plugins.yaml

- author: Colin Diesh
  description: |
    A JBrowse plugin for plotting multiple bigwig files on a single track.
    Includes a storeclass that accepts multiple bigwig URLs and a custom
    tracktype for rendering the subtracks.
  gmodProject: JBrowse
  location: https://github.com/cmdcolin/multibigwig
  name: multibigwig
  license: MIT
- author: Colin Diesh
  description: |
    A JBrowse plugin for plotting GC Content and GC Skew. The plugin consists
    of a storeClass that automatically calculates the percentage of G/C bases
    in a region, a track type that derives from the Wiggle XY or density types,
    and a dialog box to adjust the sliding window size, window step size, and
    the calculation mode (content or skew).
  gmodProject: JBrowse
  location: https://github.com/cmdcolin/gccontent
  name: gccontent
  license: MIT
  demo: "gccontent&tracks=DNA,GCContentXY"
  image: gccontent.png
- author: Colin Diesh
  description: |
   A JBrowse plugin for indexing names with elasticsearch.
  gmodProject: JBrowse
  location: https://github.com/cmdcolin/jbrowse_elasticsearch
  name: jbrowse_elasticsearch
- author: Colin Diesh
  description: |
   A JBrowse plugin to load BED tabix, VCF tabix, or BAM as a blank track if
   the index url gets a 404.
  gmodProject: JBrowse
  location: https://github.com/cmdcolin/fastloader
  name: fastloader
  license: ISC
- author: Colin Diesh
  description: |
    A JBrowse plugin that adds a few custom glyphs for variants and GWAS data.
  gmodProject: JBrowse
  location: https://github.com/cmdcolin/gwasviewer
  name: gwasviewer
  image: gwasviewer.png
  demo: "gwasviewer"
- author: Colin Diesh
  description: |
    A JBrowse plugin that fetches info from MyVariant.info and MyGene.info and
    displays them.
  gmodProject: JBrowse
  location: https://github.com/cmdcolin/myvariantviewer
  image: myvariantviewer.png
  name: myvariantviewer
  demo: "myvariantviewer&tracks=DNA,MyGenev3,clinvar"
- author: Colin Diesh
  description: |
    A JBrowse plugin for viewing data from the GA4GH APIs.
  gmodProject: JBrowse
  location: https://github.com/cmdcolin/ga4ghviewer
  name: ga4ghviewer
  demo: "ga4ghviewer&tracks=DNA,1000genomes"
- author: Colin Diesh
  description: |
    A JBrowse plugin for re-mapping coordinates "on the fly".
  gmodProject: JBrowse
  location: https://github.com/cmdcolin/projectionplugin
  name: projectionplugin
  license: MIT
- author: Andrew Wilkey
  description: |
   A JBrowse plugin to allow the browser to enter fullscreen mode.
  gmodProject: JBrowse
  location: https://github.com/awilkey/fullscreen-jbrowse
  name: Fullscreen
  license: MIT
- author: Sean Davey sdavey@email.arizona.edu
  description: |
   custom track selector for managing CoGe experiments (tracks) and notebooks,
   RESTful tracks, custom feature, SNP, alignment and marker tracks, feature
   search, track data search, track export, search export, create new
   experiments based on searches, and more.
  gmodProject: JBrowse
  location: https://github.com/LyonsLab/coge/tree/master/web/js/jbrowse/plugins/CoGe
  name: CoGe JBrowse plugin
  license: BSD-2-Clause
- author: Travis Saari
  description: |
    Interactive tool for viewing and manipulating feature sequences -
    hide/show, change text case, and highlight/unhighlight selected
    subfeatures
  gmodProject: JBrowse
  license: GPL-3.0
  location: https://github.com/tsaari88/FeatureSequence
  name: FeatureSequence
- author: Nathan Dunn
  description: |
    Genome annotation editor with a Java Server backend and a Javascript client
    that runs in a web browser as a JBrowse plugin.
