Jbrowse-plugin-quantseq NPM

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.