CD2H gitForager

The Hyve

Login: thehyve

Company: null

Location: Utrecht, Netherlands

email: office@thehyve.nl

Blog: http://www.thehyve.nl

Members

Repositories

Achilles: Automated Characterization of Health Information at Large-scale Longitudinal Evidence Systems (ACHILLES) - descriptive statistics about a OMOP CDM v4 database
acme-client: A Ruby client for the letsencrypt's ACME protocol.
angular-transmart-analysis: null
arborist: TranSMART Arborist: Graphical tool for reshaping your data for the tranSMART data warehouse.
arraycgh-galaxy: ArrayCGH tools ported from Chipster to Galaxy
arvados: an open source platform for managing and analyzing biomedical big data
base-ui-component-seed: Angular JS plugin skeleton for a transmart UI.
blast2html: A command line tool + Galaxy plugin to convert blast XML output into a nicely readable html page
blend4j: blend4j is a JVM partial reimplemenation of the Python library bioblend for interacting with Galaxy, CloudMan, and BioCloudCentral.
cbioportal: cBioPortal topic branches at The Hyve
cbioportal-docker: A context to create cBioPortal docker images
cbioportal-frontend: React Frontend of cBioPortal :tada:
cbioportal-gsva-analysis: GSVA score and p-value calculation for TCGA studies in cBioPortal
cbioportal-staging: Staging app for automatically loading studies into cBioPortal
cbioportal-staging-portal: Staging web portal for loading studies into cBioPortal
charts: Curated applications for Kubernetes
civic-server: Backend Server for CIViC Project
ckanext-configpermission: A CKAN extension for managing permissions
ckanext-extractor: A full text and metadata extractor for CKAN
clinical-timeline: Use d3-timeline to visualize clinical data
Configuration-Files: ISAconfiguration files which have been created by the ISAconfigurator. These can be used by ISAcreator, ISAvalidator, ISAconverter and the BII Data Management Tool
cookiecutter: Cookiecutter boilerplate for tranSMART data portal. Based on hack4impact flask-base
dalliance-plugin: null
datahub: A centralized location for storing curated data ready for inclusion in cBioPortal.
data-showcase: A data showcase for displaying a summary of data in TranSMART.
dataverse-client-r: R Client for Dataverse 4 Repositories
dataverse-puppet: null
dazzle: null
dbSNP-pg-helpers: null
dbxpBase: Base domain model for dbXP / study capture framework
dbxpModuleBase: Grails plugin that provides basic functionality for dbXP module plugins.
dbxpModuleStorage: Grails Plugin for storing Metabolomics files in MongoDB
dntp-portal: Request portal for Dutch pathology labs.
eid-idp: The eID Identity Provider is a simple IdP using the eID as authentication token. Forked from https://code.google.com/p/eid-idp/
enhanced-fixed-datatable: cBioPortal Enhanced Fixed Datatable topic branches at The Hyve
environment-kangaroocyber-staging: null
fairdatapoint: null
fairmetadata4j: null
folder-management-plugin: The transmart (and grails) plugin that contains the folder-management elements.
food4me-webservice: null
galaxy_blast: Galaxy wrappers for NCBI BLAST+ and related BLAST tools.
galaxy-roles-profiles: Contains roles and profiles for a Galaxy server management.
galaxytools: Galaxy Tool wrappers
garethr-docker: Puppet module for managing docker
GDT: Grails plugin called Grails Domain Templates, which materializes an EAV datamodel in a relational database for Grails domain objects.
genome-nexus: Interpreting cancer genomics data
genome-nexus-importer: Import data into MongoDB for use by https://github.com/genome-nexus/genome-nexus/
glowing-bear: A cohort-selection UI (currently using tranSMART REST API v2)
glowing-bear-backend: Merged IRCT Repository
glowing-bear-site: Github pages for Glowing Bear website
Groc-1: Beautiful documentation of your groovy sources
GSCF: Generic Study Capture Framework
GSCF-RClient: R client to connect to GSCF
GWAVA: Genome Wide Association Study Visualizer (LODZ2 project)
heim-blend4j-plugin: null
heim-folder-management-plugin: null
heim-GWAVA: null
heim-RInterface: null
heim-Rmodules: null
heim-SmartR: heim
heim-transmartApp: null
heim-transmart-core-api: null
heim-transmart-core-db: null
heim-transmart-data: null
