Repositories list

• portal-ui

  Public
  HuBMAP Data Portal front end

  user-interfacegehlenborglabhubmap+ 1hidivelab

  TypeScript

  •

  MIT License

  •2•12•200•28•Updated Oct 31, 2024Oct 31, 2024

• hra-kg

  Public
  HRA-KG: Human Reference Atlas Knowledge Graph

  human-reference-atlas

  Mermaid

  •

  MIT License

  •1•3•3•1•Updated Oct 31, 2024Oct 31, 2024

• hra-ui

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

  human-reference-atlas

  TypeScript

  •

  MIT License

  •2•4•100•3•Updated Oct 31, 2024Oct 31, 2024

• xenium-pipeline

  Public
  0•0•0•0•Updated Oct 31, 2024Oct 31, 2024

• portal-containers

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

  gehlenborglabhidivelab

  Python

  •

  MIT License

  •1•0•22•28•Updated Oct 31, 2024Oct 31, 2024

• codex-data-products

  Public
  Data product creation for HIVE processed CODEX datasets

  Python

  •0•0•1•0•Updated Oct 31, 2024Oct 31, 2024

• rna-data-products

  Public
  Python

  •

  GNU General Public License v3.0

  •0•0•3•0•Updated Oct 31, 2024Oct 31, 2024

• ingest-api

  Public
  Python

  •

  MIT License

  •0•0•19•1•Updated Oct 30, 2024Oct 30, 2024

• hra-do-processor

  Public
  hra-do-processor: HRA Digital Objects Processor

  human-reference-atlas

  JavaScript

  •

  MIT License

  •0•1•4•0•Updated Oct 30, 2024Oct 30, 2024

• py-hubmapbags

  Public
  Python package used to build the submission for the CFDE Search Portal

  data-wrangling

  Jupyter Notebook

  •2•1•20•3•Updated Oct 30, 2024Oct 30, 2024

• azimuth-annotate

  Public
  R

  •

  GNU General Public License v3.0

  •1•1•2•2•Updated Oct 30, 2024Oct 30, 2024

• ingest-pipeline

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

  Python

  •

  MIT License

  •5•4•79•14•Updated Oct 30, 2024Oct 30, 2024

• segmentations

  Public
  Python

  •

  GNU General Public License v3.0

  •1•1•1•0•Updated Oct 30, 2024Oct 30, 2024

• documentation

  Public
  General Documentation For HuBMAP

  JavaScript

  •1•0•1•0•Updated Oct 30, 2024Oct 30, 2024

• entity-api

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

  Python

  •

  MIT License

  •1•3•54•1•Updated Oct 30, 2024Oct 30, 2024

• ccf-validation-tools

  Public
  HRA ASCT+B Validation Reports

  human-reference-atlas

  Python

  •

  Apache License 2.0

  •1•6•4•3•Updated Oct 30, 2024Oct 30, 2024

• search-api

  Public
  HuBMAP search service and associated pieces to create an index

  Python

  •

  MIT License

  •2•2•46•1•Updated Oct 29, 2024Oct 29, 2024

• portal-visualization

  Public
  Given HuBMAP Dataset JSON, creates a Vitessce configuration

  visualizationgehlenborglabhidivelab

  Python

  •

  MIT License

  •1•1•11•4•Updated Oct 29, 2024Oct 29, 2024

• 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 Oct 29, 2024Oct 29, 2024

• user_workspaces_server

  Public
  Python

  •

  MIT License

  •1•0•6•0•Updated Oct 28, 2024Oct 28, 2024

• 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•42•8•Updated Oct 28, 2024Oct 28, 2024

• hra-registrations

  Public
  Manually curated HRA Dataset Graphs

  human-reference-atlas

  HTML

  •

  MIT License

  •0•1•13•0•Updated Oct 28, 2024Oct 28, 2024

• dataset-metadata-spreadsheet

  Public
  MIT License

  •0•1•2•0•Updated Oct 28, 2024Oct 28, 2024

• hra-tissue-block-annotation

  Public
  HRA Mesh Collision API

  human-reference-atlas

  C++

  •1•0•0•0•Updated Oct 28, 2024Oct 28, 2024

• phenocycler-pipeline

  Public
  PhenoCycler segmentation pipeline

  Python

  •

  GNU General Public License v3.0

  •4•0•2•0•Updated Oct 28, 2024Oct 28, 2024

• user-templates-api

  Public
  Python

  •

  MIT License

  •2•0•2•1•Updated Oct 28, 2024Oct 28, 2024

• ingest-ui

  Public
  HuBMAP Data Ingest Portal

  JavaScript

  •

  MIT License

  •0•4•94•0•Updated Oct 28, 2024Oct 28, 2024

• gateway

  Public
  dockernginxflask+ 3docker-composeuwsgipython3

  Python

  •

  MIT License

  •0•0•12•1•Updated Oct 26, 2024Oct 26, 2024

• ingest-validation-tests

  Public
  Python

  •0•0•4•2•Updated Oct 25, 2024Oct 25, 2024

• epic-obj-csv-to-mudata

  Public
  Python

  •

  GNU General Public License v3.0

  •0•1•4•0•Updated Oct 25, 2024Oct 25, 2024