{"id":21662777,"url":"https://github.com/higlass/higlass-clinvar","last_synced_at":"2025-03-20T05:48:51.201Z","repository":{"id":54299174,"uuid":"290288299","full_name":"higlass/higlass-clinvar","owner":"higlass","description":"Display ClinVar data in HiGlass","archived":false,"fork":false,"pushed_at":"2022-12-08T20:55:47.000Z","size":975,"stargazers_count":2,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-03-11T05:05:23.751Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"JavaScript","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/higlass.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2020-08-25T18:08:19.000Z","updated_at":"2024-02-07T15:48:05.000Z","dependencies_parsed_at":"2023-01-25T15:00:14.371Z","dependency_job_id":null,"html_url":"https://github.com/higlass/higlass-clinvar","commit_stats":null,"previous_names":[],"tags_count":7,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/higlass%2Fhiglass-clinvar","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/higlass%2Fhiglass-clinvar/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/higlass%2Fhiglass-clinvar/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/higlass%2Fhiglass-clinvar/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/higlass","download_url":"https://codeload.github.com/higlass/higlass-clinvar/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":244560373,"owners_count":20472219,"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":"2024-11-25T10:18:01.662Z","updated_at":"2025-03-20T05:48:51.184Z","avatar_url":"https://github.com/higlass.png","language":"JavaScript","funding_links":[],"categories":[],"sub_categories":[],"readme":"\n# Display ClinVar variants in HiGlass\n\n![ClinVar](https://aveit.s3.amazonaws.com/higlass/static/higlass-clinvar-screenshot.png)\n\n\n**Note**: This is the source code for the ClinVar track only! You might want to check out the following repositories as well:\n\n- HiGlass viewer: https://github.com/higlass/higlass\n- HiGlass server: https://github.com/higlass/higlass-server\n- HiGlass docker: https://github.com/higlass/higlass-docker\n\n## Installation\n \n```\nnpm install higlass-clinvar\n```\n\n## Data preparation\n\nIn order to bring a ClinVar vcf file (https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/) into the required BED format, the following script can be used (make sure to adjust the file names in the script). A chrom sizes file is required.\n```\npython /scripts/extract_clinvar_data.py\n```\n\nThe resulting bed file can be aggregated and ingested into a HiGlass server in the usual way:\n```\nclodius aggregate bedfile --chromsizes-filename hg38.txt --delimiter $'\\t' --importance-column 6 --max-per-tile 80 clinvar_20200824.bed \n\npython manage.py ingest_tileset --filename data/clinvar_20200824.beddb --filetype beddb --datatype bedlike --uid clinvar_20200824\n\n```\n\n## Usage\n\nThe live script can be found at:\n\n- https://unpkg.com/higlass-clinvar/dist/higlass-clinvar.js\n\n### Client\n\n1. Load this track before the HiGlass core script. For example:\n\n```\n\u003cscript src=\"/higlass-clinvar.js\"\u003e\u003c/script\u003e\n\u003cscript src=\"hglib.js\"\u003e\u003c/script\u003e\n\n\u003cscript\u003e\n  ...\n\u003c/script\u003e\n```\n\n### Options\nThe following options are available:\n```\n{\n  \"server\": \"http://localhost:8001/api/v1\",\n  \"tilesetUid\": \"awesome_clinvar\",\n  \"uid\": \"awesome_clinvar_uid\",\n  \"type\": \"horizontal-clinvar\",\n  \"options\": {\n    \"fontSize\": 10,\n    \"fontFamily\": \"Arial\",\n    \"labelTextColor\": \"#888888\",\n    \"levelDistance\": 20, // Detemines how far the different levels are visually apart\n    \"significanceColors\": {\n      \"pathogenic\": \"#ff0000\",\n      \"pathogenic_likely_pathogenic\": \"#ff3838\",\n      \"likely_pathogenic\": \"#a80000\",\n      \"uncertain_significance\": \"#808080\",\n      \"likely_benign\": \"#009600\",\n      \"benign_likely_benign\": \"#00c900\",\n      \"benign\": \"#00ff00\",\n      \"risk_factor\": \"#999999\",\n    },\n  },\n  \"width\": 768,\n  \"height\": 200\n}\n```\n\n### ECMAScript Modules (ESM)\n\nWe also build out ES modules for usage by applications who may need to import or use `higlass-clinvar` as a component.\n\nWhenever there is a statement such as the following, assuming `higlass-clinvar` is in your node_modules folder:\n```javascript\nimport { ClinvarTrack } from 'higlass-clinvar';\n```\n\nThen ClinvarTrack would automatically be imported from the `./es` directory (set via package.json's `\"module\"` value). \n\n## Support\n\nFor questions, please either open an issue or ask on the HiGlass Slack channel at http://bit.ly/higlass-slack\n\n## Development\n\n### Testing\n\nTo run the test suite:\n\n```\nnpm run test-watch\n```\n\n### Installation\n\n```bash\n$ git clone https://github.com/higlass/higlass-clinvar.git\n$ cd higlass-clinvar\n$ npm install\n```\nIf you have a local copy of higlass, you can then run this command in the higlass-clinvar directory:\n\n```bash\nnpm link higlass\n```\n\n### Commands\n\n - **Developmental server**: `npm start`\n - **Production build**: `npm run build`\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhiglass%2Fhiglass-clinvar","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fhiglass%2Fhiglass-clinvar","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhiglass%2Fhiglass-clinvar/lists"}