Repositories list

• hra-ui

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

  human-reference-atlas

  TypeScript

  •

  MIT License

  •3•4•96•6•Updated Mar 4, 2025Mar 4, 2025

• portal-ui

  Public
  HuBMAP Data Portal front end

  user-interfacegehlenborglabhubmap+ 1hidivelab

  TypeScript

  •

  MIT License

  •2•12•200•34•Updated Mar 4, 2025Mar 4, 2025

• ccf-grlc

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

  human-reference-atlas

  JavaScript

  •

  MIT License

  •1•1•1•0•Updated Mar 4, 2025Mar 4, 2025

• hra-workflows

  Public
  hra-workflows: HRA workflows for processing experimental data

  human-reference-atlas

  Python

  •

  MIT License

  •0•0•3•0•Updated Mar 4, 2025Mar 4, 2025

• hra-registrations

  Public
  Manually curated HRA Dataset Graphs

  human-reference-atlas

  HTML

  •

  MIT License

  •0•1•14•0•Updated Mar 4, 2025Mar 4, 2025

• ingest-ui

  Public
  HuBMAP Data Ingest Portal

  JavaScript

  •

  MIT License

  •0•4•105•0•Updated Mar 4, 2025Mar 4, 2025

• phenocycler-pipeline

  Public
  PhenoCycler segmentation pipeline

  Python

  •

  GNU General Public License v3.0

  •4•0•2•0•Updated Mar 4, 2025Mar 4, 2025

• portal-visualization

  Public
  Given HuBMAP Dataset JSON, creates a Vitessce configuration

  visualizationgehlenborglabhidivelab

  Python

  •

  MIT License

  •1•1•11•5•Updated Mar 3, 2025Mar 3, 2025

• hra-rui-locations-processor

  Public
  CLI to simplify creating rui_locations.jsonld files

  human-reference-atlas

  JavaScript

  •

  MIT License

  •0•3•1•0•Updated Mar 3, 2025Mar 3, 2025

• rna-data-products

  Public
  Python

  •

  GNU General Public License v3.0

  •0•0•5•0•Updated Mar 3, 2025Mar 3, 2025

• ingest-pipeline

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

  Python

  •

  MIT License

  •5•4•79•9•Updated Feb 28, 2025Feb 28, 2025

• ingest-validation-tools

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

  schemastandardsfair+ 3gehlenborglabhubmaphidivelab

  Python

  •

  MIT License

  •18•8•41•8•Updated Feb 28, 2025Feb 28, 2025

• hra-do-processor

  Public
  hra-do-processor: HRA Digital Objects Processor

  human-reference-atlas

  JavaScript

  •

  MIT License

  •0•2•9•2•Updated Feb 28, 2025Feb 28, 2025

• data-products-ui

  Public
  JavaScript

  •0•0•7•0•Updated Feb 27, 2025Feb 27, 2025

• epic-obj-csv-to-mudata

  Public
  Python

  •

  GNU General Public License v3.0

  •0•1•4•0•Updated Feb 26, 2025Feb 26, 2025

• documentation

  Public
  General Documentation For HuBMAP

  JavaScript

  •1•0•3•0•Updated Feb 26, 2025Feb 26, 2025

• user_workspaces_server

  Public
  Python

  •

  MIT License

  •1•0•6•1•Updated Feb 26, 2025Feb 26, 2025

• ccf-validation-tools

  Public
  HRA ASCT+B Validation Reports

  human-reference-atlas

  Python

  •

  Apache License 2.0

  •1•7•4•3•Updated Feb 26, 2025Feb 26, 2025

• mudata-validator

  Public
  Python package to validate Anndata objects.

  Python

  •

  GNU General Public License v3.0

  •0•0•1•0•Updated Feb 25, 2025Feb 25, 2025

• ingest-api

  Public
  Python

  •

  MIT License

  •0•0•17•1•Updated Feb 25, 2025Feb 25, 2025

• portal-containers

  Public
  Docker containers to pre-process data for visualization in the portal

  gehlenborglabhidivelab

  Python

  •

  MIT License

  •1•0•22•27•Updated Feb 24, 2025Feb 24, 2025

• hra-hubmap-kpmp-integration

  Public
  [WIP] repo for exploring HRA HuBMAP + KPMP Integration

  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Feb 24, 2025Feb 24, 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•4•0•Updated Feb 21, 2025Feb 21, 2025

• ingest-validation-tests

  Public
  Python

  •0•0•4•2•Updated Feb 19, 2025Feb 19, 2025

• entity-api

  Public
  A set of web service calls to return information about HuBMAP entities

  Python

  •

  MIT License

  •1•3•46•1•Updated Feb 18, 2025Feb 18, 2025

• deepcelltypes

  Public
  PureBasic

  •0•0•1•0•Updated Feb 14, 2025Feb 14, 2025

• expr-h5ad-adjust

  Public
  Adjustment of `expr.h5ad` for assay differences

  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Feb 14, 2025Feb 14, 2025

• azimuth-annotate

  Public
  R

  •

  GNU General Public License v3.0

  •1•1•2•2•Updated Feb 14, 2025Feb 14, 2025

• xenium-pipeline

  Public
  Python

  •0•0•0•0•Updated Feb 14, 2025Feb 14, 2025

• user-templates-api

  Public
  Python

  •

  MIT License

  •3•0•3•2•Updated Feb 13, 2025Feb 13, 2025