https://github.com/gmod/jbrowse-plugin-quantseq

External JB2 plugin implementing a QuantitativeSequence track for displaying base-resolution models.
https://github.com/gmod/jbrowse-plugin-quantseq

genomics jbrowse jbrowse-plugin visualization

Last synced: 4 months ago
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External JB2 plugin implementing a QuantitativeSequence track for displaying base-resolution models.

• Host: GitHub
• URL: https://github.com/gmod/jbrowse-plugin-quantseq
• Owner: GMOD
• License: apache-2.0
• Created: 2021-03-18T15:22:21.000Z (about 4 years ago)
• Default Branch: main
• Last Pushed: 2024-07-09T21:53:17.000Z (11 months ago)
• Last Synced: 2025-02-16T02:08:15.343Z (4 months ago)
• Topics: genomics, jbrowse, jbrowse-plugin, visualization
• Language: TypeScript
• Homepage: https://www.npmjs.com/package/jbrowse-plugin-quantseq
• Size: 445 KB
• Stars: 1
• Watchers: 11
• Forks: 0
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • Contributing: CONTRIBUTING.md
  • License: LICENSE

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README

        
![Integration](https://github.com/elliothershberg/jbrowse-plugin-quantseq/workflows/Integration/badge.svg?branch=main)

# jbrowse-plugin-quantseq

This is an external plugin for the [JBrowse 2](https://jbrowse.org/jb2/)

open-source platform for visualizing and integrating biological data.

This plugin implements a QuantitativeSequence (quantseq) track type. It builds on the concept of a "dynamic sequence (dynseq)" track that was added to the

awesome [WashU Epigenome Browser](http://epigenomegateway.wustl.edu/).

This track combines the QuantitativeTrack and the ReferenceSequenceTrack from

JBrowse 2 in order to visualize quantitative data for regulatory genomics at

base-resolution, such as the predictions of the [BPNet](https://github.com/kundajelab/bpnet) model. Here is what this new track looks like:

![image](https://user-images.githubusercontent.com/19295181/113226964-4a7cf000-9246-11eb-86f2-b7fb9645c8d8.png)

## Install

### For use in [JBrowse Web](https://jbrowse.org/jb2/docs/quickstart_web)

No installation required

### For use in [`@jbrowse/react-linear-view`](https://www.npmjs.com/package/@jbrowse/react-linear-genome-view)

```

yarn add jbrowse-plugin-quantseq

```

## Usage

Add to the "plugins" of your JBrowse Web config:

```json

{

  "plugins": [

    {

      "name": "Quantseq",

      "url": "https://unpkg.com/jbrowse-plugin-quantseq/dist/jbrowse-plugin-quantseq.umd.production.min.js"

    }

  ]

}

```

Here is an example track configuration for this view:

```json

{

  "type": "QuantitativeTrack",

  "trackId": "ngmlr_cov",

  "name": "Nanog importance counts (BPNet)",

  "assemblyNames": ["hg38"],

  "adapter": {

    "type": "QuantitativeSequenceAdapter",

    "wiggleAdapter": {

      "type": "BigWigAdapter",

      "bigWigLocation": {

        "uri": "https://jbrowse.org/genomes/GRCh38/BPNet/Nanog.importance.counts.bw"

      }

    },

    "sequenceAdapter": {

      "type": "BgzipFastaAdapter",

      "fastaLocation": {

        "uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz"

      },

      "faiLocation": {

        "uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.fai"

      },

      "gziLocation": {

        "uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.gzi"

      }

    }

  },

  "displays": [

    {

      "displayId": "QuantitativeSequence_display",

      "type": "QuantitativeSequenceDisplay"

    }

  ]

}

```

This specifies an adapter for where the sequence is derived from, in addition to the where the bigWig data is derived from, and configures the display format.

## Contributing

We welcome any contributions or PRs to this repo. Developer information for this

codebase can be found [here](https://github.com/elliothershberg/jbrowse-plugin-quantseq/blob/main/CONTRIBUTING.md)