{"id":20387054,"url":"https://github.com/cmdcolin/jbrowse-plugin-riboseq","last_synced_at":"2026-05-07T20:33:55.220Z","repository":{"id":230942574,"uuid":"780518644","full_name":"cmdcolin/jbrowse-plugin-riboseq","owner":"cmdcolin","description":"A WIP for a biostar question","archived":false,"fork":false,"pushed_at":"2024-04-01T17:10:58.000Z","size":230,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-01-15T08:45:00.153Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"TypeScript","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/cmdcolin.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null}},"created_at":"2024-04-01T16:45:10.000Z","updated_at":"2024-04-01T17:05:30.000Z","dependencies_parsed_at":"2024-04-01T18:28:23.285Z","dependency_job_id":"19a5e8fb-f074-4e60-b710-fece4540dd2b","html_url":"https://github.com/cmdcolin/jbrowse-plugin-riboseq","commit_stats":null,"previous_names":["cmdcolin/jbrowse-plugin-riboseq"],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cmdcolin%2Fjbrowse-plugin-riboseq","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cmdcolin%2Fjbrowse-plugin-riboseq/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cmdcolin%2Fjbrowse-plugin-riboseq/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cmdcolin%2Fjbrowse-plugin-riboseq/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/cmdcolin","download_url":"https://codeload.github.com/cmdcolin/jbrowse-plugin-riboseq/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":241937038,"owners_count":20045167,"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":"2024-11-15T02:42:30.073Z","updated_at":"2025-12-01T23:06:01.910Z","avatar_url":"https://github.com/cmdcolin.png","language":"TypeScript","funding_links":[],"categories":[],"sub_categories":[],"readme":"# jbrowse-plugin-ribo-seq\n\n## Dev setup\n\n```bash\n\ngit clone git@github.com:cmdcolin/jbrowse-plugin-ribo-seq\ncd jbrowse-plugin-ribo-seq\nyarn\nyarn start\n# visit http://yourjbrowse/?config=http://localhost:9000/config.json\n\n```\n\n## Production setup\n\n```json\n{\n  \"plugins\": [\n    {\n      \"name\": \"RiboSeq\",\n      \"url\": \"https://unpkg.com/jbrowse-plugin-ribo-seq/dist/jbrowse-plugin-ribo-seq.umd.production.min.js\"\n    }\n  ]\n}\n```\n\n## Screenshot\n\n![](img/1.png)\n\n## Input\n\nsample data: a bed tabix file with a column name indicating \"color\"\n\n```\n#chr\tstart\tend\tstrand\tcolor\tcount\n1\t10000000\t10000001\t+\t0\t6\n1\t10000001\t10000002\t+\t0\t1\n1\t10000004\t10000005\t+\t1\t1\n1\t10000006\t10000007\t+\t2\t1\n1\t10000007\t10000008\t+\t1\t30\n1\t10000009\t10000010\t+\t3\t2\n```\n\n## Configuration\n\nUse the RiboSeqAdapter and then use a BedTabixAdapter subadapter\n\n```json\n{\n  \"type\": \"FeatureTrack\",\n  \"trackId\": \"ribo-seq_track\",\n  \"name\": \"RiboSeq\",\n  \"assemblyNames\": [\"hg19\"],\n  \"adapter\": {\n    \"type\": \"RiboSeqAdapter\",\n    \"subadapter\": {\n      \"type\": \"BedTabixAdapter\",\n      \"scoreColumn\": \"count\",\n      \"bedGzLocation\": {\n        \"uri\": \"test.bed.gz\"\n      },\n      \"index\": {\n        \"location\": {\n          \"uri\": \"test.bed.gz.tbi\"\n        }\n      }\n    }\n  },\n  \"displays\": [\n    {\n      \"displayId\": \"ribo-seq_display\",\n      \"type\": \"LinearRiboSeqDisplay\"\n    }\n  ]\n}\n```\n\n## Footnote\n\nMotivated by https://www.biostars.org/p/9591324/#9591469\n\nThis is very demo-quality. Inspired by plugins like\nhttps://github.com/cmdcolin/mpileupplugin also\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcmdcolin%2Fjbrowse-plugin-riboseq","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcmdcolin%2Fjbrowse-plugin-riboseq","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcmdcolin%2Fjbrowse-plugin-riboseq/lists"}