{"id":19857067,"url":"https://github.com/griffithlab/civic_svi_course","last_synced_at":"2026-02-15T09:43:05.177Z","repository":{"id":166624105,"uuid":"632046216","full_name":"griffithlab/CIVIC_SVI_Course","owner":"griffithlab","description":"A hands on course explaining how to complete somatic cancer variant interpretation using CIViC and current guidelines","archived":false,"fork":false,"pushed_at":"2025-01-10T19:00:29.000Z","size":66363,"stargazers_count":0,"open_issues_count":1,"forks_count":2,"subscribers_count":15,"default_branch":"main","last_synced_at":"2025-05-02T02:38:38.627Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"CSS","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"cc-by-4.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/griffithlab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.md","code_of_conduct":"code_of_conduct.md","threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2023-04-24T15:42:11.000Z","updated_at":"2023-04-24T15:42:22.000Z","dependencies_parsed_at":"2025-01-10T19:52:53.876Z","dependency_job_id":null,"html_url":"https://github.com/griffithlab/CIVIC_SVI_Course","commit_stats":null,"previous_names":["griffithlab/civic_svi_course"],"tags_count":0,"template":false,"template_full_name":"jhudsl/OTTR_Template","purl":"pkg:github/griffithlab/CIVIC_SVI_Course","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/griffithlab%2FCIVIC_SVI_Course","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/griffithlab%2FCIVIC_SVI_Course/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/griffithlab%2FCIVIC_SVI_Course/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/griffithlab%2FCIVIC_SVI_Course/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/griffithlab","download_url":"https://codeload.github.com/griffithlab/CIVIC_SVI_Course/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/griffithlab%2FCIVIC_SVI_Course/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29475211,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-15T06:58:05.414Z","status":"ssl_error","status_checked_at":"2026-02-15T06:58:05.085Z","response_time":118,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-11-12T14:17:23.100Z","updated_at":"2026-02-15T09:43:05.160Z","avatar_url":"https://github.com/griffithlab.png","language":"CSS","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Introduction to Clinical Interpretation of Somatic Cancer Variants\n\nThis course was created from [this GitHub template](https://github.com/jhudsl/OTTR_Template).\n\nThis course was created with Bookdown and introduces best practices and tools for clinical interpretation of somatic cancer variants.\n\nYou 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). \n\n## About this course\n\nThis course will introduce background concepts, tools, resources, and relevant standard operating procedures and guidelines for the clinical interpretation of somatic cancer variants. \n\n## Learning Objectives\n\nThis course will teach learners to:  \n\n- Understand key concepts of somatic cancer variant interpretation\n- Introduce ClinGen Somatic Cancer efforts\n- Introduce key SOPs and guidelines for classifying the clinical relevance and oncogenicity of somatic cancer variants\n- Introduce CIViC as a curation platform for somatic variant interpretation\n\n## Encountering problems?\n\nIf you are encountering any problems with this course, please file a GitHub issue or [contact us at CIViC help](mailto:help@civicdb.org).\n\n## How to contribute to this course\n\nThere are extensive instructions available in the [OTTR documentation](https://www.ottrproject.org/index.html). Here are basic instructions/reminders:\n\n1. Clone the repo.\n2. Create and checkout a new branch.\n3. Add new chapters by copying and modifying one of the existing Rmd chapter files. Add an appropriate entry in the `_bookdown.yml` file. \n4. 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.\n5. 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.\n6. Once new/revised content is ready, commit and push from the branch, and create a pull request.\n7. Go to [pull requests](https://github.com/griffithlab/CIVIC_SVI_Course/pulls) and make sure all checks passing.\n8. 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.\n9. Have someone review and approve the pull request.\n10. Merge the PR and delete the branch.\n11. Make sure all build [Actions](https://github.com/griffithlab/CIVIC_SVI_Course/actions) complete successfully.\n12. Review the bookdown build at [github pages site](https://griffithlab.github.io/CIVIC_SVI_Course/index.html). \n13. Have the leanpub course admin Preview and then Publish a new version of the course.  \n\n\u003ca rel=\"license\" href=\"http://creativecommons.org/licenses/by/4.0/\"\u003e\u003cimg alt=\"Creative Commons License\" style=\"border-width:0\" src=\"https://i.creativecommons.org/l/by/4.0/88x31.png\" /\u003e\u003c/a\u003e\u003cbr /\u003eAll materials in this course are licensed under a \u003ca rel=\"license\" href=\"http://creativecommons.org/licenses/by/4.0/\"\u003eCreative Commons Attribution 4.0 International License\u003c/a\u003e unless noted otherwise.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgriffithlab%2Fcivic_svi_course","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgriffithlab%2Fcivic_svi_course","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgriffithlab%2Fcivic_svi_course/lists"}