Refinery Platform's repositories
refinery-platform
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 interpretation of results at all stages of the analysis process.
heatmap-scatter-dash
Interactive visualizations for differential expression
django_docker_engine
Django app that manages the creation of, and proxies requests to, Docker containers.
get-reference-genomes
Get reference genomes from UCSC and prepare them for use by IGV.js
sample-data
Sample data sets and generators for Refinery.
ontology-imports
Ontology batch import definition files
visualization-tools
Registry for Visualization Tool Annotations that are compatible with Refinery (https://github.com/refinery-platform/refinery-platform)
isa-tab-exporter
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
clodius-galaxy
Galaxy tool wrapper around Clodius: https://github.com/hms-dbmi/clodius
dataframer
Tries to load any file into a pandas DataFrame, with a minimum of configuration, and a focus on bioinformatics
docker_heatmap-volcano-pca
Docker wrapper around heatmap-volcano-pca
docker_igv_js
A Docker container to wrap IGV.js
igv-wrapper-for-refinery
Wrap IGV as an AMD which accepts Node IDs
intervene-refinery-docker
Wrap the Intervene shiny app for Refinery
kompatible
Python wrapper for Kubernetes which matches the interface of Docker
lineup-refinery-docker
Builds a Refinery visualization Docker image for Lineup
multiqc-refinery-docker
Creates a Docker container wrapping a Refinery visualization for Qualimap in MultiQC
refinery-developer-vis-tool
A basic Refinery-compatible visualization tool to aid prospective Refinery VisualizationTool developers.
refinery-higlass-docker
"Refinery-ified" flavor of the higlass-docker (https://github.com/hms-dbmi/higlass-docker/) project
refinery-jupyter-docker
"Refinery-ified" flavor of the base-notebook here: https://github.com/jupyter/docker-stacks
refinery-stats
Altair code for Refinery Stats plots.
shiny-docker-demo
Demonstrates how to wrap a Shiny app for Refinery
shiny-heatmap-refinery
A simple containerized Shiny App heatmap
solr-synonyms-analyzer
Solr query parser plugin that performs proper query-time synonym expansion.
split-paired-collection
A Galaxy: https://galaxyproject.org/ tool that takes an input Dataset Collection and returns two distinct outputs