heim-tranSMART-ETL: null
heim-transmart-extensions: null
heim-transmart-gwas-plugin: null
heim-transmart-ICE: null
heim-transmart-legacy-db: null
heim-transmart-metacore-plugin: null
heim-transmart-rest-api: null
heim-transmart-test: null
ISAcreator: ISAcreator is a Java desktop application which allows for creation and editing of ISATab files. Led by Eamonn Maguire and Philippe Rocca-Serra (Uni. of Oxford).
iViz: cBioPortal Study View
jbrowse-plugin: null
jstat: JavaScript Statistical Library
jx-quickstart-spring: null
logic-query-parser: null
magma: Data and meta-data abstraction layer.
matrixImporter: Grails plugin for importing tab delimited, Excel 97/2003/2007 and CSV files
maven-release-plugin: null
metabolomicsModule: Module for storing Metabolomics Data
mica: Mica is a web portal for epidemiological study consortia.
mutation-mapper: cBioPortal mutation mapper topic branches at The Hyve
mydas: mydas is an easy-to-extend Java DAS server framework.
naa-folder-management: tranSMART Folder Management Plug-in
naa-Rmodules: Rmodules
naa-SmartR: null
naa-transmartApp: mirror of the GPL 1.0 GA release of transmart
naa-transmart-core-api: null
naa-transmart-core-db: SnpSubjectRow
naa-transmart-extensions: null
naa-transmart-gwas: Pfizer Transmart GWAS module
naa-transmart-legacy-db: null
naa-transmart-rest-api: null
nb_conda: Conda environment and package access extension from within Jupyter
nbdime: Tools for diffing and merging of Jupyter notebooks.
oauthenticator: OAuth + JupyterHub Authenticator = OAuthenticator
obiba-commons: Reusable code for persistence (hibernate), security, spring and wicket.
OHDSI-Atlas: ATLAS is an open source software tool for researchers to conduct scientific analyses on standardized observational data
OHDSI-CommonDataModel: Definition and DDLs for the OMOP Common Data Model (CDM)
OHDSI-Dataprint: A Novel Visualization Tool for Database Comparison
ohdsi-DeriveVariables: R package for deriving variables from the OMOP Common Data Model.
ohdsi-drug-mapping: Drug mapping script to map drugs to RxNorm drugs. Note that the data files are contained within the repository.
ohdsi-etl-sweden: ETL procedure to OMOP CDM for Swedish health data.
OHDSI-WebAPI: [Under development] OHDSI WebAPI contains all OHDSI services that can be called from OHDSI applications
OHDSI-WebAPI: [Under development] OHDSI WebAPI contains all OHDSI services that can be called from OHDSI applications
OHDSI-WhiteRabbit: WhiteRabbit is a small application that can be used to analyse the structure and contents of a database as preparation for designing an ETL. It comes with RabbitInAHat, an application for interactive design of an ETL to the OMOP Common Data Model with the help of the the scan report generated by White Rabbit.
OHDSI-WhiteRabbit: WhiteRabbit is a small application that can be used to analyse the structure and contents of a database as preparation for designing an ETL. It comes with RabbitInAHat, an application for interactive design of an ETL to the OMOP Common Data Model with the help of the the scan report generated by White Rabbit.
oncoprintjs: OncoPrint visualization
opal: OBiBa?s core database application for biobanks or epidemiological studies.
opal-rserver: Opal Rserver Debian meta package
OpenClinica: OpenClinica is the world's first commercial open source clinical trial software for Electronic Data Capture (EDC) Clinical Data Management (CDM).
Open-Clinica-Data-Uploader: Next version of Open Clinica Data Importer
opencpu: OpenCPU system for embedded scientific computation and reproducible research
opencpuRScripts: produceUI
openphacts-java-client: OpenPHACTS API client library for Java
package_recipes: Contains package recipes for various open source tools and libraries used by The Hyve
PathVisioRPC: PathVisioRPC is an XML-RPC implementation of PathVisio that allows users to create and edit biological pathways, visualize data on pathways, perform pathway statistics, query pathways to obtain list of participants and exports results in various image formats. Since most major programming languages have an XML-RPC implementation, this application enables users to access PathVisio functionality without leaving the programming environment with which they are familiar.
