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    178 repositories

    • portal-ui

      Public
      HuBMAP Data Portal front end
      user-interfacegehlenborglabhubmaphidivelab
      TypeScript
      •
      MIT License
      •2•12•200•31•Updated Jan 23, 2025Jan 23, 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 23, 2025Jan 23, 2025

    • hra-do-processor

      Public
      hra-do-processor: HRA Digital Objects Processor
      human-reference-atlas
      JavaScript
      •
      MIT License
      •0•2•10•1•Updated Jan 23, 2025Jan 23, 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 Jan 23, 2025Jan 23, 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•85•2•Updated Jan 23, 2025Jan 23, 2025

    • codex-pipeline

      Public
      CODEX data processing code
      Python
      •
      GNU General Public License v3.0
      •4•11•8•2•Updated Jan 23, 2025Jan 23, 2025

    • ingest-pipeline

      Public
      Data ingest pipeline(s) for QA/metadata etl/post-processing
      Python
      •
      MIT License
      •5•4•79•17•Updated Jan 23, 2025Jan 23, 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•9•Updated Jan 23, 2025Jan 23, 2025

    • documentation

      Public
      General Documentation For HuBMAP
      JavaScript
      •1•0•4•0•Updated Jan 23, 2025Jan 23, 2025

    • entity-api

      Public
      A set of web service calls to return information about HuBMAP entities
      Python
      •
      MIT License
      •1•3•47•2•Updated Jan 23, 2025Jan 23, 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 23, 2025Jan 23, 2025

    • user_workspaces_server

      Public
      Python
      •
      MIT License
      •1•0•6•0•Updated Jan 23, 2025Jan 23, 2025

    • ingest-ui

      Public
      HuBMAP Data Ingest Portal
      JavaScript
      •
      MIT License
      •0•4•99•0•Updated Jan 23, 2025Jan 23, 2025

    • hra-registrations

      Public
      Manually curated HRA Dataset Graphs
      human-reference-atlas
      HTML
      •
      MIT License
      •0•1•14•0•Updated Jan 22, 2025Jan 22, 2025

    • ingest-api

      Public
      Python
      •
      MIT License
      •0•0•19•1•Updated Jan 22, 2025Jan 22, 2025

    • hra_owl_query_tester

      Public
      A framework for specifying and testing queries against CCF.owl based on competency questions.
      Python
      •
      MIT License
      •0•1•1•0•Updated Jan 22, 2025Jan 22, 2025

    • ccf-validation-tools

      Public
      HRA ASCT+B Validation Reports
      human-reference-atlas
      Python
      •
      Apache License 2.0
      •1•6•4•3•Updated Jan 22, 2025Jan 22, 2025

    • gateway

      Public
      Custom gateway service with auth check for APIs and file assets not hosted with AWS API Gateway
      dockernginxflaskdocker-composeuwsgipython3
      Python
      •
      MIT License
      •0•0•6•0•Updated Jan 21, 2025Jan 21, 2025

    • hra-hubmap-kpmp-integration

      Public
      [WIP] repo for exploring HRA HuBMAP + KPMP Integration
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jan 20, 2025Jan 20, 2025

    • sra-human-scrubber

      Public
      An SRA tool that takes as input local fastq file from a clinical infection sample, identifies and removes any significant human read, and outputs the edited (cleaned) fastq file that can safely be used for SRA submission.
      Shell
      •
      Other
      •8•0•0•0•Updated Jan 17, 2025Jan 17, 2025

    • mibi-pipeline

      Public
      Forked from celldive to create new pipeline for mibi
      Python
      •
      GNU General Public License v3.0
      •4•0•0•0•Updated Jan 17, 2025Jan 17, 2025

    • hra-workflows

      Public
      hra-workflows: HRA workflows for processing experimental data
      human-reference-atlas
      Python
      •
      MIT License
      •0•0•3•0•Updated Jan 16, 2025Jan 16, 2025

    • azimuth-annotate

      Public
      R
      •
      GNU General Public License v3.0
      •1•1•2•3•Updated Jan 16, 2025Jan 16, 2025

    • expr-h5ad-adjust

      Public
      Adjustment of `expr.h5ad` for assay differences
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jan 16, 2025Jan 16, 2025

    • user-templates-api

      Public
      Python
      •
      MIT License
      •3•0•3•1•Updated Jan 16, 2025Jan 16, 2025

    • portal-visualization

      Public
      Given HuBMAP Dataset JSON, creates a Vitessce configuration
      visualizationgehlenborglabhidivelab
      Python
      •
      MIT License
      •1•1•11•4•Updated Jan 15, 2025Jan 15, 2025

    • commons

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

    • rna-probes-pipeline

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

    • search-api

      Public
      HuBMAP search service and associated pieces to create an index
      Python
      •
      MIT License
      •2•2•19•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