{"_id":"@apr144/higlass-transcripts","name":"@apr144/higlass-transcripts","dist-tags":{"latest":"0.3.8"},"versions":{"0.3.8":{"name":"@apr144/higlass-transcripts","version":"0.3.8","description":"Gene transcripts track for HiGlass","private":false,"author":{"name":"Alexander Veit"},"license":"MIT","contributors":[{"name":"Alexander Veit","url":"http://github.com/alexander-veit"},{"name":"Alex Reynolds","url":"http://github.com/alexpreynolds"}],"main":"./src/index.js","unpkg":"./dist/higlass-transcripts.js","module":"./es","repository":{"type":"git","url":"git+https://github.com/higlass/higlass-transcripts.git"},"devDependencies":{"babel-cli":"^6.26.0","babel-core":"^6.26.3","babel-loader":"^7.1.5","babel-plugin-transform-runtime":"^6.23.0","babel-polyfill":"^6.26.0","babel-preset-env":"^1.7.0","babel-preset-react":"^6.24.1","chai":"^4.2.0","cheerio":"=1.0.0-rc.3","enzyme":"^3.11.0","enzyme-adapter-react-16":"^1.6.0","file-loader":"^1.1.11","higlass":"^1.11.11","html-loader":"^0.5.5","html-webpack-plugin":"^3.1.0","jasmine":"^2.99.0","karma":"^4.4.1","karma-chrome-launcher":"^3.1.0","karma-jasmine":"^3.1.1","karma-phantomjs-launcher":"^1.0.4","karma-sourcemap-loader":"^0.3.7","karma-verbose-reporter":"0.0.6","karma-webpack":"^4.0.2","robust-point-in-polygon":"^1.0.3","sourcemap":"^0.1.0","style-loader":"^0.20.3","terser-webpack-plugin":"^3.0.1","unminified-webpack-plugin":"^2.0.0","webpack":"^4.43.0","webpack-cli":"^3.3.11","webpack-dev-server":"^3.10.3"},"scripts":{"build-es":"rm -rf ./es/* && npx babel ./src/scripts/ --out-dir ./es/ --env-name esm","build":"npm run build-es && NODE_ENV=production ./node_modules/webpack/bin/webpack.js --mode production","build-debug":"NODE_ENV=development; ./node_modules/webpack/bin/webpack.js --mode=development","start":"./node_modules/webpack-dev-server/bin/webpack-dev-server.js --mode development --open","test":"NODE_ENV=development; npm run build-debug && ./node_modules/karma/bin/karma start karma.conf.js","prerelease":"rm -rf dist/*; npm run build; zip -r dist.zip dist","clean":"rm -rf dist/*; rm -rf es/*; rm -rf node_modules/*","reinstall":"npm run clean; npm install"},"dependencies":{"@gmod/indexedfasta":"^2.0.0","d3-color":"^3.1.0","d3-scale":"^4.0.2","generic-filehandle":"^3.0.0","higlass-register":"^0.3.0"},"gitHead":"1cda7efe793c33acb2c4f526547afc0d4f358ce3","bugs":{"url":"https://github.com/higlass/higlass-transcripts/issues"},"homepage":"https://github.com/higlass/higlass-transcripts#readme","_id":"@apr144/higlass-transcripts@0.3.8","_nodeVersion":"16.20.2","_npmVersion":"8.19.4","dist":{"integrity":"sha512-UI6HuvtCBdmqkQpD2srsTmBgsY9ylJrVV2HJKnPqk6YhUhS9t3ogQGNChyBM4HSJ5jdCjqY9ahMRSTV81YiTYA==","shasum":"27c68221b3dbaef205886c102759eff0e9791889","tarball":"https://registry.npmjs.org/@apr144/higlass-transcripts/-/higlass-transcripts-0.3.8.tgz","fileCount":15,"unpackedSize":411852,"signatures":[{"keyid":"SHA256:DhQ8wR5APBvFHLF/+Tc+AYvPOdTpcIDqOhxsBHRwC7U","sig":"MEUCIQCKyjDbJ9aCjYO6c5h0DrmkVEoYGmNudcZfMU1KBccuPwIgJ4iiQOu2pKKMkVGEik6drYNcgauqkBM95qDQTqNE/+s="}]},"_npmUser":{"name":"apr144","email":"alexpreynolds@gmail.com"},"directories":{},"maintainers":[{"name":"apr144","email":"alexpreynolds@gmail.com"}],"_npmOperationalInternal":{"host":"s3://npm-registry-packages-npm-production","tmp":"tmp/higlass-transcripts_0.3.8_1738882993750_0.8056089834751938"},"_hasShrinkwrap":false}},"time":{"created":"2025-02-06T23:03:13.666Z","0.3.8":"2025-02-06T23:03:13.944Z","modified":"2025-02-06T23:03:14.208Z"},"maintainers":[{"name":"apr144","email":"alexpreynolds@gmail.com"}],"description":"Gene transcripts track for HiGlass","homepage":"https://github.com/higlass/higlass-transcripts#readme","repository":{"type":"git","url":"git+https://github.com/higlass/higlass-transcripts.git"},"contributors":[{"name":"Alexander Veit","url":"http://github.com/alexander-veit"},{"name":"Alex Reynolds","url":"http://github.com/alexpreynolds"}],"author":{"name":"Alexander Veit"},"bugs":{"url":"https://github.com/higlass/higlass-transcripts/issues"},"license":"MIT","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<script src=\"/higlass-transcripts.js\"></script>\n<script src=\"hglib.js\"></script>\n<script>\n  ...\n</script>\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    \"showTooltip\": true,\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","readmeFilename":"README.md"}