  gmodProject: JBrowse
  location: https://github.com/GMOD/Apollo
  name: Apollo
  license: BSD-3-Clause
- author: Colin Diesh
  description: |
    A JBrowse plugin for creating sashimi or junction style plots from RNA-seq
    data
  gmodProject: JBrowse
  location: https://github.com/cmdcolin/sashimiplot
  name: sashimiplot
  image: sashimiplot.png
  license: MIT
- author: Brigitte Hofmeister
  description: |
    Adds a 'select all from category' checkbox to all categories in
    hierarchical tracklist  When you check/uncheck the box, it applies to all
    tracks in that category and any subcategories
  gmodProject: JBrowse
  location: https://github.com/bhofmei/jbplugin-hierarchicalcheckbox
  name: Hierarchical Checkbox Plugin
  license: MIT
- author: Brigitte Hofmeister
  description: |
    This plugin is to be used to add a menu option for XYPlot and MethylXYPlot
    tracks that allows the user to change the y-axis limits without needing to
    edit the config file.
  gmodProject: JBrowse
  location: https://github.com/bhofmei/jbplugin-trackscores
  name: Track Score Plugin
  license: MIT
- author: Brigitte Hofmeister
  description: |
    This plugin is to be used with whole-genome bisulfite sequencing data.
    Unlike almost all other browsers, this pluging allows you to see all
    methylation contexts on one track.
  gmodProject: JBrowse
  location: https://github.com/bhofmei/jbplugin-methylation
  name: Methylation Plugin
  license: Apache-2.0
- author: Brigitte Hofmeister
  description: |
    JBrowse plugin to support small RNA visualization.
  gmodProject: JBrowse
  location: https://github.com/bhofmei/jbplugin-smallrna
  name: Small RNA Plugin
  license: MIT
- author: Andrew Wilkey
  description: |
    Moves scrollbar on genome viewer up DOM to make it play well with others
    when using JBrowse outside of an iframe.
  gmodProject: JBrowse
  location: https://github.com/awilkey/scrollpos-jbrowse
  name: Scrollpos
  license: MIT
- author: Maria Kim, Vivek Krishnakumar
  description: |
    SeqLighter is a dynamic sequence viewer plugin implemented using the BioJS
    framework, built for/by the Arabidopsis Information Portal (Araport) project.
  gmodProject: JBrowse
  license: MIT
  location: https://github.com/Arabidopsis-Information-Portal/SeqLighter
  name: SeqLighter
- author: Maria Kim, Vivek Krishnakumar
  description: |
    ComboTrackSelector is a plugin to allow the co-existence of the
    Hierarchical and Faceted Track selectors in JBrowse, built for/by
    the Arabidopsis Information Portal (Araport) project.
  gmodProject: JBrowse
  license: MIT
  location: https://github.com/Arabidopsis-Information-Portal/ComboTrackSelector
  name: ComboTrackSelector
- author: Keiran Raine
  description: |
    JBrowse plugin to display multiple BigWig tracks as a stacked proportion of count with
    a wiggleXY plot overlaid to show the count at that location e.g. allele fraction.
  gmodProject: JBrowse
  license: AGPL-3.0
  location: https://github.com/cancerit/proportionalmultibw
  name: ProportionalMultiBw
- author: Colin Diesh
  description: |
    A JBrowse plugin for coloring BAM reads according to quality scores
  gmodProject: JBrowse
  location: https://github.com/cmdcolin/qualityglyphs
  name: qualityglyphs
- author: Colin Diesh
  description: |
    A JBrowse plugin with a custom variant track for multi-VCF files and optionally plotting LD scores
  gmodProject: JBrowse
  location: https://github.com/cmdcolin/multivariantviewer
  name: multivariantviewer
- author: Colin Diesh
  description: |
    A JBrowse plugin to parse AGP files and display them
  gmodProject: JBrowse
  location: https://github.com/cmdcolin/agp_parser
  name: agp_parser
- author: Colin Diesh
  description: |
    A JBrowse plugin to view GC content % overlaid on a BAM coverage plot
  gmodProject: JBrowse
  license: ISC
  location: https://github.com/cmdcolin/gccoverage
  name: gccoverage
- author: Brigitte Hofmeister
  description: |
    JBrowse plugin to makes configurable screenshots easy using PhantomJS Cloud
  gmodProject: JBrowse
  location: https://github.com/bhofmei/jbplugin-screenshot
  name: Screenshots Plugin
  license: MIT
- author: Eric Rasche
  description: |
    JBrowse plugin to render gff3 formatted Blast results nicely and provide useful help menus
  gmodProject: JBrowse
  location: https://github.com/TAMU-CPT/blastview
  name: BlastView
  license: AGPL-3.0
  demo: "blastview&tracks=DNA,Feature,Blast&loc=ctgA:5235..6268"
  image: blastviewer.png