pedigree_schema_design: Assumptions about the pedigree file format and it's content
pg_bitcount: PostgreSQL extension providing a bitcount function.
podium: Podium Request Portal
podium-api-docs: API documentation for the Podium request portal
podium-example-config: Example configuration repository for the Podium registry.
podium-registry: BBMRI Podium Microservices Registry
puppet-3scale-proxy: Puppet module to configure 3scale proxy.
puppet-afp: https://forge.puppetlabs.com/swizzley88/afp
puppet-aptly: Puppet module to deploy and manage aptly, a Debian repository management tool http://www.aptly.info/
puppet-bamboo_artifact: Deploy artifacts directly from Bamboo
puppet-confluent: Puppet module for setting up confluent.io kafka/zookeeper/restservice/schemaregistry
puppet-data_showcase: Puppet module for the data showcase application
puppet-galaxy: Root repository for the puppet galaxy project.
puppet-glowing_bear: Puppet module for Glowing Bear
puppet-grafana: Puppet module to manage Grafana
puppet-hadoop: Hadoop Module for Basic Installation of Core/Common Package
puppet-i2b2: Puppet module for installing i2b2.
puppet-jenkins: Puppet module for Jenkins
puppet-logrotate: Puppet logrotate module
puppet-phenotype-database: Puppet module to install Phenotype Database application suite
puppet-podium: Puppet module for the Podium request portal
puppet-rabbitmq: RabbitMQ Puppet Module
puppet-samba: Puppet module to manage Samba Server
puppet-transmartApp: Puppet module to automatically install the TransmartApp
puppet-yaml_settings: Puppet type for editing YAML files
qsp-dev-portal: QSP dev portal based on AWS API Gateway
qualify: null
qualify-devportal: QuaLiFY developer portal
qualify-provider-portal: Provider portal used for the QualiFY Server Platform
quisper-configuration-public: Configuration for the quisper nginx proxy.
RADAR-Android-ActiGraphLink: null
RADAR-AndroidApplication: Application to be run on a Raspberry Pi3 to interact with the wearable devices
radar-android-application-status: Application statistics plugin for RADAR passive remote monitoring app
RADAR-Android-Phone: Basic phone sensor plugin for RADAR passive remote monitoring app
RADAR-Android-Wear: Android Wear support for RADAR
RADAR-Backend: Kafka backend for processing device data
RADAR-Commons-Android: Base android functionality for the RADAR passive application plugins
radar-docker: null
radar-puppet: RADAR puppet module
RADAR-Schemas: Catalog of the schemas for RADAR-CNS
react-select-checked: A React select component based on JedWatson/React-Select with checkmarks on selected options.
rest_api: Flask-based Rest API for OpenTargets CoreDB Data
RInterface: An R module for interacting with tranSMART's RESTful API
Rmodules: A R statistical analysis module plugin for tranSMART
Rmodules_oncoprint: null
rserver-admin: R server REST controller
SAM: Simple Assay Module
sas-convert: Simple SAS7BDAT to CSV conversion tool based on the Parso library.
schemas: Work on data models and APIs for Genomic data.
selenese-runner-java: Selenium IDE native format interpreter.
seleniumTests: Selenium scripts for automated tests
sensu-community-plugins: Sensu community plugins for checks, handlers, & mutators.
sensu-puppet: Sensu Puppet module.
sesi_site: Mica Drupal site for SESI project. It contains modules and themes.
singularity-jupyter: null
SmartR: null
smart-r-js: null
spssio: Automatically exported from code.google.com/p/spssio
spss-sav-pseudonymization: Small utility to replace numeric identifiers from SPSS sav files.
tf_to_pf_17_1: null
tm2cbio: Utility to translate tranSMART export files to a directory ready for import to cBioPortal
tMDataLoader: new Groovy-based tranSMART ETL
tmtk: tranSMART Arborist ETL toolkit
to-tsv-scripts: Collection of scripts to extract content from different formats to tsv (tab separated values) format.
trait_odm_to_i2b2: TraIT ODM to i2b2 (OpenClinica to transMART converter)
translocation-users: null
transmart-android: Android Client for TranSMART
transmart-api-client-py: python client for transmart rest api
