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@ncihtan NCI Human Tumor Atlas Network (HTAN)

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    41 repositories

    • htan-portal

      Public
      The HTAN Data Portal
      cancer-genomicscancer-researchcancer-imaging
      TypeScript
      •11•9•128•14•Updated Oct 31, 2024Oct 31, 2024

    • htan_missing_manual

      Public
      The HTAN Manual
      JavaScript
      •1•0•0•0•Updated Oct 29, 2024Oct 29, 2024

    • htan-linkml

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 29, 2024Oct 29, 2024

    • data_curator_config

      Public
      Project configurations for the Data Curator App
      19•0•0•0•Updated Oct 20, 2024Oct 20, 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•32•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
      •26•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