Repositories list

• hra-ui

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

  human-reference-atlasot2od030545

  human-reference-atlasot2od030545

  TypeScript

  •

  MIT License

  •33 forks•77 stars•115115 issues•55 pull requests•Updated Apr 24, 2026Apr 24, 2026

• ingest-pipeline

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

  ot2od030545

  ot2od030545

  Python

  •

  MIT License

  •66 forks•44 stars•7979 issues•44 pull requests•Updated Apr 24, 2026Apr 24, 2026

• hra-registrations

  Public
  Manually curated HRA Dataset Graphs

  human-reference-atlasot2od030545

  human-reference-atlasot2od030545

  HTML

  •

  MIT License

  •00 forks•11 star•1616 issues•00 pull requests•Updated Apr 23, 2026Apr 23, 2026

• search-api

  Public
  HuBMAP search service and associated pieces to create an index

  ot2od030545

  ot2od030545

  Python

  •

  MIT License

  •22 forks•22 stars•1919 issues•11 pull request•Updated Apr 23, 2026Apr 23, 2026

• salmon-rnaseq

  Public
  scRNA-seq pipeline using Salmon for quantification

  ot2od030545

  ot2od030545

  Python

  •

  GNU General Public License v3.0

  •66 forks•44 stars•88 issues•55 pull requests•Updated Apr 23, 2026Apr 23, 2026

• multiome-rna-atac-pipeline

  Public
  Pipeline for unified processing of joint RNA-seq and ATAC-seq measurements for single cells

  ot2od030545

  ot2od030545

  Python

  •

  GNU General Public License v3.0

  •00 forks•00 stars•77 issues•00 pull requests•Updated Apr 23, 2026Apr 23, 2026

• spatialdata-io

  Public
  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •5858 forks•00 stars•00 issues•00 pull requests•Updated Apr 23, 2026Apr 23, 2026

• hra-kg

  Public
  Human Reference Atlas Knowledge Graph

  human-reference-atlasot2od030545

  human-reference-atlasot2od030545

  Mermaid

  •

  MIT License

  •11 fork•44 stars•1111 issues•11 pull request•Updated Apr 23, 2026Apr 23, 2026

• portal-ui

  Public
  HuBMAP Data Portal front end

  user-interfacehubmaphidivelab+ 1

  user-interfacehubmaphidivelabot2od030545

  TypeScript

  •

  MIT License

  •33 forks•1313 stars•175175 issues•1717 pull requests•Updated Apr 22, 2026Apr 22, 2026

• documentation

  Public
  General Documentation For HuBMAP

  ot2od030545

  ot2od030545

  JavaScript

  •11 fork•11 star•1313 issues•33 pull requests•Updated Apr 22, 2026Apr 22, 2026

• SectionAligner

  Public
  ot2od030545

  ot2od030545

  Python

  •

  GNU General Public License v3.0

  •00 forks•11 star•11 issue•00 pull requests•Updated Apr 22, 2026Apr 22, 2026

• hra-do-processor

  Public
  hra-do-processor: HRA Digital Objects Processor

  human-reference-atlasot2od030545

  human-reference-atlasot2od030545

  JavaScript

  •

  MIT License

  •11 fork•44 stars•1616 issues•33 pull requests•Updated Apr 22, 2026Apr 22, 2026

• ccf-validation-tools

  Public
  HRA ASCT+B Validation Reports

  human-reference-atlasot2od030545

  human-reference-atlasot2od030545

  Python

  •

  Apache License 2.0

  •11 fork•66 stars•44 issues•44 pull requests•Updated Apr 22, 2026Apr 22, 2026

• portal-containers

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

  hidivelabot2od030545

  hidivelabot2od030545

  Python

  •

  MIT License

  •11 fork•00 stars•2222 issues•2222 pull requests•Updated Apr 21, 2026Apr 21, 2026

• entity-api

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

  ot2od030545

  ot2od030545

  Python

  •

  MIT License

  •11 fork•44 stars•4343 issues•33 pull requests•Updated Apr 21, 2026Apr 21, 2026

• ingest-api

  Public
  HuBMAP Data Ingest API

  ot2od030545

  ot2od030545

  Python

  •

  MIT License

  •00 forks•00 stars•1111 issues•11 pull request•Updated Apr 21, 2026Apr 21, 2026

• gateway

  Public
  Custom gateway service with auth check for APIs and file assets not hosted with AWS API Gateway

  dockernginxflask+ 4

  dockernginxflaskdocker-composeuwsgipython3ot2od030545

  Python

  •

  MIT License

  •11 fork•00 stars•77 issues•11 pull request•Updated Apr 20, 2026Apr 20, 2026

• user_workspaces_server

  Public
  ot2od030545

  ot2od030545

  Python

  •

  MIT License

  •11 fork•00 stars•33 issues•00 pull requests•Updated Apr 20, 2026Apr 20, 2026

• phenocycler-integrated-maps

  Public
  Python

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 20, 2026Apr 20, 2026

• phenocycler-pipeline

  Public
  PhenoCycler segmentation pipeline

  ot2od030545

  ot2od030545

  Python

  •

  GNU General Public License v3.0

  •44 forks•00 stars•11 issue•00 pull requests•Updated Apr 20, 2026Apr 20, 2026

• ingest-validation-tools

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

  schemastandardsfair+ 3

  schemastandardsfairhubmaphidivelabot2od030545

  Python

  •

  MIT License

  •1818 forks•99 stars•3939 issues•44 pull requests•Updated Apr 20, 2026Apr 20, 2026

• ingest-ui

  Public
  HuBMAP Data Ingest Portal

  ot2od030545

  ot2od030545

  JavaScript

  •

  MIT License

  •00 forks•44 stars•6464 issues•00 pull requests•Updated Apr 20, 2026Apr 20, 2026

• user-templates-api

  Public
  hidivelabot2od030545

  hidivelabot2od030545

  Jupyter Notebook

  •

  MIT License

  •55 forks•00 stars•44 issues•33 pull requests•Updated Apr 17, 2026Apr 17, 2026

• commons

  Public
  The common code supporting the HuBMAP web services

  ot2od030545

  ot2od030545

  Python

  •

  MIT License

  •00 forks•11 star•66 issues•00 pull requests•Updated Apr 16, 2026Apr 16, 2026

• geomx-pipeline

  Public
  ot2od030545

  ot2od030545

  Python

  •

  MIT License

  •00 forks•00 stars•44 issues•00 pull requests•Updated Apr 16, 2026Apr 16, 2026

• pan-organ-azimuth-annotate

  Public
  ot2od030545

  ot2od030545

  Python

  •00 forks•00 stars•00 issues•11 pull request•Updated Apr 16, 2026Apr 16, 2026

• hra-workflows-runner

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

  human-reference-atlasot2od030545

  human-reference-atlasot2od030545

  JavaScript

  •

  MIT License

  •11 fork•00 stars•44 issues•00 pull requests•Updated Apr 16, 2026Apr 16, 2026

• xenium-pipeline

  Public
  ot2od030545

  ot2od030545

  Python

  •11 fork•00 stars•22 issues•00 pull requests•Updated Apr 16, 2026Apr 16, 2026

• ingest-validation-tests

  Public
  ot2od030545

  ot2od030545

  Python

  •00 forks•00 stars•44 issues•00 pull requests•Updated Apr 15, 2026Apr 15, 2026

• sprm

  Public
  ot2od030545

  ot2od030545

  Python

  •

  GNU General Public License v3.0

  •00 forks•44 stars•22 issues•11 pull request•Updated Apr 14, 2026Apr 14, 2026