transmart-api-training: Data science with tranSMART REST API in Python and R
transmartApp: tranSMART is a knowledge management platform that enables scientists to develop and refine research hypotheses by investigating correlations between genetic and phenotypic data, and assessing their analytical results in the context of published literature and other work.
transmartApp-DB: Database schema and database dumps for tranSMART application
transmartApp-doc: null
transmartAppInstaller: Installation script for transmartApp and i2b2 using GAnt (Ant in Groovy)
transmart-arborist-deprecated: Superseded by https://github.com/thehyve/arborist
transmart-base-ui: Boilerplate code for tranSMART UI
transmart-batch: tranSMART pipeline alternative to ETL, using Spring Batch
transmart-core: Core components and documentation of the tranSMART platform. http://transmartfoundation.org
transmart-core-api: null
transmart-core-db: Implementation of transmart-core-api for PostgreSQL/Oracle/H2
transmart-curation-scripts_public: public transmart-curation-scripts
transmart-data: Tools for managing tranSMART's database
tranSMART_Data_Curation: Temporary repository for sharing curation scripts for public datasets.
transmart-dev: Repo manifests for tranSMART development
tranSMART-ETL: tranSMART ETL pipelines and configurations
transmart-extensions: Elements that are being collected for refactoring but do not yet have a home. This project needs to be reviewed often!
transmart-fair-data-point: TranSMART FAIR data point
transmart-galaxy: Transmart plugin to execute jobs on the galaxy
transmart-gwas-plink: Plink integration for tranSMART
transmart-gwas-plugin: The transmart (and grails) plugin that contains the GWAS elements.
transmart-i2b2-migration: Scripts for running transmart on i2b2 data
transmart-images: Scripts for building an deploying tranSMART VM images
transmart-legacy-db: Contains the Grails domain declarations of the legacy transmart schema
transmart-loader: tranSMART import functionality implemented in Groovy
transmart-mydas: null
transmart-pro-design: Design artefacts for Transmart Pro
transmart-rest-api: HTTP available tranSMART RESTful API
transmart-test: Functional tests for tranSMART
transmart-test-dataset: A public test dataset intended to use for testing of the loading scripts and interface functionalities of tranSMART and for data curators to understand the expected data format.
transmart-travis: Helper scripts for travis builds
transmart-tutorials: A collection of transmart-related Jupyter Notebook tutorials
transmart-xnat-viewer: Connector to link tranSMART to an XNAT server
utrecht-campus-party-2016: Campus Party Workshop Materials
variant: A database for storing genotype-phenotype mappings from literature. This project was commissioned by TNO Quality of Life under the EU FP7 EURRECA project.
vcf2maf: Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
OHDSI-WebAPI: [Under development] OHDSI WebAPI contains all OHDSI services that can be called from OHDSI applications
OHDSI-WebAPI: [Under development] OHDSI WebAPI contains all OHDSI services that can be called from OHDSI applications
webapp: open targets platform angular.js front end
OHDSI-WhiteRabbit: WhiteRabbit is a small application that can be used to analyse the structure and contents of a database as preparation for designing an ETL. It comes with RabbitInAHat, an application for interactive design of an ETL to the OMOP Common Data Model with the help of the the scan report generated by White Rabbit.
OHDSI-WhiteRabbit: WhiteRabbit is a small application that can be used to analyse the structure and contents of a database as preparation for designing an ETL. It comes with RabbitInAHat, an application for interactive design of an ETL to the OMOP Common Data Model with the help of the the scan report generated by White Rabbit.
xnat-QIB-TranSMART-import: null
zscore-analyses: null

This work is supported by the National Institutes of Health's National Center for Advancing Translational Sciences, Grant Number U24TR002306. This work is solely the responsibility of the creators and does not necessarily represent the official views of the National Institutes of Health.