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- 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
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