Repositories list

• xenium-pipeline

  Public
  Common Workflow Language

  •0•0•0•0•Updated Nov 15, 2024Nov 15, 2024

• ingest-pipeline

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

  Python

  •

  MIT License

  •5•4•79•16•Updated Nov 15, 2024Nov 15, 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•105•6•Updated Nov 15, 2024Nov 15, 2024

• ingest-validation-tests

  Public
  Python

  •0•0•4•1•Updated Nov 15, 2024Nov 15, 2024

• soft-assay-rules

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

  Python

  •

  MIT License

  •0•0•0•2•Updated Nov 15, 2024Nov 15, 2024

• hra-do-processor

  Public
  hra-do-processor: HRA Digital Objects Processor

  human-reference-atlas

  JavaScript

  •

  MIT License

  •0•1•4•1•Updated Nov 14, 2024Nov 14, 2024

• multiome-data-products

  Public
  Python

  •0•0•0•0•Updated Nov 14, 2024Nov 14, 2024

• portal-ui

  Public
  HuBMAP Data Portal front end

  user-interfacegehlenborglabhubmap+ 1hidivelab

  TypeScript

  •

  MIT License

  •2•12•201•31•Updated Nov 14, 2024Nov 14, 2024

• kaggle-2-segmentation

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Nov 14, 2024Nov 14, 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•41•8•Updated Nov 14, 2024Nov 14, 2024

• user_workspaces_server

  Public
  Python

  •

  MIT License

  •1•0•6•0•Updated Nov 14, 2024Nov 14, 2024

• member-ui

  Public
  Forms and service for HuBMAP user registration and profile edit

  HTML

  •

  MIT License

  •0•0•11•2•Updated Nov 14, 2024Nov 14, 2024

• rna-data-products

  Public
  Python

  •

  GNU General Public License v3.0

  •0•0•3•0•Updated Nov 14, 2024Nov 14, 2024

• py-hubmapbags

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

  data-wrangling

  Jupyter Notebook

  •2•1•20•2•Updated Nov 13, 2024Nov 13, 2024

• portal-containers

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

  gehlenborglabhidivelab

  Python

  •

  MIT License

  •1•0•22•27•Updated Nov 13, 2024Nov 13, 2024

• portal-visualization

  Public
  Given HuBMAP Dataset JSON, creates a Vitessce configuration

  visualizationgehlenborglabhidivelab

  Python

  •

  MIT License

  •1•1•11•4•Updated Nov 13, 2024Nov 13, 2024

• gateway

  Public
  dockernginxflask+ 3docker-composeuwsgipython3

  Python

  •

  MIT License

  •0•0•12•2•Updated Nov 13, 2024Nov 13, 2024

• ingest-api

  Public
  Python

  •

  MIT License

  •0•0•19•2•Updated Nov 13, 2024Nov 13, 2024

• ccf-validation-tools

  Public
  HRA ASCT+B Validation Reports

  human-reference-atlas

  Python

  •

  Apache License 2.0

  •1•6•4•3•Updated Nov 13, 2024Nov 13, 2024

• documentation

  Public
  General Documentation For HuBMAP

  JavaScript

  •1•0•3•0•Updated Nov 12, 2024Nov 12, 2024

• pas-ftu-segmentation-pipeline

  Public
  Python

  •

  MIT License

  •0•0•3•0•Updated Nov 12, 2024Nov 12, 2024

• hra-registrations

  Public
  Manually curated HRA Dataset Graphs

  human-reference-atlas

  HTML

  •

  MIT License

  •0•1•13•0•Updated Nov 11, 2024Nov 11, 2024

• 3DCellComposer

  Public
  3DCellComposer - A Versatile Pipeline Utilizing 2D Cell Segmentation Methods for 3D Cell Segmentation

  Python

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Nov 11, 2024Nov 11, 2024

• data-products-ui

  Public
  JavaScript

  •0•0•8•0•Updated Nov 11, 2024Nov 11, 2024

• imc-3d-segmentation

  Public
  imc-3d-segmentation

  Python

  •

  MIT License

  •0•0•1•0•Updated Nov 8, 2024Nov 8, 2024

• deepcelltypes

  Public
  PureBasic

  •0•0•1•0•Updated Nov 8, 2024Nov 8, 2024

• search-api

  Public
  HuBMAP search service and associated pieces to create an index

  Python

  •

  MIT License

  •2•2•44•1•Updated Nov 8, 2024Nov 8, 2024

• sprm

  Public
  Python

  •

  GNU General Public License v3.0

  •0•4•9•1•Updated Nov 8, 2024Nov 8, 2024

• hra-kg

  Public
  HRA-KG: Human Reference Atlas Knowledge Graph

  human-reference-atlas

  Mermaid

  •

  MIT License

  •1•3•3•1•Updated Nov 7, 2024Nov 7, 2024

• entity-api

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

  Python

  •

  MIT License

  •1•3•55•1•Updated Nov 7, 2024Nov 7, 2024