Repositories list

• hra-workflows-runner

  Public
  hra-workflows-runner: Pipeline to download, annotate, and summarize experimental data using hra-workflows

  human-reference-atlasot2od030545

  JavaScript

  •

  MIT License

  •0•0•11•2•Updated Jun 25, 2025Jun 25, 2025

• documentation

  Public
  General Documentation For HuBMAP

  ot2od030545

  JavaScript

  •1•0•5•0•Updated Jun 25, 2025Jun 25, 2025

• user_workspaces_server

  Public
  ot2od030545

  Python

  •

  MIT License

  •1•0•6•0•Updated Jun 25, 2025Jun 25, 2025

• hra-ui

  Public
  HRA UIs Monorepo (includes HRA Portal, EUI, RUI, ASCT+B Reporter, and more)

  human-reference-atlasot2od030545

  TypeScript

  •

  MIT License

  •3•5•84•5•Updated Jun 25, 2025Jun 25, 2025

• portal-ui

  Public
  HuBMAP Data Portal front end

  user-interfacehubmaphidivelab+ 1ot2od030545

  TypeScript

  •

  MIT License

  •2•13•200•21•Updated Jun 25, 2025Jun 25, 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.

  ot2od030545

  MIT License

  •0•1•1•0•Updated Jun 25, 2025Jun 25, 2025

• ingest-api

  Public
  HuBMAP Data Ingest API

  ot2od030545

  Python

  •

  MIT License

  •0•0•23•1•Updated Jun 25, 2025Jun 25, 2025

• pan-organ-azimuth-annotate

  Public
  ot2od030545

  Python

  •1•0•2•0•Updated Jun 25, 2025Jun 25, 2025

• codex-pipeline

  Public
  CODEX data processing code

  ot2od030545

  Python

  •

  GNU General Public License v3.0

  •5•12•5•2•Updated Jun 25, 2025Jun 25, 2025

• rna-data-products

  Public
  ot2od030545

  Python

  •

  GNU General Public License v3.0

  •0•1•5•0•Updated Jun 25, 2025Jun 25, 2025

• ingest-pipeline

  Public
  Data ingest pipeline(s) for QA/metadata etl/post-processing

  ot2od030545

  Python

  •

  MIT License

  •6•4•79•10•Updated Jun 25, 2025Jun 25, 2025

• ccf-validation-tools

  Public
  HRA ASCT+B Validation Reports

  human-reference-atlasot2od030545

  Python

  •

  Apache License 2.0

  •1•7•4•3•Updated Jun 25, 2025Jun 25, 2025

• stellar

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Jun 24, 2025Jun 24, 2025

• hra-kg

  Public
  Human Reference Atlas Knowledge Graph

  human-reference-atlasot2od030545

  Mermaid

  •

  MIT License

  •1•4•9•1•Updated Jun 24, 2025Jun 24, 2025

• search-python-sdk

  Public
  Python SDK to access HuBMAP Search API

  ot2od030545

  Python

  •

  MIT License

  •0•0•1•1•Updated Jun 24, 2025Jun 24, 2025

• entity-python-sdk

  Public
  Python SDK to access HuBMAP Entity API

  ot2od030545

  Python

  •

  MIT License

  •0•0•1•1•Updated Jun 24, 2025Jun 24, 2025

• scfind

  Public
  ot2od030545

  Shell

  •

  MIT License

  •0•0•0•0•Updated Jun 23, 2025Jun 23, 2025

• hra-registrations

  Public
  Manually curated HRA Dataset Graphs

  human-reference-atlasot2od030545

  HTML

  •

  MIT License

  •0•1•14•0•Updated Jun 23, 2025Jun 23, 2025

• ccf-grlc

  Public
  ccf-grlc: Useful SPARQL queries for HRA work + API via grlc.io

  human-reference-atlasot2od030545

  JavaScript

  •

  MIT License

  •1•1•3•0•Updated Jun 23, 2025Jun 23, 2025

• ingest-ui

  Public
  HuBMAP Data Ingest Portal

  ot2od030545

  JavaScript

  •

  MIT License

  •0•4•92•2•Updated Jun 23, 2025Jun 23, 2025

• sprm

  Public
  ot2od030545

  Python

  •

  GNU General Public License v3.0

  •0•4•9•1•Updated Jun 23, 2025Jun 23, 2025

• rna-probes-pipeline

  Public
  ot2od030545

  Python

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Jun 19, 2025Jun 19, 2025

• visium-pipeline

  Public
  ot2od030545

  Python

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Jun 19, 2025Jun 19, 2025

• hra-do-processor

  Public
  hra-do-processor: HRA Digital Objects Processor

  human-reference-atlasot2od030545

  JavaScript

  •

  MIT License

  •0•3•13•3•Updated Jun 18, 2025Jun 18, 2025

• commons

  Public
  The common code supporting the HuBMAP web services

  ot2od030545

  Python

  •

  MIT License

  •0•1•6•1•Updated Jun 18, 2025Jun 18, 2025

• hra-rui-locations-processor

  Public
  CLI to simplify creating rui_locations.jsonld files

  human-reference-atlasot2od030545

  JavaScript

  •

  MIT License

  •0•3•1•0•Updated Jun 18, 2025Jun 18, 2025

• segmentations

  Public
  ot2od030545

  Python

  •

  GNU General Public License v3.0

  •1•1•1•1•Updated Jun 18, 2025Jun 18, 2025

• azimuth-annotate

  Public
  ot2od030545

  R

  •

  GNU General Public License v3.0

  •1•1•2•2•Updated Jun 18, 2025Jun 18, 2025

• ingest-validation-tools

  Public
  HuBMAP data submission guidelines, and tools which check that submissions adhere to those guidelines.

  schemastandardsfair+ 3hubmaphidivelabot2od030545

  Python

  •

  MIT License

  •18•8•40•7•Updated Jun 17, 2025Jun 17, 2025

• antibody-api

  Public
  API for the Antibody DB.

  ot2od030545

  Python

  •0•0•32•9•Updated Jun 16, 2025Jun 16, 2025