Repositories list

• adama

  Public
  Adaptible Data And Microservices API

  JavaScript

  •

  Other

  •3•6•39•17•Updated Dec 26, 2022Dec 26, 2022

• adamalib

  Public
  A Python library for using Adama

  Jupyter Notebook

  •

  Other

  •3•3•0•4•Updated Dec 26, 2022Dec 26, 2022

• atted-displayer

  Public
  JavaScript

  •1•0•0•11•Updated Dec 6, 2022Dec 6, 2022

• ComboTrackSelector

  Public
  Plugin to allow the co-existence of the Hierarchical and Faceted Track Selectors in the GMOD JBrowse Genome Browser

  jbrowse-pluginjbrowse

  JavaScript

  •

  MIT License

  •4•7•2•0•Updated Mar 18, 2019Mar 18, 2019

• thalemine

  Public
  ThaleMine - an InterMine with Arabidopsis genomic data

  bioinformaticsgenomicsbiological-data-analysis+ 2interminegenomics-visualization

  Java

  •0•0•0•0•Updated Mar 22, 2018Mar 22, 2018

• thalemine-bio-sources

  Public
  Data Sources for ThaleMine - an InterMine with Arabidopsis genomic data

  Java

  •1•0•0•0•Updated Mar 16, 2018Mar 16, 2018

• intermine-scripts

  Public
  All scripts that used to be in the main intermine repository in bio/scripts and intermine/scripts

  PLpgSQL

  •

  GNU Lesser General Public License v2.1

  •10•0•0•0•Updated Mar 16, 2018Mar 16, 2018

• jbrowse-contrib

  Public
  Configuration and miscellaneous support files for Araport JBrowse installation

  jbrowse

  Shell

  •

  GNU Lesser General Public License v2.1

  •3•3•0•0•Updated Feb 12, 2018Feb 12, 2018

• intermine

  Public
  This is the code base for Thalemine, a data warehouse system based on InterMine and used in Araport, the Arabidopsis Information Portal.

  Java

  •

  Other

  •347•4•0•0•Updated Feb 7, 2018Feb 7, 2018

• small_orfs_to_jbrowse

  Public
  ADAMA web-service wrapper to transform "Translated small ORFs" GFF3 data (Hsu et al. 2016) into JBrowse compatible JSON

  jbrowse-rest-apijbrowseadama

  Python

  •

  Other

  •0•0•0•0•Updated Jan 14, 2018Jan 14, 2018

• CDN

  Public
  JavaScript, Cascading Style Sheet Content Delivery Network

  JavaScript

  •23•0•0•0•Updated Nov 20, 2017Nov 20, 2017

• atted_webservices

  Public
  Illustrative web service for ATTED II coexpression web service

  Python

  •5•0•0•0•Updated Aug 2, 2017Aug 2, 2017

• GAG

  Public
  Generates an NCBI .tbl file of annotations on a genome.

  Python

  •

  MIT License

  •20•0•0•0•Updated May 15, 2017May 15, 2017

• jbrowse

  Public
  A modern genome browser built with JavaScript and HTML5.

  visualizationgenomicsgmod+ 3genome-browserjbrowsejavascript

  JavaScript

  •

  GNU Lesser General Public License v2.1

  •198•2•0•0•Updated May 4, 2017May 4, 2017

• AraportJBPlugin

  Public
  Custom JBrowse plugin to map JBrowse/Store/SeqFeature/REST to the Araport Adama API endpoints

  jbrowsejbrowse-plugin

  JavaScript

  •

  MIT License

  •0•0•0•0•Updated May 4, 2017May 4, 2017

• EnsemblVariants

  Public
  JBrowse plugin enabling the ability to enrich the Ensembl Variants (VCF) track with metadata from rest.ensemblgenomes.org API

  jbrowsejbrowse-plugin

  JavaScript

  •

  MIT License

  •0•0•0•0•Updated May 4, 2017May 4, 2017

• 1001GenomesVariants

  Public
  JBrowse plugin enabling the ability to enrich the 1001 Genomes Variants track with metadata from 1001genomes.org Master Accession List API

  jbrowsejbrowse-plugin

  JavaScript

  •

  MIT License

  •0•0•0•0•Updated May 4, 2017May 4, 2017

• CyverseRemoteTracks

  Public
  JBrowse plugin enabling the ability to dynamically load tracks from data/configurations stored in the Cyverse Data Store

  jbrowsejbrowse-plugin

  JavaScript

  •

  MIT License

  •0•1•0•0•Updated Apr 21, 2017Apr 21, 2017

• deploy-community-tracks

  Public
  Shell

  •0•0•4•0•Updated Jan 11, 2017Jan 11, 2017

• jcvi-araport11-services

  Public
  ADAMA adapters for querying Araport11 annotation data

  Python

  •

  Other

  •1•0•0•0•Updated Jan 5, 2017Jan 5, 2017

• araport-portal

  Public
  Docker image for the Araport portal.

  PHP

  •0•0•0•0•Updated Dec 22, 2016Dec 22, 2016

• science_apps_workspace

  Public
  Drupal module for the Araport Science Apps Workspace.

  PHP

  •1•1•10•0•Updated Dec 22, 2016Dec 22, 2016

• araport_features

  Public
  Drupal modules developed for Araport functionality.

  PHP

  •0•0•0•0•Updated Dec 22, 2016Dec 22, 2016

• araport-theme

  Public
  Arabadopsis Information Portal Theme, a Bootstrap 3 theme based on http://drupal.org/project/bootstrap.

  CSS

  •0•0•0•0•Updated Dec 22, 2016Dec 22, 2016

• tree-viewer-app

  Public
  Viewer app for rendering phylogenetic trees.

  JavaScript

  •0•0•0•0•Updated Oct 10, 2016Oct 10, 2016

• PMR_API

  Public
  Adapter for PMR web services.

  Python

  •

  GNU General Public License v2.0

  •0•1•0•0•Updated Sep 26, 2016Sep 26, 2016

• phytozome_webservices

  Public
  ADAMA adapters for various Phytozome webservices

  0•1•0•0•Updated Aug 31, 2016Aug 31, 2016

• jbrowse-tabix-howto

  Public
  Visualizing tabix-indexed files located on the CyVerse Data Store using the JBrowse Genome Browser

  0•2•0•0•Updated Jul 28, 2016Jul 28, 2016

• generator-aip-science-app

  Public
  Yeoman Generator for building Science Apps for the Arabidopsis Information Portal.

  JavaScript

  •2•2•1•0•Updated Jul 26, 2016Jul 26, 2016

• ebi-interaction-viewer-app

  Public
  Araport demo science app that uses the ADAMA layer to query interaction data from EBI

  JavaScript

  •0•0•0•0•Updated Jul 20, 2016Jul 20, 2016