Repositories list

• refinery-platform

  Public
  The Refinery Platform is a data management, analysis and visualization system for bioinformatics and computational biology applications. The platforms consists …

  galaxy-projectrefineryrefinery-platform+ 1hidivelab

  Python

  •

  Other

  •21•106•299•34•Updated Jan 11, 2023Jan 11, 2023

• dataframer

  Public
  Tries to load any file into a pandas DataFrame, with a minimum of configuration, and a focus on bioinformatics

  Python

  •

  MIT License

  •0•0•2•2•Updated Dec 26, 2022Dec 26, 2022

• django_docker_engine

  Public
  Django app that manages the creation of, and proxies requests to, Docker containers.

  dockerdjangoproxy-server

  Python

  •

  MIT License

  •2•6•47•2•Updated Dec 26, 2022Dec 26, 2022

• heatmap-scatter-dash

  Public
  Interactive visualizations for differential expression

  visualizationdockerrefinery+ 1differential-expression

  Python

  •

  MIT License

  •1•25•41•8•Updated Dec 8, 2022Dec 8, 2022

• lineup-refinery-docker

  Public
  Builds a Refinery visualization Docker image for Lineup

  Python

  •

  MIT License

  •0•0•9•0•Updated Feb 18, 2022Feb 18, 2022

• refinery-higlass-docker

  Public
  "Refinery-ified" flavor of the higlass-docker (https://github.com/hms-dbmi/higlass-docker/) project

  dockerhiglassrefinery-platform

  Python

  •

  MIT License

  •0•0•5•0•Updated Feb 18, 2022Feb 18, 2022

• solr-synonyms-analyzer

  Public
  Solr query parser plugin that performs proper query-time synonym expansion.

  Java

  •0•0•0•2•Updated May 12, 2021May 12, 2021

• kompatible

  Public
  Python wrapper for Kubernetes which matches the interface of Docker

  Python

  •

  MIT License

  •0•0•1•1•Updated Mar 25, 2021Mar 25, 2021

• visualization-tools

  Public
  Registry for Visualization Tool Annotations that are compatible with Refinery (https://github.com/refinery-platform/refinery-platform)

  visualizationdockerrefinery+ 1hidivelab

  Python

  •

  MIT License

  •1•2•3•0•Updated Nov 19, 2019Nov 19, 2019

• docker_igv_js

  Public
  A Docker container to wrap IGV.js

  docker-imageigv

  Python

  •

  MIT License

  •1•0•11•2•Updated Nov 19, 2019Nov 19, 2019

• isa-tab-exporter

  Public
  AWS API Gateway deployment with backing Lambda used to generate ISA-Tab Archives from POST data containing valid ISA-JSON https://isa-specs.readthedocs.io/en/la…

  pythondockerlambda+ 4api-gatewayterraformisatabisatab-archives

  Python

  •

  MIT License

  •0•0•0•0•Updated Feb 13, 2019Feb 13, 2019

• galaxy-tools

  Public
  R

  •0•4•2•0•Updated Nov 29, 2018Nov 29, 2018

• intervene-refinery-docker

  Public
  Wrap the Intervene shiny app for Refinery

  R

  •

  Other

  •0•0•4•0•Updated Oct 2, 2018Oct 2, 2018

• shiny-heatmap-refinery

  Public
  A simple containerized Shiny App heatmap

  Shell

  •

  MIT License

  •0•0•1•0•Updated Sep 6, 2018Sep 6, 2018

• refinery-stats

  Public
  Altair code for Refinery Stats plots.

  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Sep 6, 2018Sep 6, 2018

• shiny-docker-demo

  Public
  Demonstrates how to wrap a Shiny app for Refinery

  Shell

  •

  MIT License

  •0•0•0•0•Updated Sep 6, 2018Sep 6, 2018

• multiqc-refinery-docker

  Public
  Creates a Docker container wrapping a Refinery visualization for Qualimap in MultiQC

  Shell

  •

  MIT License

  •0•0•2•0•Updated Jul 31, 2018Jul 31, 2018

• qualimap2

  Public
  Qualimap 2 is a platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facili…

  Python

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Jul 30, 2018Jul 30, 2018

• split-paired-collection

  Public
  A Galaxy: https://galaxyproject.org/ tool that takes an input Dataset Collection and returns two distinct outputs

  galaxy-projectdataset-collections

  MIT License

  •0•0•0•0•Updated Jul 10, 2018Jul 10, 2018

• satori

  Public
  SATORI - A System for Ontology-Guided Visual Exploration of Biomedical Data Repositories

  visualizationsearchontology+ 5explorationrefinerybiomedicalsatoridata-repository

  CSS

  •0•2•0•0•Updated Apr 9, 2018Apr 9, 2018

• refinery-developer-vis-tool

  Public
  A basic Refinery-compatible visualization tool to aid prospective Refinery VisualizationTool developers.

  Python

  •

  MIT License

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

• get-reference-genomes

  Public
  Get reference genomes from UCSC and prepare them for use by IGV.js

  Python

  •

  MIT License

  •0•3•4•0•Updated Oct 26, 2017Oct 26, 2017

• clodius-galaxy

  Public
  Galaxy tool wrapper around Clodius: https://github.com/hms-dbmi/clodius

  galaxy-projectclodiusclodius-galaxy+ 1hidivelab

  MIT License

  •0•0•0•0•Updated Oct 18, 2017Oct 18, 2017

• refinery-jupyter-docker

  Public
  "Refinery-ified" flavor of the base-notebook here: https://github.com/jupyter/docker-stacks

  Python

  •

  MIT License

  •0•0•0•0•Updated Jul 6, 2017Jul 6, 2017

• ontology-imports

  Public
  Ontology batch import definition files

  neo4jowlontology+ 2importrefinery

  Web Ontology Language

  •

  MIT License

  •1•3•0•0•Updated May 3, 2017May 3, 2017

• heatmap-volcano-pca

  Public
  JavaScript

  •

  BSD 3-Clause "New" or "Revised" License

  •0•1•6•0•Updated Mar 23, 2017Mar 23, 2017

• docker_heatmap-volcano-pca

  Public
  Docker wrapper around heatmap-volcano-pca

  Python

  •

  MIT License

  •0•0•0•0•Updated Mar 23, 2017Mar 23, 2017

• tool-api

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Feb 14, 2017Feb 14, 2017

• igv-wrapper-for-refinery

  Public
  Wrap IGV as an AMD which accepts Node IDs

  JavaScript

  •

  MIT License

  •0•0•3•0•Updated Jan 5, 2017Jan 5, 2017

• sample-data

  Public
  Sample data sets and generators for Refinery.

  Python

  •

  MIT License

  •1•3•0•0•Updated May 3, 2016May 3, 2016