, and embed in chapters following example code in existing chapters.
5. Add references in BibTex format to the `book.bib` file. BibTex entries can be obtained with [doi2bib.org](https://www.doi2bib.org/). Cite references inline using `@key` where `key` is the citation key in the first line of the BibTex entry.
6. Once new/revised content is ready, commit and push from the branch, and create a pull request.
7. Go to [pull requests](https://github.com/griffithlab/CIVIC_SVI_Course/pulls) and make sure all checks passing.
8. 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.
9. Have someone review and approve the pull request.
10. Merge the PR and delete the branch.
11. Make sure all build [Actions](https://github.com/griffithlab/CIVIC_SVI_Course/actions) complete successfully.
12. Review the bookdown build at [github pages site](https://griffithlab.github.io/CIVIC_SVI_Course/index.html).
13. 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.