{"id":20387119,"url":"https://github.com/cmdcolin/colorbycds","last_synced_at":"2025-09-12T15:35:46.532Z","repository":{"id":137212231,"uuid":"99132581","full_name":"cmdcolin/colorbycds","owner":"cmdcolin","description":"A JBrowse plugin to color the features and DNA track according the coding frame","archived":false,"fork":false,"pushed_at":"2018-10-11T15:48:44.000Z","size":5410,"stargazers_count":2,"open_issues_count":3,"forks_count":1,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-03-04T23:31:42.978Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"JavaScript","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":"ChangeLog.md","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":"2017-08-02T15:29:12.000Z","updated_at":"2018-10-11T01:05:01.000Z","dependencies_parsed_at":null,"dependency_job_id":"7aef40aa-b01a-4486-8c35-8a81152de885","html_url":"https://github.com/cmdcolin/colorbycds","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"purl":"pkg:github/cmdcolin/colorbycds","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cmdcolin%2Fcolorbycds","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cmdcolin%2Fcolorbycds/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cmdcolin%2Fcolorbycds/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cmdcolin%2Fcolorbycds/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/cmdcolin","download_url":"https://codeload.github.com/cmdcolin/colorbycds/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cmdcolin%2Fcolorbycds/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":270885362,"owners_count":24662453,"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","status":"online","status_checked_at":"2025-08-17T02:00:09.016Z","response_time":129,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"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":"2024-11-15T02:43:17.594Z","updated_at":"2025-08-17T18:07:53.486Z","avatar_url":"https://github.com/cmdcolin.png","language":"JavaScript","funding_links":[],"categories":[],"sub_categories":[],"readme":"# colorbycds\n\nA JBrowse plugin for viewing the frame that a coding sequences of a gene is in and coloring the DNA track and gene appropriately\n\n## Screenshot\n\n![](img/1.png)\n\nFigure: Picture of genes and the DNA track with the plugin enabled. The coloring of the CDS boxes corresponds to the colored rows of the DNA track\n\n## Example\n\n    {\n     \"label\" : \"genes\",\n     \"urlTemplate\" : \"tracks/genes/{refseq}/trackData.json\",\n     \"storeClass\" : \"JBrowse/Store/SeqFeature/NCList\",\n     \"type\" : \"CanvasFeatures\",\n     \"glyph\" : \"ColorByCDS/View/FeatureGlyph/Gene\"\n    }\n\nNote that if you loaded your data with two levels e.g. mRNA-\u003eexon/cds instead of three levels e.g. gene-\u003emRNA-\u003eexon/cds then use \"ColorByCDS/View/FeatureGlyph/ProcessedTranscript\" as the glyph, otherwise you will see your feature is exploded into tiny pieces and not connected by introns.\n\n## Installation\n\nDownload to plugins/ColorByCDS and add\n\n    \"plugins\": [\"ColorByCDS\"]\n\nto jbrowse_conf.json or trackList.json. See JBrowse FAQ on installing plugins for more details\n\n\n## Notes\n\nRelies on the phase field (column 8) of your GFF to be calculated correctly. Use genometools `gt gff3 -tidy yourfile.gff \u003e yourfile_fixed.gff` to recalculate phase properly\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcmdcolin%2Fcolorbycds","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcmdcolin%2Fcolorbycds","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcmdcolin%2Fcolorbycds/lists"}