{"id":21662819,"url":"https://github.com/higlass/higlass-orthologs","last_synced_at":"2025-07-23T10:04:49.026Z","repository":{"id":54298539,"uuid":"283230610","full_name":"higlass/higlass-orthologs","owner":"higlass","description":null,"archived":false,"fork":false,"pushed_at":"2022-12-08T21:39:03.000Z","size":8077,"stargazers_count":4,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-07-19T18:43:21.232Z","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":null,"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":"2020-07-28T14:06:42.000Z","updated_at":"2023-01-27T13:49:47.000Z","dependencies_parsed_at":"2022-08-13T11:20:37.268Z","dependency_job_id":null,"html_url":"https://github.com/higlass/higlass-orthologs","commit_stats":null,"previous_names":[],"tags_count":6,"template":false,"template_full_name":null,"purl":"pkg:github/higlass/higlass-orthologs","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/higlass%2Fhiglass-orthologs","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/higlass%2Fhiglass-orthologs/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/higlass%2Fhiglass-orthologs/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/higlass%2Fhiglass-orthologs/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/higlass","download_url":"https://codeload.github.com/higlass/higlass-orthologs/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/higlass%2Fhiglass-orthologs/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":266657952,"owners_count":23963602,"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":"2025-07-23T02:00:09.312Z","response_time":66,"last_error":null,"robots_txt_status":null,"robots_txt_updated_at":null,"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":"2024-11-25T10:18:13.958Z","updated_at":"2025-07-23T10:04:48.977Z","avatar_url":"https://github.com/higlass.png","language":"JavaScript","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Gene orthologs for HiGlass\n\nDisplay orthologous amino acids in HiGlass!\n\nZoomed out (shows amino acids that match with the human):\n\n![Orthologs](https://aveit.s3.amazonaws.com/higlass/static/higlass-orthologs-zoomed-out.png)\n\nZoomed in:\n\n![Orthologs](https://aveit.s3.amazonaws.com/higlass/static/higlass-orthologs-zoomed-in.png)\n\n**Note**: This is the source code for the orthologs 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-orthologs\n```\n\n## Data preparation\n\nThe orthologs data is loaded from Ensembl via their Rest API in the client (example URL: https://rest.ensembl.org/homology/id/ENSG00000139618?type=orthologues\u0026content-type=application/json\u0026cigar_line=0\u0026target_species=cat\u0026target_species=dog). In order to determine where to display the individual amino acids in the track, we need to know the representative (human) transcript that was used to create the aligned sequences. The sequences from Ensembl are then distributed onto the exons of that transcript.\n\nIn order to obtain the representative sequences we use Ensemble Biomart (https://m.ensembl.org/biomart) with the following attributes:\n\n![Biomart](https://aveit.s3.amazonaws.com/higlass/static/Ensembl-biomart-settings.png)\n\nThe \"Query protein or transcript ID\" fields contain the information to identify the correct transcript that we need to use in the track. Store this data to a file and run\n\n```\npython /scripts/get_representative_transcripts.py\n```\nto obtain the `bed` file that will serve as base for the orthologs track.\n\nTo create an aggregated `beddb` file from that data, you can use the script\n```\npython /scripts/aggregate_transcripts.py\n```\nAn example `beddb` file can be found in the `examples` folder.\n\nTo ingest the data into higlass-server:\n```\npython manage.py ingest_tileset \\\n    --filename /data/representative_transcripts.beddb \\\n    --filetype beddb \\\n    --coordSystem hg38 \\\n    --datatype gene-annotation \\\n    --uid canonical_transcripts_hg38\n```\n\n## Usage\n\nThe live script can be found at:\n\n- https://unpkg.com/higlass-orthologs/dist/higlass-orthologs.js\n\n### Client\n\n1. Make sure you load this track after the HiGlass core script. For example:\n\n```\n\u003cscript src=\"hglib.js\"\u003e\u003c/script\u003e\n\u003cscript src=\"/higlass-orthologs.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_orthologs\",\n  \"uid\": \"awesome_orthologs_uid\",\n  \"type\": \"horizontal-orthologs\",\n  \"options\": {\n    \"aminoAcidColor\": \"#333333\", // font color of amino acids that match with the human one\n    \"aminoAcidColorNoMatch\": \"#b0b0b0\", // font color of amino acids that don't match with the human one\n    \"fontSize\": 10, // font size for labels and amino acids\n    \"fontFamily\": \"Arial\", // font family for labels and amino acids\n    \"gapsColor\": \"#eb9c00\", // color to indicate gaps in the sequence alignment\n    \"labelTextColor\": \"#888888\", // color of labels\n    \"minusStrandColor1\": \"#ffe0e2\", // background color 1 of amino acids on the negative strand\n    \"minusStrandColor2\": \"#fff0f1\", // background color 2 of amino acids on the negative strand\n    \"minusStrandColorZoomedOut\": \"#fabec2\", // color of horizontal bars, when zoomed out\n    \"plusStrandColor1\": \"#ebebff\", // background color 1 of amino acids on the positive strand\n    \"plusStrandColor2\": \"#dedeff\", // background color 2 of amino acids on the positive strand\n    \"plusStrandColorZoomedOut\": \"#bdbfff\", // color of horizontal bars, when zoomed out\n    \"rowHeight\": 11, // height of each row in the table\n    \"rowSpacing\": 2, // space between rows\n    \"species\": [\n      \"human\",\n      \"macaca_mulatta\",\n      \"mouse\",\n      \"dog\",\n      \"elephant\",\n      \"chicken\",\n      \"zebrafish\",\n    ], // the species to compare. Currently only a certain species are supported. More can be added in the EnsemblHelper class\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-orthologs` as a component.\n\nWhenever there is a statement such as the following, assuming `higlass-orthologs` is in your node_modules folder:\n```javascript\nimport { OrthologsTrack } from 'higlass-orthologs';\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### Installation\n\n```bash\n$ git clone https://github.com/higlass/higlass-orthologs.git\n$ cd higlass-orthologs\n$ npm install\n```\nIf you have a local copy of higlass, you can then run this command in the higlass-orthologs 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-orthologs","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fhiglass%2Fhiglass-orthologs","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhiglass%2Fhiglass-orthologs/lists"}