jbrowse-plugin-quantseq

This is an external plugin for the JBrowse 2 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.

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 model. Here is what this new track looks like:

Install

For use in JBrowse Web

No installation required

For use in @jbrowse/react-linear-view

yarn add jbrowse-plugin-quantseq

Usage

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

{
  "plugins": [
    {
      "name": "Quantseq",
      "url": "https://unpkg.com/jbrowse-plugin-quantseq/dist/jbrowse-plugin-seq.umd.production.min.js"
    }
  ]
}

Here is an example track configuration for this view:

{
  "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