Plugin Store

About the plugin store

This store contains the current list of white-listed JBrowse 2 plugins. Plugins can add functionality that doesn't exist in the core application, such as a new data adapter or a custom track type.

The configuration specified for each plugin can be added to the plugins array as a top-level entry. For example:

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

Plugins can also be added directly inside the app via the File menu.

Developer information

We welcome developers who want to create a new JBrowse 2 plugin. The primary resource for getting started is the plugin template .

If you build a plugin you'd like featured in this store, follow the instructions found here .

MsaView

GitHub

Colin Diesh Apache License 2.0

multiple sequence alignment browser plugin for JBrowse 2

Configuration

                    {
  "name": "MsaView",
  "url": "https://jbrowse.org/plugins/jbrowse-plugin-msaview/dist/jbrowse-plugin-msaview.umd.production.min.js"
}

GDC

GitHub

Garrett Stevens, Colin Diesh, Rob Buels, Caroline Bridge MIT

JBrowse 2 plugin for integrating with GDC resources

Configuration

                    {
  "name": "GDC",
  "url": "https://jbrowse.org/plugins/jbrowse-plugin-gdc/dist/jbrowse-plugin-gdc.umd.production.min.js"
}

Quantseq

GitHub

Elliot Hershberg Apache License 2.0

External JB2 plugin implementing a QuantitativeSequence track for displaying base-resolution models.

Configuration

                    {
  "name": "Quantseq",
  "url": "https://jbrowse.org/plugins/jbrowse-plugin-quantseq/dist/jbrowse-plugin-quantseq.umd.production.min.js"
}

GWAS

GitHub

Colin Diesh MIT

Plugin for displaying GWAS results such as manhattan plot renderings

Configuration

                    {
  "name": "GWAS",
  "url": "https://jbrowse.org/plugins/jbrowse-plugin-gwas/dist/jbrowse-plugin-gwas.umd.production.min.js"
}

UCSC

GitHub

Colin Diesh MIT

A JBrowse 2 plugin for accessing the UCSC API

Configuration

                    {
  "name": "UCSC",
  "url": "https://jbrowse.org/plugins/jbrowse-plugin-ucsc/dist/jbrowse-plugin-ucsc.umd.production.min.js"
}

Biothings

GitHub

Colin Diesh MIT

Adapts to APIs like mygene.info to get super rich gene annotations

Configuration

                    {
  "name": "Biothings",
  "url": "https://jbrowse.org/plugins/jbrowse-plugin-biothings/dist/jbrowse-plugin-biothings.umd.production.min.js"
}

Ideogram

GitHub

Colin Diesh, Caroline Bridge Apache License 2.0

JBrowse 2 plugin for rendering ideograms

Configuration

                    {
  "name": "Ideogram",
  "url": "https://jbrowse.org/plugins/jbrowse-plugin-ideogram/dist/jbrowse-plugin-ideogram.umd.production.min.js"
}

CIVIC

GitHub

Colin Diesh Apache License 2.0

JBrowse 2 plugin for fetching data from the CIVIC clinical interpretation of cancer variants

Configuration

                    {
  "name": "CIVIC",
  "url": "https://jbrowse.org/plugins/jbrowse-plugin-civic/dist/jbrowseplugincivic.umd.production.min.js"
}

ICGC

GitHub

Caroline Bridge Apache License 2.0

JBrowse 2 plugin to integrate resources from the ICGC

Configuration

                    {
  "name": "ICGC",
  "url": "https://jbrowse.org/plugins/jbrowse-plugin-icgc/dist/jbrowse-plugin-icgc.umd.production.min.js"
}

Reactome

GitHub

Caroline Bridge Apache License 2.0

JBrowse 2 plugin to integrate resources from Reactome

Configuration

                    {
  "name": "Reactome",
  "url": "https://jbrowse.org/plugins/jbrowse-plugin-reactome/dist/jbrowse-plugin-reactome.umd.production.min.js"
}

MultilevelLinearView

GitHub

Caroline Bridge Apache License 2.0

JBrowse 2 plugin that adds a linear genome view that can show multiple zoom levels

Configuration

                    {
  "name": "MultilevelLinearView",
  "url": "https://jbrowse.org/plugins/jbrowse-plugin-multilevel-linear-view2/dist/jbrowse-plugin-multilevel-linear-view2.umd.production.min.js"
}

TrackHubRegistry

GitHub

Colin Diesh Apache License 2.0

JBrowse 2 plugin that adds ability to connect to hubs from the trackhub registry. Note: only for use with v2.3.0 or greater

Configuration

                    {
  "name": "TrackHubRegistry",
  "url": "https://jbrowse.org/plugins/jbrowse-plugin-trackhub-registry/dist/jbrowse-plugin-trackhub-registry.umd.production.min.js"
}

RefGet

GitHub

Emilio Righi ISC

JBrowse 2 plugin that adds ability to retrieve sequences from refget API compliant servers

Configuration

                    {
  "name": "RefGet",
  "url": "https://jbrowse.org/plugins/jbrowse-plugin-refget-api/dist/jbrowse-plugin-refget-api.umd.production.min.js"
}

Linkout

GitHub

NAL-i5K Apache License 2.0

JBrowse 2 plugin that links out to feature page based on dbxref

Configuration

                    {
  "name": "Linkout",
  "url": "https://jbrowse.org/plugins/jbrowse-plugin-linkout/dist/jbrowse-plugin-linkout.umd.production.min.js"
}

MafViewer

GitHub

Colin Diesh MIT

View multiple alignment format (MAF) files as tracks

Configuration

                    {
  "name": "MafViewer",
  "url": "https://jbrowse.org/plugins/jbrowse-plugin-mafviewer/dist/jbrowse-plugin-mafviewer.umd.production.min.js"
}

Protein3d

GitHub

Colin Diesh MIT

View 3-D protein structures in JBrowse 2

Configuration

                    {
  "name": "Protein3d",
  "url": "https://jbrowse.org/plugins/jbrowse-plugin-protein3d/dist/jbrowse-plugin-protein3d.umd.production.min.js"
}