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    153 repositories

    • flying_nimbus

      Public
      Go
      •
      MIT License
      •0•1•5•1•Updated Apr 22, 2026Apr 22, 2026

    • peds-brain-auto-seg-public

      Public
      D3b PedsBrainAutoSeg tool (public realease)
      Python
      •
      Other
      •1•7•0•0•Updated Apr 22, 2026Apr 22, 2026

    • flywheel-soft-data-copy

      Public
      Commands to use smart-copy functionality on Flywheel
      Python
      •0•0•0•1•Updated Apr 10, 2026Apr 10, 2026

    • D3b-RADIANT-Annotation

      Public
      VCF annotation workflow for the RADIANT program
      Nextflow
      •
      Apache License 2.0
      •0•0•0•0•Updated Apr 10, 2026Apr 10, 2026

    • fw-move-session-to-proj

      Public
      Flywheel gear to move session to a destination project
      Python
      •0•0•0•0•Updated Mar 26, 2026Mar 26, 2026

    • bixtools

      Public
      🐳 Dockerfiles for bioinformatics tools
      dockerbioinformaticsbix
      dockerbioinformaticsbix
      Dockerfile
      •4•17•0•2•Updated Mar 26, 2026Mar 26, 2026

    • ambra-code

      Public
      Code examples for all things Ambra Health
      Python
      •0•0•0•0•Updated Mar 26, 2026Mar 26, 2026

    • d3b-flywheel-routine-missing-classifications

      Public
      routine QC job for data hosted on Flywheel
      Python
      •0•0•0•0•Updated Mar 13, 2026Mar 13, 2026

    • fw-d3b-ped-auto-deface

      Public
      Flywheel gear implementing pediatric defacing (model inference with pretrained weights (nnUnet))
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Mar 10, 2026Mar 10, 2026

    • d3b-api-client-cli

      Public
      👨🏻‍💻 CLI client for APIs frequently used in D3b
      Python
      •
      Apache License 2.0
      •0•0•7•3•Updated Mar 4, 2026Mar 4, 2026

    • d3b-tiru-flywheel-code-repo

      Public
      Flywheel SDK example scripts
      Python
      •0•0•0•0•Updated Feb 26, 2026Feb 26, 2026

    • annoFuse

      Public
      Filter and prioritize fusion calls
      R
      •
      Other
      •3•20•11•0•Updated Feb 24, 2026Feb 24, 2026

    • image-deid-etl

      Public
      A WIP tool to assist with reading DICOM images from Ambra/Orthanc, conversion to anonymized NIfTI images, and uploading to Flywheel.
      awsetlterraform
      awsetlterraformdicombatchnifti
      Python
      •
      Apache License 2.0
      •0•5•22•0•Updated Feb 20, 2026Feb 20, 2026

    • AlleleCouNT

      Public
      Development repo for LOH
      Python
      •
      Apache License 2.0
      •1•1•2•0•Updated Jan 23, 2026Jan 23, 2026

    • annoFuseData

      Public
      R
      •
      Other
      •0•0•0•0•Updated Jan 23, 2026Jan 23, 2026

    • d3b-flywheel-routine-empty-containers

      Public
      Routine QC job for data hosted on Flywheel
      Python
      •0•0•0•0•Updated Jan 23, 2026Jan 23, 2026

    • D3b-Pathogenicity-Assessment

      Public
      In collaboration with the Diskin lab, this repo houses a workflow designed to take in KF annotated vcf files, and further annotate for pathogenicity prediction
      Common Workflow Language
      •
      Apache License 2.0
      •2•0•1•0•Updated Jan 8, 2026Jan 8, 2026

    • fw-captk-brats-pipeline

      Public
      Flywheel gear for CaPTk-BraTSPipeline command
      Shell
      •
      Apache License 2.0
      •0•0•1•0•Updated Jan 6, 2026Jan 6, 2026

    • flywheel-sdk-gear-template

      Public
      Template for developing a Flywheel SDK gear
      Python
      •0•0•0•0•Updated Dec 16, 2025Dec 16, 2025

    • fw-fsl-slicer

      Public
      Flywheel gear for FSL slicer command
      Shell
      •0•0•0•0•Updated Dec 12, 2025Dec 12, 2025

    • fw-dynamic-range-mri

      Public
      Flywheel gear to calculate the dynamic range of an MRI
      Python
      •0•0•0•0•Updated Dec 11, 2025Dec 11, 2025

    • fw-histomicsTK-generate-tissue-mask

      Public
      Flywheel gear to generate tissue mask for WSI with HistomicsTK
      Python
      •0•0•0•0•Updated Dec 11, 2025Dec 11, 2025

    • d3b-flywheel-warehousing

      Public
      Warehousing from flywheel
      Python
      •0•0•0•0•Updated Dec 11, 2025Dec 11, 2025

    • peds-brain-seg-pipeline-public

      Public
      Preprocessing and automatic tumor segmentation for pediatric brain tumor subjects
      Other
      •1•6•0•0•Updated Oct 14, 2025Oct 14, 2025

    • INCLUDE-Ch21-Variant-Calling-Dev

      Public
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Sep 19, 2025Sep 19, 2025

    • fw-d3b-get-tumor-seg-measurements

      Public
      Flywheel gear for extracting tumor measurements from segmentation files and storing as session metadata
      Python
      •0•0•0•0•Updated Aug 8, 2025Aug 8, 2025

    • fw-captk-feature-extraction

      Public
      Flywheel gear that implements CaPTk feature extraction tool
      Shell
      •
      Apache License 2.0
      •0•0•1•0•Updated Aug 5, 2025Aug 5, 2025

    • pediatric-auto-defacer-public

      Public
      Release of pretrained pediatric de-facing model for MRI file de-identification
      Other
      •0•3•0•0•Updated Aug 1, 2025Aug 1, 2025

    • tap-jira

      Public
      Python
      •
      Other
      •28•0•0•0•Updated Jul 29, 2025Jul 29, 2025

    • celllines-profiling-analysis

      Public
      Stemness analysis in HGG Suspension vs Adhesion cell lines
      R
      •1•3•0•0•Updated Jul 29, 2025Jul 29, 2025
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