Refinery Platform

All

37 repositories

refinery-platform
Public
The Refinery Platform is a data management, analysis and visualization system for bioinformatics and computational biology applications. The platforms consists of three major components: a data repository with rich metadata capabilities, a workflow engine based on the popular Galaxy system, and visualization tools to support the exploration and …
galaxy-project gehlenborglab refinery refinery-platform
Python
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Other
•24•102•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
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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.
proxy-server docker django
Python
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MIT License
•2•6•47•2•Updated Dec 26, 2022Dec 26, 2022
heatmap-scatter-dash
Public
Interactive visualizations for differential expression
visualization docker refinery differential-expression
Python
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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
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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
docker higlass refinery-platform
Python
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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
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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)
docker gehlenborglab visualization refinery
Python
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MIT License
•1•2•3•0•Updated Nov 19, 2019Nov 19, 2019
docker_igv_js
Public
A Docker container to wrap IGV.js
docker-image igv
Python
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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/latest/isajson.html
terraform python docker lambda api-gateway isatab isatab-archives
Python
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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
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Other
•0•0•4•0•Updated Oct 2, 2018Oct 2, 2018
shiny-heatmap-refinery
Public
A simple containerized Shiny App heatmap
Shell
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MIT License
•0•0•1•0•Updated Sep 6, 2018Sep 6, 2018
refinery-stats
Public
Altair code for Refinery Stats plots.
Jupyter Notebook
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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
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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
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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 facilitate the quality control of alignment sequencing data and its derivatives like feature counts.
Python
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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-project dataset-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
visualization search ontology exploration refinery biomedical data-repository satori
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
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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
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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-project gehlenborglab clodius clodius-galaxy
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
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MIT License
•0•0•0•0•Updated Jul 6, 2017Jul 6, 2017
ontology-imports
Public
Ontology batch import definition files
neo4j owl ontology import refinery
Web Ontology Language
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MIT License
•1•2•0•0•Updated May 3, 2017May 3, 2017
heatmap-volcano-pca
Public
JavaScript
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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
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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
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MIT License
•0•0•3•0•Updated Jan 5, 2017Jan 5, 2017
sample-data
Public
Sample data sets and generators for Refinery.
Python
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MIT License
•1•3•0•0•Updated May 3, 2016May 3, 2016