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•86•6•Updated Jan 31, 2025Jan 31, 2025

• user_workspaces_server

  Public
  Python

  •

  MIT License

  •1•0•6•1•Updated Jan 31, 2025Jan 31, 2025

• ingest-ui

  Public
  HuBMAP Data Ingest Portal

  JavaScript

  •

  MIT License

  •0•4•100•3•Updated Jan 31, 2025Jan 31, 2025

• hra-do-processor

  Public
  hra-do-processor: HRA Digital Objects Processor

  human-reference-atlas

  JavaScript

  •

  MIT License

  •0•2•9•0•Updated Jan 31, 2025Jan 31, 2025

• portal-ui

  Public
  HuBMAP Data Portal front end

  user-interfacegehlenborglabhubmap+ 1hidivelab

  TypeScript

  •

  MIT License

  •2•12•200•30•Updated Jan 31, 2025Jan 31, 2025

• documentation

  Public
  General Documentation For HuBMAP

  JavaScript

  •1•0•4•0•Updated Jan 31, 2025Jan 31, 2025

• ingest-api

  Public
  Python

  •

  MIT License

  •0•0•18•2•Updated Jan 31, 2025Jan 31, 2025

• gateway

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

  dockernginxflask+ 3docker-composeuwsgipython3

  Python

  •

  MIT License

  •0•0•6•1•Updated Jan 31, 2025Jan 31, 2025

• azimuth-annotate

  Public
  R

  •

  GNU General Public License v3.0

  •1•1•2•2•Updated Jan 31, 2025Jan 31, 2025

• hra-registrations

  Public
  Manually curated HRA Dataset Graphs

  human-reference-atlas

  HTML

  •

  MIT License

  •0•1•14•0•Updated Jan 31, 2025Jan 31, 2025

• user-templates-api

  Public
  Python

  •

  MIT License

  •3•0•3•2•Updated Jan 31, 2025Jan 31, 2025

• phenocycler-pipeline

  Public
  PhenoCycler segmentation pipeline

  Python

  •

  GNU General Public License v3.0

  •4•0•2•0•Updated Jan 31, 2025Jan 31, 2025

• entity-api

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

  Python

  •

  MIT License

  •1•3•48•1•Updated Jan 31, 2025Jan 31, 2025

• SectionAligner

  Public
  Python

  •

  GNU General Public License v3.0

  •0•1•1•0•Updated Jan 30, 2025Jan 30, 2025

• mudata-validator

  Public
  Python package to validate Anndata objects.

  Python

  •

  GNU General Public License v3.0

  •0•0•3•0•Updated Jan 30, 2025Jan 30, 2025

• portal-containers

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

  gehlenborglabhidivelab

  Python

  •

  MIT License

  •1•0•22•27•Updated Jan 29, 2025Jan 29, 2025

• ccf-validation-tools

  Public
  HRA ASCT+B Validation Reports

  human-reference-atlas

  Python

  •

  Apache License 2.0

  •1•6•4•3•Updated Jan 29, 2025Jan 29, 2025

• hubmap-ontology

  Public
  CCF Ontology v1.x

  human-reference-atlas

  Python

  •

  Creative Commons Attribution 4.0 International

  •0•3•9•1•Updated Jan 28, 2025Jan 28, 2025

• hra-kg

  Public
  HRA-KG: Human Reference Atlas Knowledge Graph

  human-reference-atlas

  Mermaid

  •

  MIT License

  •1•3•5•1•Updated Jan 28, 2025Jan 28, 2025

• ingest-pipeline

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

  Python

  •

  MIT License

  •5•4•79•17•Updated Jan 27, 2025Jan 27, 2025

• hra-hubmap-kpmp-integration

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

  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Jan 27, 2025Jan 27, 2025

• soft-assay-rules

  Public
  Rules for "soft" assay classification, and tools to generate and test them.

  Python

  •

  MIT License

  •0•0•0•1•Updated Jan 24, 2025Jan 24, 2025

• hra-workflows-runner

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

  human-reference-atlas

  JavaScript

  •

  MIT License

  •0•0•8•1•Updated Jan 24, 2025Jan 24, 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-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•9•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•4•0•Updated Jan 23, 2025Jan 23, 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

• 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