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•116116 issues•66 pull requests•Updated May 1, 2026May 1, 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•3333 pull requests•Updated May 1, 2026May 1, 2026

• ingest-api

  Public
  HuBMAP Data Ingest API

  ot2od030545

  ot2od030545

  Python

  •

  MIT License

  •00 forks•00 stars•1010 issues•22 pull requests•Updated Apr 30, 2026Apr 30, 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 30, 2026Apr 30, 2026

• sprm

  Public
  ot2od030545

  ot2od030545

  Python

  •

  GNU General Public License v3.0

  •00 forks•44 stars•22 issues•11 pull request•Updated Apr 30, 2026Apr 30, 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 30, 2026Apr 30, 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 30, 2026Apr 30, 2026

• ingest-validation-tests

  Public
  ot2od030545

  ot2od030545

  Python

  •00 forks•00 stars•44 issues•00 pull requests•Updated Apr 30, 2026Apr 30, 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•4040 issues•22 pull requests•Updated Apr 30, 2026Apr 30, 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•33 pull requests•Updated Apr 30, 2026Apr 30, 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 29, 2026Apr 29, 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•33 pull requests•Updated Apr 29, 2026Apr 29, 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 29, 2026Apr 29, 2026

• 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 corr…

  ot2od030545

  ot2od030545

  MIT License

  •00 forks•11 star•00 issues•00 pull requests•Updated Apr 28, 2026Apr 28, 2026

• pan-organ-azimuth-annotate

  Public
  ot2od030545

  ot2od030545

  Python

  •00 forks•00 stars•00 issues•11 pull request•Updated Apr 28, 2026Apr 28, 2026

• spatialdata-io

  Public
  Python

  •

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

  •5858 forks•00 stars•00 issues•00 pull requests•Updated Apr 27, 2026Apr 27, 2026

• geomx-pipeline

  Public
  ot2od030545

  ot2od030545

  Python

  •

  MIT License

  •00 forks•00 stars•44 issues•00 pull requests•Updated Apr 27, 2026Apr 27, 2026

• documentation

  Public
  General Documentation For HuBMAP

  ot2od030545

  ot2od030545

  JavaScript

  •11 fork•11 star•1212 issues•22 pull requests•Updated Apr 27, 2026Apr 27, 2026

• user_workspaces_server

  Public
  ot2od030545

  ot2od030545

  Python

  •

  MIT License

  •11 fork•00 stars•33 issues•00 pull requests•Updated Apr 24, 2026Apr 24, 2026

• aws-api-gateway

  Public
  API definitions, Lambda functions/authorizers/layer, and documentations to work with AWS API Gateway

  ot2od030545

  ot2od030545

  Python

  •00 forks•11 star•00 issues•00 pull requests•Updated Apr 24, 2026Apr 24, 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•66 issues•11 pull request•Updated Apr 24, 2026Apr 24, 2026

• ingest-ui

  Public
  HuBMAP Data Ingest Portal

  ot2od030545

  ot2od030545

  JavaScript

  •

  MIT License

  •00 forks•44 stars•6060 issues•00 pull requests•Updated Apr 24, 2026Apr 24, 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 24, 2026Apr 24, 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 24, 2026Apr 24, 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

• 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

• 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

• 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