{"id":19857082,"url":"https://github.com/griffithlab/pvactools_intro_course","last_synced_at":"2025-05-02T02:30:34.051Z","repository":{"id":164644497,"uuid":"632049144","full_name":"griffithlab/pVACtools_Intro_Course","owner":"griffithlab","description":"Getting started with pVACtools - pVACseq, pVACbind and pVACview","archived":false,"fork":false,"pushed_at":"2025-01-10T19:00:31.000Z","size":72070,"stargazers_count":0,"open_issues_count":1,"forks_count":2,"subscribers_count":13,"default_branch":"main","last_synced_at":"2025-04-06T21:04:07.168Z","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}},"created_at":"2023-04-24T15:49:17.000Z","updated_at":"2023-07-17T21:40:18.000Z","dependencies_parsed_at":null,"dependency_job_id":"79636b24-5b23-4928-8757-35c64792b022","html_url":"https://github.com/griffithlab/pVACtools_Intro_Course","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":"jhudsl/OTTR_Template","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/griffithlab%2FpVACtools_Intro_Course","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/griffithlab%2FpVACtools_Intro_Course/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/griffithlab%2FpVACtools_Intro_Course/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/griffithlab%2FpVACtools_Intro_Course/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/griffithlab","download_url":"https://codeload.github.com/griffithlab/pVACtools_Intro_Course/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":251972410,"owners_count":21673599,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","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":"2024-11-12T14:17:26.391Z","updated_at":"2025-05-02T02:30:29.039Z","avatar_url":"https://github.com/griffithlab.png","language":"CSS","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Introduction to pVACtools\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 neoantigen identification.\n\nYou can see the [bookdown rendered course material here (GitHub pages site)](https://griffithlab.github.io/pVACtools_Intro_Course/) or the [leanpub rendered version here](https://leanpub.com/c/intropvac). \n\n## About this course\n\nThis course will introduce background concepts, tools, resources, and practical advice on designing cancer vaccines and prioritizing neoantigens with pVACtools. \n\n## Learning Objectives\n\nThis course will teach learners to:  \n\n- Understand key concepts of neoantigen identification\n- Install and run pVACtools\n- Demonstrate pVACview\n\n## Encountering problems?\n\nIf you are encountering any problems with this course, please file a GitHub issue or [contact us at pVACtools help](mailto:help@pvactools.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/1uz39zaObDGKhEVCGzO0JO35CTbC0oRAM0mxgLcMAA9Y/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/pVACtools_Intro_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/pVACtools_Intro_Course/actions) complete successfully.\n12. Review the bookdown build at [github pages site](https://griffithlab.github.io/pVACtools_Intro_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%2Fpvactools_intro_course","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgriffithlab%2Fpvactools_intro_course","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgriffithlab%2Fpvactools_intro_course/lists"}