Discover thehyve/arborist Open Source project by The Hyve (@thehyve)

Core components and documentation of the tranSMART platform. https://i2b2transmart.org/

transmart-core

A light weight adaptation React based mutation lollipop plot from cBioPortal frontend.

react-mutation-plot

Podium request portal for biobanks

podium

Fairspace provides a secure environment for managing research data.

fairspace

tranSMART pipeline alternative to ETL, using Spring Batch

transmart-batch

A React select component based on JedWatson/React-Select with checkmarks on selected options.

react-select-checked

PostgreSQL extension providing a bitcount function.

pg_bitcount

python_claml

A ClaML reader for Python

Docker scripts for Glowing Bear

glowing-bear-docker

Shell

ukbiobank-omop-etl

Resources and documentation for UK Biobank to OMOP CDM v5.3.1 conversion

HTML

cbioportal-docker

A context to create cBioPortal docker images

Dockerfile

transmart-api-client-py

🐍 Python client for tranSMART Glowing Bear

tranSMART Arborist ETL toolkit

tmtk

HTTP available tranSMART RESTful API

transmart-rest-api

Transformation scripts for Inclivia's Abucasis EHR data | BigData@Heart consortium

ohdsi-etl-abucasis

davfs2

Mount a WebDAV resource as a regular file system. This repository is a copy of the original repository with project specific patches in the fairspace branch.

ohdsi-drug-mapping

Drug mapping script to map drugs to RxNorm drugs. Note that the data files are contained within the repository.

PLpgSQL

ohdsi-DeriveVariables

R package for deriving variables from the OMOP Common Data Model.

dbxpModuleBase

Grails plugin that provides basic functionality for dbXP module plugins.

Request portal for Dutch pathology labs.

dntp-portal

ETL scripts for caliber data

ohdsi-etl-caliber

transmart-data

Tools for managing tranSMART's database

PLSQL

ohdsi-etl-sweden

ETL procedure to OMOP CDM for Swedish health data.

Grails plugin for importing tab delimited, Excel 97/2003/2007 and CSV files

matrixImporter

Scripts for converting CSR data to TranSMART

python_csr2transmart

A terraform config for provisioning of Idm

tr_idm

HCL

python_transmart_loader

TranSMART loader library for Python

Data science with tranSMART REST API in Python and R

transmart-api-training

Jupyter Notebook

transmart-hyper-dicer

Export a subset of data from a TranSMART instance based on a query, and upload them to a different (empty) TranSMART instance using transmart-copy. Short for TranSMART hypercube dicer.

SAM

Simple Assay Module

Next version of Open Clinica Data Importer

Open-Clinica-Data-Uploader

Small utility to replace numeric identifiers from SPSS sav files.

spss-sav-pseudonymization

React components for visualisations from the GTEx web portal

react-gtex-viz

TranSMART FAIR data point

transmart-fair-data-point

A data showcase for displaying a summary of data in TranSMART.

data-showcase

Puppet module for TranSMART

puppet-transmart_core

Puppet

python_claml2transmart

ClaML ontology to TranSMART loader

food4me-webservice

dalliance-plugin

GSVA score and p-value calculation for TCGA studies in cBioPortal

cbioportal-gsva-analysis

transmart-arborist-deprecated

Superseded by https://github.com/thehyve/arborist

A command line tool + Galaxy plugin to convert blast XML output into a nicely readable html page

blast2html

coding-dojo

Android Client for TranSMART

transmart-android

Data extraction, transformation and loading pipeline for the Princess Maxima Center

pmc-conversion

Transformation from PRIAS to the OMOP CDM

ohdsi-etl-prias

transmart-core-db

Implementation of transmart-core-api for PostgreSQL/Oracle/H2

Data warehouse Inventory Management System

whereabouts

OHDSI COVID-19 studyathon website

ohdsi-covid19-site

HTML

heim-SmartR

heim

Backend application for Glowing Bear UI, supporting user queries management, subscription and notification functionality

gb-backend

ohdsi-schemas

transmart-mydas

transmart-packer

data jobs for transmart

A database for storing genotype-phenotype mappings from literature. This project was commissioned by TNO Quality of Life under the EU FP7 EURRECA project.

variant

Variant store connector for the TranSMART API

transmart-variant-store-connector

python_fhir2transmart

FHIR to TranSMART loader

a cBioPortal adapter for the BioCypher framework

biocypher-cbioportal

Configuration for the quisper nginx proxy.

quisper-configuration-public

Lua

transmart-lib

TranSMART API client library and proxy

Github pages for Glowing Bear website

glowing-bear-site

HTML

transmartApp-doc

Example ontology to TranSMART loader

python_ontology2transmart

Sharks gotta swim. Bats gotta fly. And I'll need a weekly planning till I die.

amazing-planning-generator

Code for connecting JupyterHub to Fairspace

fairspace-jupyter

smart-r-js