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
  image: multibigwig.png
- 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
  image: jbrowse_elasticsearch.png
  license: NONE
- 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"
  license: NONE
- 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"
  license: NONE
- 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"
  image: ga4ghviewer.png
  license: NONE
- 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
  image: projectionplugin.png
- 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_plugin
  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 user checks/unchecks 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
  image: hierarchicalcheckbox.png
  license: Apache-2.0
- author: Brigitte Hofmeister
  description: |
    This plugin 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
  image: trackscores.png
  license: Apache-2.0
- author: Brigitte Hofmeister
  description: |
    JBrowse plugin for whole-genome bisulfite sequencing data.
    This pluging allows the user to see all methylation contexts on one track.
  gmodProject: JBrowse
  location: https://github.com/bhofmei/jbplugin-methylation
  name: Methylation Plugin
  image: methylation.png
  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: Apache-2.0
  image: smallrna.png
- 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
  image: seqlighter.png
- 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
  demo: "combotrackselector&loc=Chr1:25097503..25120860&tracks=DNA,Genes,1005,159,1013,285,1201"
  image: combotrackselector.png
- 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
  image: proportionalmultibw.png
- 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
  image: qualityglyphs.png
  license: NONE
- 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
  image: multivariant.png
  license: NONE
- 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
  license: NONE
- 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
  image: gccoverage.png
- 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
  image: screenshot.png
  license: Apache-2.0
- author: Helena 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
- author: Matthias Monfort, Charles Girardot
  description: |
    JBrowse plugin for dynamic visualization by automatic selection of
    informative tracks from hundreds of genomic data sets. Dynamix takes
    advantage of a priori knowledge to automatically display data tracks
    with signal within a genomic region of interest. Dynamix also
    introduces a new carousel view that optimises screen utilisation by
    enabling users to independently scroll through groups of tracks.
  gmodProject: JBrowse
  location: https://git.embl.de/monfort/dynamix/
  name: Dynamix
  demo: "http://furlonglab.embl.de/DynamixDemo"
  image: dynamix.png
  license: MIT
- author: Colin Diesh
  description:  |
      A JBrowse plugin to view multiple whole-genome alignment data
  name: mafviewer
  image: mafviewer.png
  gmodProject: JBrowse
  location: https://github.com/cmdcolin/mafviewer
  license: NONE
- author: Andrew Wilkey
  description:  |
      JBrowse plugin allowing users to manage a persistent list of bookmarks kept in localstorage
  name: Bookmarks
  image: bookmarks.png
  gmodProject: JBrowse
  location: https://github.com/awilkey/bookmarks-jbrowse/
  license: MIT
- author: Helena Rasche
  description:  |
      Dark/Flat theme for JBrowse
  name: Dark/Flat Theme
  image: darkflat.png
  gmodProject: JBrowse
  location: https://github.com/erasche/jbrowse-dark-theme/
  license: GPL-3.0
  demo: "darkflat&tracks=DNA,ExampleFeatures&loc=ctgA:1..6268"
- author: Helena Rasche
  description:  |
      Afra/Minimalist theme for JBrowse
  name: Minimalist Theme
  image: minimalist.png
  gmodProject: JBrowse
  location: https://github.com/erasche/jbrowse-minimalist-theme/
  license: GPL-3.0
  demo: "minimalist&tracks=DNA,ExampleFeatures&loc=ctgA:1..6268"
- author: JBrowse Themes
  demo: ThemeComponent-Colors-BlackWhite-BlueGreen&tracks=DNA,ExampleFeatures&loc=ctgA:1..6268
  description: A pleasant minimalist black, white and fresh colour scheme
  image: ThemeComponent-Colors-BlackWhite-BlueGreen.png
  license: GPL-3.0
  location: https://github.com/jbrowse-themes/ThemeComponent-Colors-BlackWhite-BlueGreen
  name: ThemeComponent-Colors-BlackWhite-BlueGreen
  gmodProject: JBrowse
- author: JBrowse Themes
  demo: ThemeComponent-DisableGrid&tracks=DNA,ExampleFeatures&loc=ctgA:1..6268
  description: A JBrowse 'Theme Component' which disables the grid
  image: ThemeComponent-DisableGrid.png
  license: GPL-3.0
  location: https://github.com/jbrowse-themes/ThemeComponent-DisableGrid
  gmodProject: JBrowse
  name: ThemeComponent-DisableGrid
- author: JBrowse Themes
  demo: ThemeComponent-Flat&tracks=DNA,ExampleFeatures&loc=ctgA:1..6268
  description: Flatten many curved surfaces
  image: ThemeComponent-Flat.png
  license: GPL-3.0
  location: https://github.com/jbrowse-themes/ThemeComponent-Flat
  name: ThemeComponent-Flat
  gmodProject: JBrowse
- author: JBrowse Themes
  demo: ThemeComponent-RearrangedRulers&tracks=DNA,ExampleFeatures&loc=ctgA:1..6268
  description: Rearranges the rulers to be next to each other, and removes the "zoomed
    region" blue bar.
