Repositories list

• htan2-data-model

  Public
  Data Model for HTAN Phase 2

  Python

  •

  MIT License

  •1•1•36•0•Updated Jan 23, 2026Jan 23, 2026

• htan2_project_setup

  Public
  Python

  •0•0•1•1•Updated Jan 22, 2026Jan 22, 2026

• htan_missing_manual

  Public
  The HTAN Manual

  2•1•3•0•Updated Jan 22, 2026Jan 22, 2026

• htan2-to-crdc-nextflow-uploader

  Public
  The pipeline for uploading HTAN2 data to NCI Cancer Research Data Commons (CRDC) via the General Commons (GC).

  Nextflow

  •0•0•1•0•Updated Jan 18, 2026Jan 18, 2026

• htan-portal

  Public
  The HTAN Data Portal

  cancer-genomicscancer-researchcancer-imaging

  TypeScript

  •13•10•137•13•Updated Jan 9, 2026Jan 9, 2026

• h5ad

  Public
  HTAN h5ad Validator

  Python

  •

  MIT License

  •0•0•0•0•Updated Nov 10, 2025Nov 10, 2025

• snowflake-bigquery-jobs

  Public
  Cloud Run Jobs to connect Snowflake and BigQuery

  Python

  •0•0•0•0•Updated Oct 31, 2025Oct 31, 2025

• hdash_air

  Public
  Python

  •

  MIT License

  •0•1•9•0•Updated Oct 17, 2025Oct 17, 2025

• data-models

  Public archive
  Schema.org Data Models for HTAN

  schema-orgbiothings

  HTML

  •

  MIT License

  •8•15•0•0•Updated Sep 4, 2025Sep 4, 2025

• nf-cdstransfer

  Public archive
  Nextflow pipeline to transfer data from Synapse to a CDS AWS bucket

  Nextflow

  •0•0•1•0•Updated Sep 3, 2025Sep 3, 2025

• phase2_biospecimen_data_model

  Public
  HTAN Phase 2 Biospecimen Data Model

  Python

  •0•0•0•0•Updated Aug 30, 2025Aug 30, 2025

• htan-imaging-assets-lambda

  Public template
  Lambda function to generate mapping file of HTAN imaging assets for use on portal based on s3 inventory

  Python

  •

  Apache License 2.0

  •5•0•0•0•Updated Aug 28, 2025Aug 28, 2025

• htan-artist-launcher

  Public
  Python

  •0•0•0•0•Updated Aug 28, 2025Aug 28, 2025

• Community-Notebooks

  Public
  Jupyter Notebook

  •

  Apache License 2.0

  •6•1•0•0•Updated Jul 16, 2025Jul 16, 2025

• data-release-cloud-run

  Public
  Google Cloud Run job to validate unreleased data files

  Python

  •2•1•0•1•Updated May 6, 2025May 6, 2025

• id-provenance

  Public
  Google Cloud Function to update BigQuery ID Provenance table

  HCL

  •

  MIT License

  •1•0•0•0•Updated Apr 14, 2025Apr 14, 2025

• phase2_clinical_data_model

  Public
  HTAN Phase 2 Clinical Data Model

  Python

  •0•1•0•0•Updated Apr 3, 2025Apr 3, 2025

• nf-htan-qc

  Public
  Python

  •0•0•4•1•Updated Mar 19, 2025Mar 19, 2025

• vitessce-demo-gh-pages

  Public
  JavaScript

  •0•0•0•0•Updated Feb 11, 2025Feb 11, 2025

• dbgapmonitor

  Public
  Script and action to monitor dbGaP authorized requestors

  Python

  •

  MIT License

  •0•0•1•0•Updated Feb 11, 2025Feb 11, 2025

• s3-synapse-sync

  Public
  Lambda function code to index files in S3 bucket by creating filehandles on Synapse

  Python

  •0•0•1•4•Updated Jan 17, 2025Jan 17, 2025

• data_curator_config

  Public
  Project configurations for the Data Curator App

  23•0•0•0•Updated Oct 20, 2024Oct 20, 2024

• nf-imagecleaner

  Public
  nf-imagecleaner is a Nextflow pipeline that prepares images for upload to HTAN by removing sensitive data

  Python

  •0•0•2•2•Updated Jul 4, 2024Jul 4, 2024

• channel_metadata

  Public
  Scripts and notebooks on collating, exposing and harmonising channel metadata

  Python

  •0•0•0•0•Updated May 15, 2024May 15, 2024

• bq-metadata-cloud-run

  Public
  Set up a scheduled Cloud Run job to update HTAN metadata tables in BigQuery daily.

  Python

  •1•0•1•0•Updated May 8, 2024May 8, 2024

• synapse_acl_reset

  Public
  🔥 HTAN x Synapse ACL reset

  Python

  •0•0•3•0•Updated Apr 23, 2024Apr 23, 2024

• gcs-synapse-sync

  Public
  Google Cloud Function code to index files in GC bucket by creating filehandles on Synapse, triggered by changes to bucket.

  Python

  •

  Apache License 2.0

  •1•0•0•0•Updated Apr 12, 2024Apr 12, 2024

• readthedocs

  Public
  Documentation for the ISB-CGC on Read the Docs.

  Python

  •

  Apache License 2.0

  •16•0•0•0•Updated Mar 1, 2024Mar 1, 2024

• htan-monitor

  Public
  Python

  •0•0•0•0•Updated Jan 3, 2024Jan 3, 2024

• hdash

  Public archive
  Command line tool for generating HTAN dashboard.

  Python

  •

  MIT License

  •1•1•5•2•Updated Dec 21, 2023Dec 21, 2023