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    178 repositories

    • ingest-api

      Public
      Python
      •
      MIT License
      •0•0•21•1•Updated Jan 15, 2025Jan 15, 2025

    • commons

      Public
      The common code supporting the HuBMAP web services
      Python
      •
      MIT License
      •0•1•6•1•Updated Jan 15, 2025Jan 15, 2025

    • codex-pipeline

      Public
      CODEX data processing code
      Python
      •
      GNU General Public License v3.0
      •4•11•8•2•Updated Jan 15, 2025Jan 15, 2025

    • hra-ui

      Public
      HRA UIs Monorepo (includes HRA Portal, EUI, RUI, ASCT+B Reporter, and more)
      human-reference-atlas
      TypeScript
      •
      MIT License
      •2•4•81•3•Updated Jan 14, 2025Jan 14, 2025

    • portal-ui

      Public
      HuBMAP Data Portal front end
      user-interfacegehlenborglabhubmaphidivelab
      TypeScript
      •
      MIT License
      •2•12•200•28•Updated Jan 14, 2025Jan 14, 2025

    • ingest-validation-tools

      Public
      HuBMAP data submission guidelines, and tools which check that submissions adhere to those guidelines.
      schemastandardsfairgehlenborglabhubmaphidivelab
      Python
      •
      MIT License
      •18•8•41•8•Updated Jan 14, 2025Jan 14, 2025

    • user_workspaces_server

      Public
      Python
      •
      MIT License
      •1•0•6•0•Updated Jan 14, 2025Jan 14, 2025

    • ingest-pipeline

      Public
      Data ingest pipeline(s) for QA/metadata etl/post-processing
      Python
      •
      MIT License
      •5•4•79•17•Updated Jan 14, 2025Jan 14, 2025

    • rna-probes-pipeline

      Public
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Jan 14, 2025Jan 14, 2025

    • portal-visualization

      Public
      Given HuBMAP Dataset JSON, creates a Vitessce configuration
      visualizationgehlenborglabhidivelab
      Python
      •
      MIT License
      •1•1•11•5•Updated Jan 14, 2025Jan 14, 2025

    • portal-containers

      Public
      Docker containers to pre-process data for visualization in the portal
      gehlenborglabhidivelab
      Python
      •
      MIT License
      •1•0•22•29•Updated Jan 14, 2025Jan 14, 2025

    • entity-api

      Public
      A set of web service calls to return information about HuBMAP entities
      Python
      •
      MIT License
      •1•3•50•2•Updated Jan 14, 2025Jan 14, 2025

    • hra-do-processor

      Public
      hra-do-processor: HRA Digital Objects Processor
      human-reference-atlas
      JavaScript
      •
      MIT License
      •0•2•9•0•Updated Jan 13, 2025Jan 13, 2025

    • dataset-metadata-spreadsheet

      Public
      This repository stores all the next-generation dataset metadata specification produced by the Data Coordination Working Group (DCWG). Every distinct folder corresponds to a particular assay or tissue sample used to produce the dataset.
      MIT License
      •0•1•1•0•Updated Jan 13, 2025Jan 13, 2025

    • hra-hubmap-kpmp-integration

      Public
      [WIP] repo for exploring HRA HuBMAP + KPMP Integration
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jan 13, 2025Jan 13, 2025

    • search-api

      Public
      HuBMAP search service and associated pieces to create an index
      Python
      •
      MIT License
      •2•2•20•1•Updated Jan 12, 2025Jan 12, 2025

    • visium-pipeline

      Public
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Jan 10, 2025Jan 10, 2025

    • hra-kg

      Public
      HRA-KG: Human Reference Atlas Knowledge Graph
      human-reference-atlas
      Mermaid
      •
      MIT License
      •1•2•3•0•Updated Jan 10, 2025Jan 10, 2025

    • sc-atac-seq-pipeline

      Public
      ATAC-seq pipelines for HuBMAP
      Python
      •
      MIT License
      •4•2•11•3•Updated Jan 10, 2025Jan 10, 2025

    • imc-3d-segmentation

      Public
      imc-3d-segmentation
      Python
      •
      MIT License
      •0•0•1•0•Updated Jan 10, 2025Jan 10, 2025

    • ingest-ui

      Public
      HuBMAP Data Ingest Portal
      JavaScript
      •
      MIT License
      •0•4•100•0•Updated Jan 9, 2025Jan 9, 2025

    • py-hubmapbags

      Public
      Python package used to build the submission for the CFDE Search Portal
      data-wrangling
      Jupyter Notebook
      •2•1•17•1•Updated Jan 9, 2025Jan 9, 2025

    • member-ui

      Public
      Forms and service for HuBMAP user registration and profile edit
      HTML
      •
      MIT License
      •0•0•9•2•Updated Jan 8, 2025Jan 8, 2025

    • metadata-schema-mapping

      Public
      This repository contains a collection of JSON files representing mappings between legacy schemas and updated schemas stored as CEDAR templates.
      0•0•1•0•Updated Jan 8, 2025Jan 8, 2025

    • documentation

      Public
      General Documentation For HuBMAP
      JavaScript
      •1•0•4•0•Updated Jan 8, 2025Jan 8, 2025

    • ccf-validation-tools

      Public
      HRA ASCT+B Validation Reports
      human-reference-atlas
      Python
      •
      Apache License 2.0
      •1•6•4•3•Updated Jan 8, 2025Jan 8, 2025

    • rna-data-products

      Public
      Python
      •
      GNU General Public License v3.0
      •0•0•3•0•Updated Jan 7, 2025Jan 7, 2025

    • tissue-bar-graphs

      Public
      TypeScript
      •
      MIT License
      •1•1•8•0•Updated Jan 7, 2025Jan 7, 2025

    • hra-tissue-block-annotation

      Public
      HRA Mesh Collision API
      human-reference-atlas
      C++
      •1•1•0•0•Updated Jan 7, 2025Jan 7, 2025

    • soft-assay-rules

      Public
      Rules for "soft" assay classification, and tools to generate and test them.
      Python
      •
      MIT License
      •0•0•0•2•Updated Dec 19, 2024Dec 19, 2024