  image: ThemeComponent-RearrangedRulers.png
  license: GPL-3.0
  location: https://github.com/jbrowse-themes/ThemeComponent-RearrangedRulers
  name: ThemeComponent-RearrangedRulers
  gmodProject: JBrowse
- author: JBrowse Themes
  demo: ThemeComponent-RightAlignedControls&tracks=DNA,ExampleFeatures&loc=ctgA:1..6268
  description: Align the zoom controls to the right.
  image: ThemeComponent-RightAlignedControls.png
  license: GPL-3.0
  location: https://github.com/jbrowse-themes/ThemeComponent-RightAlignedControls
  name: ThemeComponent-RightAlignedControls
  gmodProject: JBrowse
- author: Helena Rasche
  name: Site-wide Notices
  demo: sitewide
  description: |
      This allows you to proactively inform users about upcoming maintenance
      events. It displays a highly visible button and a popup with further
      information loaded from a JSON file, allowing your users to plan around
      downtimes.
  image: sitewide.png
  license: AGPL-3.0
  location: https://github.com/TAMU-CPT/SitewideNotices/
  gmodProject: JBrowse
- author: Colin Diesh
  description: |
    JBrowse plugin to make a list of tracks from a base track config and list of file URLs
  gmodProject: JBrowse
  location: https://github.com/cmdcolin/manytracks
  license: ISC
  name: manytracks
- author: BioNano Genomics
  description: |
      JBrowse plugin to support BioNano Genomics files
  gmodProject: JBrowse
  location: https://github.com/bionanogenomics/JBrowsePlugin/
  license: MIT
  name: BioNanoGenomics
- author: Brigitte Hofmeister
  description: |
      JBrowse plugin that allows the user to manually switch between
      feature/read views and histogram views
  gmodProject: JBrowse
  location: https://github.com/bhofmei/jbplugin-seqview
  license: Apache-2.0
  image: seqviews.png
  name: Sequence Views
- author: Brigitte Hofmeister
  description: |
      JBrowse plugin that show sequence motif density as a heatmap for one or more
      sequence contexts in one track.
  gmodProject: JBrowse
  location: https://github.com/bhofmei/jbplugin-motifdens
  license: Apache-2.0
  image: motifdensity.png
  name: Sequence Motif Density Density
- author: Colin Diesh
  description: |
      A JBrowse plugin to color the features and DNA track according the coding frame
  gmodProject: JBrowse
  location: https://github.com/cmdcolin/colorbycds
  license: ISC
  name: colorbycds
  image: colorbycds.png
- author: Brigitte Hofmeister
  description: |
    Same visualization as the built in XYPlot and Density plot but renders the plot using HTML SVG which is better for PDF/SVG screenshots
  gmodProject: Apache-2.0
  location: https://github.com/bhofmei/jbplugin-wigglesvg
  name: Wiggle SVG Plot Plugin
  license: Apache-2.0
- author: Deepak Unni
  description: |
    A simple JBrowse plugin that renames the key of a displayed track to a value from track metadata
  gmodProject: JBrowse
  location: https://github.com/deepakunni3/RenameTracks
  name: Rename Tracks
  license: MIT
  image: renametracks.png
- author: Hans Vasquez-Gross
  description: |
    A JBrowse plugin that parses the ANN field from a VCF file that has been generated by SnpEff or VEP tools to color code
    SNPs based on mutation effect.
  gmodProject: JBrowse
  location: https://github.com/hans-vg/jbplugin-varianteffect
  name: Variant Effect
  license: MIT
  image: varianteffect.png
- author: NAL i5k workspace
  description: |
    A JBrowse plugin to color the features according the feature type. This plugin is derived from the Apollo plugin DraggableHTMLFeatures.
  gmodProject: JBrowse
  location: https://github.com/NAL-i5K/ColorByType
  name: ColorByType
  license: (CC0-1.0 AND BSD-3-Clause)
- author: Colin Diesh
  description: |
    A JBrowse plugin to highlight areas of a wiggle track based on another feature track
  gmodProject: JBrowse
  location: https://github.com/cmdcolin/wigglehighlighter
  name: WiggleHighlighter
  license: MIT
- author: Scott Cain
  description: |
    A JBrowse plugin to find sequence motifs with a Position Weight Matrix
  gmodProject: JBrowse
  location: https://github.com/scottcain/MotifSearch
  name: MotifSearch
  license: Apache-2.0
  image: MotifSearch-small.png
- author: Colin Diesh
  description: |
    A JBrowse plugin to draw little pie charts for the variant glyphs
  gmodProject: JBrowse
  location: https://github.com/cmdcolin/jbrowse_piechart
  name: PiechartPlugin
  license: MIT
- author: Colin Diesh
  description: |
    A JBrowse plugin to design primers. Requires setup with primer3 running on the server. Original author Nathan Liles. Note: somewhat tricky to setup
  gmodProject: JBrowse
  location: https://github.com/cmdcolin/JBrowse-PrimerDesigner
  name: PrimerDesigner
  license: MIT