{"id":21662795,"url":"https://github.com/higlass/higlass-transcripts","last_synced_at":"2025-04-11T23:43:25.685Z","repository":{"id":38986821,"uuid":"266123141","full_name":"higlass/higlass-transcripts","owner":"higlass","description":"Gene transcripts track for HiGlass","archived":false,"fork":false,"pushed_at":"2023-01-11T21:53:45.000Z","size":2435,"stargazers_count":6,"open_issues_count":5,"forks_count":2,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-03-25T19:40:38.171Z","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":"2020-05-22T13:55:18.000Z","updated_at":"2023-01-26T14:39:08.000Z","dependencies_parsed_at":"2023-02-09T07:15:32.421Z","dependency_job_id":null,"html_url":"https://github.com/higlass/higlass-transcripts","commit_stats":null,"previous_names":[],"tags_count":13,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/higlass%2Fhiglass-transcripts","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/higlass%2Fhiglass-transcripts/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/higlass%2Fhiglass-transcripts/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/higlass%2Fhiglass-transcripts/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/higlass","download_url":"https://codeload.github.com/higlass/higlass-transcripts/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248497903,"owners_count":21113982,"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":"2024-11-25T10:18:06.776Z","updated_at":"2025-04-11T23:43:25.658Z","avatar_url":"https://github.com/higlass.png","language":"JavaScript","funding_links":[],"categories":[],"sub_categories":[],"readme":"# HiGlass Transcripts Track\n\nDisplay gene transcripts in HiGlass!\n\nZoomed out:\n\n![Transcripts track](https://aveit.s3.amazonaws.com/higlass/static/higlass-transcripts-zoomed-out.png)\n\nZoomed in:\n\n![Transcripts track](https://aveit.s3.amazonaws.com/higlass/static/higlass-transcripts-zoomed-in.png)\n\n**Note**: This is the source code for the transcripts 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-transcripts\n```\n\n## Data preparation\n\nTo extract trancript data from a Gencode GTF file, the following script can be used (make sure to adjust the file names in the script)\n```\npython /scripts/extract_transcript_data.py\n```\n\nTo create an aggregated `beddb` file from that data, you can use the script\n```\npython /scripts/aggregate_transcripts.py\n```\nExample `bed` and `beddb` files can be found in the `examples` folder.\n\nTo ingest the data into higlass-server:\n```\npython manage.py ingest_tileset --filename data/transcripts.beddb --filetype beddb --datatype gene-annotation --uid aweseome_transcripts\n```\n\n\n## Usage\n\nThe live script can be found at:\n\n- https://unpkg.com/higlass-transcripts/dist/higlass-transcripts.js\n\n### Client\n\n1. Make sure you load this track prior to `hglib.js`. For example:\n\n```\n\u003cscript src=\"/higlass-transcripts.js\"\u003e\u003c/script\u003e\n\u003cscript src=\"hglib.js\"\u003e\u003c/script\u003e\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_transcripts\",\n  \"uid\": \"awesome_transcripts_uid\",\n  \"type\": \"horizontal-transcripts\",\n  \"options\": {\n    \"fontSize\": 9, // font size for labels and amino acids (if available)\n    \"fontFamily\": \"Helvetica\",\n    \"labelFontColor\": \"#333333\",\n    \"labelBackgroundPlusStrandColor\": \"#ffffff\",\n    \"labelBackgroundMinusStrandColor\": \"#ffffff\",\n    \"labelStrokePlusStrandColor\": \"#999999\",\n    \"labelStrokeMinusStrandColor\": \"#999999\",\n    \"plusStrandColor\": \"#bdbfff\", // color of coding parts of the exon on the plus strand\n    \"minusStrandColor\": \"#fabec2\", // color of coding parts of the exon on the negative strand\n    \"utrColor\": \"#C0EAAF\", // color of untranslated regions of the exons\n    \"backgroundColor\": \"#ffffff\", // color of track background\n    \"transcriptHeight\": 12, // height of the transcripts\n    \"transcriptSpacing\": 2, // space in between the transcripts\n    \"name\": \"Gene transcripts\",\n    \"maxTexts\": 50, // Maximum number of labels shown on the screen\n    \"showToggleTranscriptsButton\": true, // If the \"Show fewer transcripts\"/\"Show more transcripts\" is shown\n    \"trackHeightAdjustment\": \"automatic\", // if \"automatic\", the height of the track is adjusted to the number of visible transcripts.\n    \"startCollapsed\": false, // if true, only one transcript is shown\n    \"sequenceData\": { // If this is set, transcribed amino acids are displayed when sufficiently zoomed in\n      \"type\": \"fasta\",\n      \"fastaUrl\": \"https://aveit.s3.amazonaws.com/higlass/data/sequence/hg38.fa\",\n      \"faiUrl\": \"https://aveit.s3.amazonaws.com/higlass/data/sequence/hg38.fa.fai\",\n      \"chromSizesUrl\": \"https://aveit.s3.amazonaws.com/higlass/data/sequence/hg38.mod.chrom.sizes\"\n    },\n  },\n  \"width\": 768,\n  \"height\": 40\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-transcripts` as a component.\n\nWhenever there is a statement such as the following, assuming `higlass-transcripts` is in your node_modules folder:\n```javascript\nimport { TranscriptsTrack } from 'higlass-transcripts';\n```\n\nThen `TranscriptsTrack` 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\n### Installation\n\n```bash\n$ git clone https://github.com/higlass/higlass-transcripts.git\n$ cd higlass-transcripts\n$ npm install\n```\nIf you have a local copy of higlass, you can then run this command in the higlass-transcripts directory:\n\n```bash\nnpm link higlass\n```\n\n### Commands\n\n - **Developmental server**: `npm start`\n - **Production build**: `npm run build`\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhiglass%2Fhiglass-transcripts","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fhiglass%2Fhiglass-transcripts","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhiglass%2Fhiglass-transcripts/lists"}