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@HumanCellAtlas Human Cell Atlas

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    121 repositories

    • upload-service

      Public
      DCP Ingestion File Upload Service
      Python
      •
      MIT License
      •4•4•26•215•Updated Jun 21, 2025Jun 21, 2025

    • data-consumer-vignettes

      Public
      Simple walk-throughs of interacting with the DCP as a downstream data consumer.
      Jupyter Notebook
      •
      MIT License
      •5•17•25•98•Updated Jun 21, 2025Jun 21, 2025

    • ingest-broker-api

      Public
      RESTful API for the Ingest Broker
      JavaScript
      •
      Apache License 2.0
      •2•0•0•2•Updated Jun 21, 2025Jun 21, 2025

    • matrix-service

      Public
      DCP Expression Matrix Service
      Python
      •
      MIT License
      •4•12•31•309•Updated Jun 21, 2025Jun 21, 2025

    • ingest-central

      Public
      Ingest Central is the hub repository for the ingest service
      Jupyter Notebook
      •
      Apache License 2.0
      •1•0•203•6•Updated Jun 21, 2025Jun 21, 2025

    • logs

      Public
      Infrastructure for centralizing and indexing logs
      Python
      •
      MIT License
      •2•2•3•153•Updated Jun 21, 2025Jun 21, 2025

    • data-store-scale-test

      Public
      Scalability tests for the HCA Data Storage System ("blue box")
      Python
      •
      MIT License
      •1•2•1•22•Updated Jun 21, 2025Jun 21, 2025

    • lira

      Public
      Notification listener for secondary analyses
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•5•0•32•Updated Jun 20, 2025Jun 20, 2025

    • dcplib

      Public
      A library of modules shared among multiple Data Coordination Platform components
      Python
      •
      MIT License
      •4•4•8•1•Updated Jun 20, 2025Jun 20, 2025

    • matrix_semantic_map

      Public
      Specification for a JSON schema to map expression matrix annotations to ontology terms
      Python
      •
      Apache License 2.0
      •2•1•1•3•Updated Jun 20, 2025Jun 20, 2025

    • schema-template-generator

      Public
      Interactive UI for generating metadata schema templates
      Python
      •2•2•8•86•Updated Jun 20, 2025Jun 20, 2025

    • ingest-staging-manager

      Public
      Client for handling the creation of staging areas triggered by the ingest service
      Python
      •
      Apache License 2.0
      •1•0•0•2•Updated Jun 20, 2025Jun 20, 2025

    • data-monitoring-dashboard

      Public
      Python
      •1•2•9•59•Updated Jun 20, 2025Jun 20, 2025

    • falcon

      Public
      The workflow starter of secondary analysis service
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•3•0•32•Updated Jun 20, 2025Jun 20, 2025

    • query-service

      Public
      Prototype implementation of the DCP Query Service, a metadata search engine for HCA
      sqlpostgresqlaurorajsonbhcadcpmetadata-searchhumancellatlas
      Python
      •
      MIT License
      •2•7•48•76•Updated Jun 20, 2025Jun 20, 2025

    • secondary-analysis

      Public
      Secondary Analysis Service of the Human Cell Atlas Data Coordination Platform
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•3•124•136•Updated Jun 20, 2025Jun 20, 2025

    • dcp-cli

      Public
      DEPRECATED - HCA Data Coordination Platform Command Line Interface
      Python
      •
      MIT License
      •7•6•48•12•Updated Jun 20, 2025Jun 20, 2025

    • connexion

      Public
      Swagger/OpenAPI First framework for Python on top of Flask with automatic endpoint validation & OAuth2 support
      Python
      •
      Other
      •772•0•0•9•Updated Jun 20, 2025Jun 20, 2025

    • metadata-schema

      Public
      This repo is for the metadata schemas associated with the HCA
      Python
      •
      Apache License 2.0
      •32•67•85•52•Updated Jun 18, 2025Jun 18, 2025

    • bronze

      Public
      A minimal alarm that reads data from Google Sheets and alerts people via Slack
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•2•1•2•Updated Jun 16, 2025Jun 16, 2025

    • sctools

      Public
      Utilities for large scale distributed single cell data processing
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •8•24•13•28•Updated Jun 12, 2025Jun 12, 2025

    • dcp-diag

      Public
      Development and operations diagnostic tools and libraries
      Python
      •
      MIT License
      •1•2•6•27•Updated Jun 12, 2025Jun 12, 2025

    • metadata-migration

      Public
      Proof of concept library for migrating metadata.
      Python
      •
      MIT License
      •1•0•0•14•Updated Jun 12, 2025Jun 12, 2025

    • data-store

      Public
      Design specs and prototypes for the HCA Data Storage System (DSS, "blue box")
      hcaprod
      Python
      •
      Other
      •6•41•212•89•Updated Jun 12, 2025Jun 12, 2025

    • ingest-fastq-validator

      Public
      Python
      •
      Apache License 2.0
      •1•0•0•13•Updated Jun 10, 2025Jun 10, 2025

    • fusillade

      Public
      Federated User Identity Login & Access Decision Engine
      aws-iamaccess-decision-engine
      Python
      •
      Other
      •1•8•33•67•Updated Jun 10, 2025Jun 10, 2025

    • ingest-validator-js

      Public
      Javascript validator for HCA metadata
      JavaScript
      •
      Apache License 2.0
      •6•3•1•36•Updated May 30, 2025May 30, 2025

    • dcp

      Public
      Data Coordination Platform manifest and integration tests.
      Python
      •1•3•115•19•Updated May 7, 2025May 7, 2025

    • skylab

      Public
      Soon to be deprecated in favor of broadinstitute/warp github repo. Previously: Secondary analysis pipelines
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •34•48•1•19•Updated Mar 13, 2025Mar 13, 2025

    • dcp2

      Public
      Shared artifacts concerning the Human Cell Atlas (HCA) Data Coordination Platform (DCP)
      boardwalk
      2•4•4•0•Updated Feb 26, 2025Feb 26, 2025