Repositories list

• htan-portal

  Public
  The HTAN Data Portal

  cancer-genomicscancer-researchcancer-imaging

  TypeScript

  •11•9•130•11•Updated Oct 18, 2024Oct 18, 2024

• data_curator_config

  Public
  Project configurations for the Data Curator App

  18•0•0•1•Updated Oct 18, 2024Oct 18, 2024

• htan_missing_manual

  Public
  The HTAN Manual

  JavaScript

  •1•0•1•0•Updated Oct 18, 2024Oct 18, 2024

• htan2_project_setup

  Public
  Python

  •0•0•0•0•Updated Oct 15, 2024Oct 15, 2024

• hdash_air

  Public
  Python

  •

  MIT License

  •0•0•8•0•Updated Oct 2, 2024Oct 2, 2024

• data-models

  Public
  Schema.org Data Models for HTAN

  schema-orgbiothings

  HTML

  •

  MIT License

  •7•14•31•1•Updated Sep 11, 2024Sep 11, 2024

• nf-cdstransfer

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

  Nextflow

  •0•0•0•0•Updated Aug 29, 2024Aug 29, 2024

• data-release-cloud-run

  Public
  Google Cloud Run job to validate unreleased data files

  Python

  •1•0•0•1•Updated Jul 23, 2024Jul 23, 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

• Community-Notebooks

  Public
  Jupyter Notebook

  •

  Apache License 2.0

  •2•0•0•0•Updated May 14, 2024May 14, 2024

• dbgapmonitor

  Public
  Script and action to monitor dbGaP authorized requestors

  Python

  •

  MIT License

  •0•0•0•0•Updated May 10, 2024May 10, 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

• id-provenance

  Public
  Google Cloud Function to update BigQuery ID Provenance table

  HCL

  •

  MIT License

  •1•0•0•0•Updated Apr 19, 2024Apr 19, 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
  Command line tool for generating HTAN dashboard.

  Python

  •

  MIT License

  •1•0•4•2•Updated Dec 21, 2023Dec 21, 2023

• schema_visualization

  Public
  This repository is for extracting D3 and Javascript code from observable to produce schema visualization

  JavaScript

  •6•0•0•0•Updated Nov 29, 2023Nov 29, 2023

• nf-vectra-to-htan

  Public
  A NextFlow workflow to prepare Vectra mIF qptiff files for the HTAN DCC

  Nextflow

  •

  MIT License

  •1•2•1•0•Updated Oct 12, 2023Oct 12, 2023

• htan-orator

  Public
  Natural language descriptions of HTAN metadata

  Python

  •1•0•1•0•Updated Aug 18, 2023Aug 18, 2023

• HTAN-data-curator

  Public
  HTAN Data Ingest Shiny App

  R

  •

  Apache License 2.0

  •21•1•9•0•Updated Aug 2, 2023Aug 2, 2023

• HTAN-Data-Ingress-Docs-ARCHIVED

  Public archive
  A draft of the HTAN dataset ingress workflow - to share with tester teams and early adopters.

  10•0•5•0•Updated Jul 24, 2023Jul 24, 2023

• schematic

  Public
  Package for biomedical data model and data ingress management

  Python

  •

  MIT License

  •25•1•0•1•Updated Apr 12, 2023Apr 12, 2023

• mcmicro

  Public
  Multiple-choice microscopy pipeline

  Nextflow

  •

  MIT License

  •58•0•0•0•Updated Apr 6, 2023Apr 6, 2023

• scn2ometiff

  Public
  Shell

  •1•0•1•0•Updated Feb 16, 2023Feb 16, 2023

• dsa-htan

  Public
  Analytics and Integration Scripts for Digital Slide Integration with Synapse for the Human Tumor Atlas Network (HTAN)

  Jupyter Notebook

  •0•1•0•24•Updated Jan 6, 2023Jan 6, 2023

• synapsemonitor

  Public
  Enable monitoring of updates or newly created entities in Synapse

  Python

  •

  Apache License 2.0

  •4•0•0•0•Updated Dec 8, 2022Dec 8, 2022

• htan-artist

  Public
  A NextFlow pipeline to run image rendering process to generate resources for the HTAN Portal.

  Nextflow

  •4•0•0•0•Updated Dec 7, 2022Dec 7, 2022