Explore @uc-cdis Open Source projects

Center for Translational Data Science (@uc-cdis)

uc-cdis

Stars
375
Global Org. Rank 28,152 (Top 9 %)
Registered over 8 years ago
Most used languages

Python
62.7 %

Go
10.7 %

HTML
6.7 %

JavaScript
6.7 %

TypeScript
2.7 %

Common Workflow Language 2.7 %

Shell
1.3 %

Dockerfile
1.3 %

HCL 1.3 %

Jupyter Notebook
1.3 %

Smarty 1.3 %

Groovy
1.3 %
Location 🇺🇸 United States
Country Total Rank 18,297
Country Ranking

Common Workflow Language 28

Smarty 179

Groovy
688

HCL 3,028

Go
3,245

Shell
3,371

Dockerfile
3,993

HTML
4,682

Python
5,035

cloud-automation

Automation for standing up Gen3 commons

fence

AuthN/AuthZ OIDC Service

data-portal

Windmill: data portal for metadata submission and query

indexd

Index service server

compose-services

Deploy Gen3 using Docker compose

metadata-service

The Metadata Service provides API for retrieving JSON metadata of GUIDs.

peregrine

GraphQL search API service

gen3sdk-python

Gen3 SDK for Python

arborist

Gen3 policy engine

gen3.org

The website for gen3.org

mariner

The Gen3 Workflow Execution Service

sheepdog

API for herding data submissions

pypfb

Python library & CLI to create, view and edit PFB files

gen3-fuse

an S3 file system built on jacobsa/fuse that uses the workspace-token-service

gen3-helm

Helm charts for Gen3 Deployments

cdis-data-client

data access client

hatchery

guppy

Server that supports GraphQL queries on data from Elasticsearch

cdis-jenkins-lib

Little groovy helper for Jenkins pipelines

ndh-demo

Jupyter notebook and shinyR apps for NIAID Data Hub demo

dcfdictionary

audit-service

cdis-manifest

Manifests tracking service versions to release to each environment

data-simulator

gitops-dev

midrc_dictionary

A data dictionary for the Medical Imaging Resource Data Commons (MIDRC).

dictionaryutils

python wrapper and metaschema for datadictionary

userdatamodel

PDC data model for user management

gen3-qa

Integration Tests for Gen3

indexclient

Prototype index service client.

requestor

API to manage access requests

release-helper

Python CLI to generate release notes by scanning a repo's pull requests descriptions

planx-bioinfo-tools

Collection of helpful scripts for mapping, ETL, automation and others related to PlanX bioinformatics team. It includes tools for data model and data dictionary creation as well as data submission.

acronym-bot

Expand CTDS acronyms

cirrus

Cloud Management Library (Wrapping Cloud APIs)

create-gen3-app

Create Gen3 apps without configuration.

sower

Job dispatcher for Kubernetes

commons-frontend-app

Gen3 Data Commons template repository for gen3 frontend framework

covid19-tools

tube

gen3_dictionary_tools

A collection of python functions for converting data dictionaries between YAML and TSV formats.

gitops-qa

gen3-ui-component

Base UI component in gen3

argo-wrapper

Wrapping Argo into nice API for VADC GWAS app

ndhdictionary

Data dictionary for NIAID Commons project

gen3-userservices-info

Information gathered by the Gen3 User Service Team for Documentation

gtex-dictionary

Data dictionary to collect GTEx dataset

workspace-token-service

pelican

Sower jobs for PFB export & import

ssjdispatcher

SQS S3 Job Dispatcher

pidgin

key value metadata service

covid19_datadictionary

dbgap-extract

Extract sample data from NCBI's dbGaP site

gen3-frontend-framework

A Frontend Framework for Gen3 data portals

drsclient

This is the client library for making requests to the GA4GH DRS compatible services and returning an Indexd compatible document.

tcga_dictionary

A light-weight Gen3 data dictionary for representing TCGA/PCAWG/ICGC studies.

genomel_pipelines

GenoMEL pipelines in Bionimbus

cdis-python-utils

utilities to ease python code development

IBDGC_demos

Demonstrations for the IBDGC Commons

gen3-user-doc

gen3authz

sc19-pfb-artifacts

Artifacts for SC19 paper about PFB

genomel-dictionary

Data dictionary for GenoMEL project

Microbiome_datadictionary

New NDE Microbiome data dictionary

topmed-cwl

This is cwl pipeline for alignment potentially used for TopMed data analysis

Common Workflow Language

gen3-release-utils

Gen3 release process automation tools

dcp-demo

Jupyter notebook for GTEx and TOPMed projects at Data Commons Pilot (DCP) project

gen3-terraform

vadictionary

Data dictionary for VA Precision Oncology project

cwl.go

forked from https://github.com/otiai10/cwl.go/

flask-postgres-session

server side user session for flask app with postgres as backend

cdislogging

JCOIN_datadictionary

JCOIN Data Dictionary

bc-jupyterNotebook

Jupyter Notebook

gen3-spark

bc-cwl

Common Workflow Language

gen3utils

Utils for Gen3 commons management