{"id":27349543,"url":"https://github.com/cmdcolin/jbrowse-plugin-ldviewer","last_synced_at":"2025-04-12T19:17:48.451Z","repository":{"id":274746543,"uuid":"923869287","full_name":"cmdcolin/jbrowse-plugin-ldviewer","owner":"cmdcolin","description":null,"archived":false,"fork":false,"pushed_at":"2025-03-15T16:30:16.000Z","size":416,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-04-12T19:17:45.395Z","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,"publiccode":null,"codemeta":null}},"created_at":"2025-01-29T00:53:25.000Z","updated_at":"2025-03-15T16:30:19.000Z","dependencies_parsed_at":null,"dependency_job_id":"649438e7-d21b-4b46-8cc4-6691121a9f28","html_url":"https://github.com/cmdcolin/jbrowse-plugin-ldviewer","commit_stats":null,"previous_names":["cmdcolin/jbrowse-plugin-ldviewer"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cmdcolin%2Fjbrowse-plugin-ldviewer","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cmdcolin%2Fjbrowse-plugin-ldviewer/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cmdcolin%2Fjbrowse-plugin-ldviewer/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cmdcolin%2Fjbrowse-plugin-ldviewer/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/cmdcolin","download_url":"https://codeload.github.com/cmdcolin/jbrowse-plugin-ldviewer/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248618222,"owners_count":21134202,"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":"2025-04-12T19:17:47.950Z","updated_at":"2025-04-12T19:17:48.441Z","avatar_url":"https://github.com/cmdcolin.png","language":"TypeScript","funding_links":[],"categories":[],"sub_categories":[],"readme":"# jbrowse-plugin-ldviewer\n\nA JBrowse 2 plugin for viewing linkage disequilibrium data\n\nUses a server side plink component\n\n## Screenshot\n\n![](img/1.png)\n\n## Usage\n\n```bash\ngit clone https://github.com/cmdcolin/jbrowse-plugin-ldviewer\ncd jbrowse-plugin-ldviewer\nyarn #get main plugin deps\n\ncd ldserver\nyarn #get server deps\nyarn start #start server, dfault on 4730\n```\n\n## Config\n\nThis server starts on localhost:4730\n\nIf you need to use it on a public server, you can edit your jbrowse config .g.\n\n```json\n{\n  \"configuration\": {\n    \"LDViewerPlugin\": {\n      \"ldserver\": \"https://yourhost/ldserver\"\n    }\n  }\n}\n```\n\n## Future/ideas\n\nThe ldserver is a barrier to easy plug-n-play usage of th plugin since it\nrequires some 'server side admin' (normal jbrowse usage is very client side\nfocused)\n\nHowever, I welcome you to try it out!\n\nThe server just runs plink2 aka plink 1.9 on some vcf data. I don't know all the\nconsiderations for LD calculations so it may be limited, but gives plausible\nresults on human 1000g data\n\nWe could also consider\n\n- calculating whatever plink is doing on the client side\n- if not calculate client sid, we could host ldserver as a public utility, and\n  set default config to point at it\n- support efficient file format like LDmat. it is currently aimed as smallish\n  regions\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcmdcolin%2Fjbrowse-plugin-ldviewer","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcmdcolin%2Fjbrowse-plugin-ldviewer","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcmdcolin%2Fjbrowse-plugin-ldviewer/lists"}