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@HumanCellAtlas Human Cell Atlas

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    121 repositories

    • 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•47•1•18•Updated Dec 26, 2024Dec 26, 2024

    • data-store

      Public
      Design specs and prototypes for the HCA Data Storage System (DSS, "blue box")
      hcaprod
      Python
      •
      Other
      •6•41•212•87•Updated Dec 26, 2024Dec 26, 2024

    • data-consumer-vignettes

      Public
      Simple walk-throughs of interacting with the DCP as a downstream data consumer.
      Jupyter Notebook
      •
      MIT License
      •5•17•25•90•Updated Dec 25, 2024Dec 25, 2024

    • matrix-service

      Public
      DCP Expression Matrix Service
      Python
      •
      MIT License
      •4•12•31•294•Updated Dec 25, 2024Dec 25, 2024

    • metadata-schema

      Public
      This repo is for the metadata schemas associated with the HCA
      Python
      •
      Apache License 2.0
      •32•65•83•51•Updated Dec 20, 2024Dec 20, 2024

    • ingest-validator-js

      Public
      Javascript validator for HCA metadata
      JavaScript
      •
      Apache License 2.0
      •6•3•1•35•Updated Dec 8, 2024Dec 8, 2024

    • lira

      Public
      Notification listener for secondary analyses
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•5•0•27•Updated Nov 4, 2024Nov 4, 2024

    • 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•125•Updated Nov 3, 2024Nov 3, 2024

    • upload-service

      Public
      DCP Ingestion File Upload Service
      Python
      •
      MIT License
      •4•4•26•203•Updated Nov 2, 2024Nov 2, 2024

    • data-monitoring-dashboard

      Public
      Python
      •1•2•9•55•Updated Nov 2, 2024Nov 2, 2024

    • data-store-scale-test

      Public
      Scalability tests for the HCA Data Storage System ("blue box")
      Python
      •
      MIT License
      •1•2•1•18•Updated Nov 1, 2024Nov 1, 2024

    • falcon

      Public
      The workflow starter of secondary analysis service
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•3•0•29•Updated Nov 1, 2024Nov 1, 2024

    • query-service

      Public
      Prototype implementation of the DCP Query Service, a metadata search engine for HCA
      sqlpostgresqlaurorajsonbhcadcpmetadata-searchhumancellatlas
      Python
      •
      MIT License
      •2•7•48•72•Updated Oct 31, 2024Oct 31, 2024

    • schema-template-generator

      Public
      Interactive UI for generating metadata schema templates
      Python
      •2•2•8•83•Updated Oct 31, 2024Oct 31, 2024

    • connexion

      Public
      Swagger/OpenAPI First framework for Python on top of Flask with automatic endpoint validation & OAuth2 support
      Python
      •
      Other
      •767•0•0•7•Updated Oct 29, 2024Oct 29, 2024

    • metadata-schema-publisher

      Public
      Script for creating a repo of schemas in response to Github commits
      Python
      •3•1•0•30•Updated Sep 6, 2024Sep 6, 2024

    • fusillade

      Public
      Federated User Identity Login & Access Decision Engine
      aws-iamaccess-decision-engine
      Python
      •
      Other
      •1•8•33•64•Updated Jul 16, 2024Jul 16, 2024

    • dcp-cli

      Public
      DEPRECATED - HCA Data Coordination Platform Command Line Interface
      Python
      •
      MIT License
      •8•6•48•10•Updated Jul 16, 2024Jul 16, 2024

    • eb-locustio-sample

      Public
      AWS Elastic Beanstalk sample code to run the load testing tool, locust.
      Python
      •
      Apache License 2.0
      •59•0•0•10•Updated Jul 16, 2024Jul 16, 2024

    • sctools

      Public
      Utilities for large scale distributed single cell data processing
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •8•24•13•26•Updated Jul 16, 2024Jul 16, 2024

    • pipeline-tools

      Public
      Pipeline-tools for HCA DCP Secondary Analyses Service
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •6•5•1•10•Updated Jul 16, 2024Jul 16, 2024

    • dcp

      Public
      Data Coordination Platform manifest and integration tests.
      Python
      •1•3•115•18•Updated Jul 16, 2024Jul 16, 2024

    • logs

      Public
      Infrastructure for centralizing and indexing logs
      Python
      •
      MIT License
      •2•2•3•144•Updated Jul 16, 2024Jul 16, 2024

    • dcp-diag

      Public
      Development and operations diagnostic tools and libraries
      Python
      •
      MIT License
      •1•2•6•25•Updated Jul 16, 2024Jul 16, 2024

    • 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•2•Updated Jul 10, 2024Jul 10, 2024

    • metadata-migration

      Public
      Proof of concept library for migrating metadata.
      Python
      •
      MIT License
      •1•0•0•13•Updated Jul 10, 2024Jul 10, 2024

    • dcp-pyjsongen

      Public
      Tools for generating random JSON data from JSON schemas.
      Python
      •
      MIT License
      •1•1•0•1•Updated Jul 10, 2024Jul 10, 2024

    • cloud-blobstore

      Public
      Simple API that abstracts out differences between the blobstores across different cloud providers.
      Python
      •
      MIT License
      •3•7•1•8•Updated Jul 10, 2024Jul 10, 2024

    • ingest-hca-to-ena

      Public
      Converts and submits HCA metadata to ENA
      Python
      •
      Apache License 2.0
      •1•0•0•5•Updated Jul 3, 2024Jul 3, 2024

    • metadata-spreadsheet-tools

      Public
      Tools for generating metadata spreadsheets
      Python
      •
      Apache License 2.0
      •1•0•1•6•Updated Jul 3, 2024Jul 3, 2024