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https://github.com/alexpreynolds/higlass-bigbed-datafetcher

Provide remote access to remotely-hosted bigBed files to HiGlass client applications

https://github.com/alexpreynolds/higlass-bigbed-datafetcher

Science Score: 26.0%

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    CITATION.cff file
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    Scientific vocabulary similarity
    Low similarity (6.1%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Provide remote access to remotely-hosted bigBed files to HiGlass client applications

Basic Info
  • Host: GitHub
  • Owner: alexpreynolds
  • License: mit
  • Language: JavaScript
  • Default Branch: main
  • Size: 2.26 MB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created almost 2 years ago · Last pushed over 1 year ago
Metadata Files
Readme License

README.md

higlass-bigbed-datafetcher

Provide remote access to remotely-hosted bigBed files to HiGlass client applications

Usage

This enables access to a web-hosted bigBed file for use with the higlass-transcripts (https://github.com/higlass/higlass-transcripts) plug-in.

Register the data fetcher in your HiGlass application:

``` import register from "higlass-register"; import { BigBedDataFetcher } from "higlass-bigbed-datafetcher";

register ( { dataFetcher: BigBedDataFetcher, config: BigBedDataFetcher.config, }, { pluginType: "dataFetcher", } ); ```

Configure the view configuration's horizontal-transcripts object with data attributes pointing to the web-hosted tabix file:

{ "name": "My bigBed elements", "type": "horizontal-transcripts", "uid": "my_bigbed_uid", "options": { "fontSize": 9, // font size for labels and amino acids (if available) "fontFamily": "Helvetica", "labelFontColor": "#333333", "labelBackgroundPlusStrandColor": "#ffffff", "labelBackgroundMinusStrandColor": "#ffffff", "labelStrokePlusStrandColor": "#999999", "labelStrokeMinusStrandColor": "#999999", "plusStrandColor": "#bdbfff", // color of coding parts of the exon on the plus strand "minusStrandColor": "#fabec2", // color of coding parts of the exon on the negative strand "utrColor": "#C0EAAF", // color of untranslated regions of the exons "backgroundColor": "#ffffff", // color of track background "transcriptHeight": 12, // height of the transcripts "transcriptSpacing": 2, // space in between the transcripts "name": "Gene transcripts", "maxTexts": 50, // Maximum number of labels shown on the screen "showToggleTranscriptsButton": true, // If the "Show fewer transcripts"/"Show more transcripts" is shown "trackHeightAdjustment": "automatic", // if "automatic", the height of the track is adjusted to the number of visible transcripts. "startCollapsed": false, // if true, only one transcript is shown }, "data" : { "type": "bigbed", "url": "https://example.com/bigBed/my_elements.bb", "chromSizesUrl": "https://example.com/bigBed/hg38.chromSizes.gz", }, }

The format of data is currently driven by the formatTranscriptData function in higlass-transcripts, where transcript metadata are stored in thirteen columns:

``` formatTranscriptData(ts) { const strand = ts[5]; const stopCodonPos = ts[12] === "." ? "." : (strand === "+" ? +ts[12] + 2 : +ts[12] - 1); const startCodonPos = ts[11] === "." ? "." : (strand === "+" ? +ts[11] - 1 : +ts[11] + 2); const exonStarts = ts[9].split(",").map((x) => +x - 1); const exonEnds = ts[10].split(",").map((x) => +x); const txStart = +ts[1] - 1; const txEnd = +ts[2] - 1;

const result = { transcriptId: this.transcriptId(ts), transcriptName: ts[3], txStart: txStart, txEnd: txEnd, strand: strand, chromName: ts[0], codingType: ts[8], exonStarts: exonStarts, exonEnds: exonEnds, startCodonPos: startCodonPos, stopCodonPos: stopCodonPos, importance: +ts[4], }; return result; } ```

Placeholders are used to change rendering behavior when fields are missing data.

Owner

  • Name: Alex Reynolds
  • Login: alexpreynolds
  • Kind: user
  • Location: Seattle, WA USA
  • Company: Altius Institute for Biomedical Sciences

Pug caregiver, curler, cyclist, gardener, beginning French scholar

GitHub Events

Total
  • Push event: 3
  • Create event: 3
Last Year
  • Push event: 3
  • Create event: 3

Committers

Last synced: about 1 year ago

All Time
  • Total Commits: 6
  • Total Committers: 1
  • Avg Commits per committer: 6.0
  • Development Distribution Score (DDS): 0.0
Past Year
  • Commits: 6
  • Committers: 1
  • Avg Commits per committer: 6.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Alex Reynolds a****s@g****m 6

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Last synced: 10 months ago

All Time
  • Total issues: 0
  • Total pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Total issue authors: 0
  • Total pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
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Packages

  • Total packages: 1
  • Total downloads: unknown
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 2
  • Total maintainers: 1
npmjs.org: @apr144/higlass-bigbed-datafetcher

BigBed Data Fetcher for HiGlass

  • Versions: 2
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 0 Last month
Rankings
Dependent repos count: 25.1%
Average: 30.7%
Dependent packages count: 36.3%
Maintainers (1)
apr144
Last synced: 10 months ago

Dependencies

package.json npm
  • @esbuild-plugins/node-globals-polyfill ^0.1.1 development
  • @esbuild-plugins/node-modules-polyfill ^0.1.4 development
  • cross-env ^7.0.0 development
  • esbuild ^0.14.42 development
  • jsdom ^20.0.0 development
  • npm-run-all ^4.1.5 development
  • rimraf ^3.0.2 development
  • vite ^4.3.0 development
  • vitest ^0.23.4 development
  • @gmod/bbi ^4.0.5
  • @gmod/bed ^2.1.3
  • apr144-generic-filehandle 3.1.1-042624-003
  • d3-dsv ^3.0.1
  • d3-request ^1.0.6
  • d3-scale ^1.0.7
  • higlass-register ^0.3.0
  • slugid ^3.0.0