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    149 repositories

    • 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•2•0•0•Updated Aug 1, 2025Aug 1, 2025

    • d3b-flywheel-routine-empty-containers

      Public
      Routine QC job for data hosted on Flywheel
      Python
      •0•0•0•0•Updated Jul 30, 2025Jul 30, 2025

    • image-deid-etl

      Public
      A WIP tool to assist with reading DICOM images from Orthanc, conversion to anonymized NIfTI images, and uploading to Flywheel.
      awsetlterraformdicombatchnifti
      Python
      •
      Apache License 2.0
      •0•5•22•0•Updated Jul 30, 2025Jul 30, 2025

    • tap-jira

      Public
      Python
      •
      Other
      •26•0•0•0•Updated Jul 29, 2025Jul 29, 2025

    • celllines-profiling-analysis

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

    • fw-move-session-to-proj

      Public
      Flywheel gear to move session to a destination project
      Python
      •0•0•0•0•Updated Jul 11, 2025Jul 11, 2025

    • bixtools

      Public
      🐳 Dockerfiles for bioinformatics tools
      bioinformaticsbixdocker
      Dockerfile
      •4•17•0•0•Updated Jul 10, 2025Jul 10, 2025

    • terraform-aws-vpc

      Public
      A Terraform module to create anAmazon Web Services (AWS) Virtual Private Cloud (VPC).
      awsterraformvpcamazon-web-servicesterraform-modules
      HCL
      •0•0•0•1•Updated Jul 10, 2025Jul 10, 2025

    • OpenPedCan-analysis

      Public
      The analysis repository for the Open Pediatric Cancer Project
      HTML
      •
      Other
      •84•23•3•0•Updated Jul 9, 2025Jul 9, 2025

    • fw-binarize-image

      Public
      Flywheel gear for binarizing an image
      Python
      •0•0•0•0•Updated Jul 7, 2025Jul 7, 2025

    • fw-skullstrip-normalize

      Public
      Flywheel gear for running skull stripping & z-score normalization
      Python
      •0•0•0•0•Updated Jul 7, 2025Jul 7, 2025

    • fw-unify-masks

      Public
      Flywheel gear to combine two mask files.
      Python
      •0•0•0•0•Updated Jul 7, 2025Jul 7, 2025

    • fw-d3b-convert-nii2dcm

      Public
      Flywheel curation gear to be run at the project-level
      Python
      •
      MIT License
      •0•0•0•0•Updated Jul 1, 2025Jul 1, 2025

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

      Public
      Flywheel gear to extract tumor measurements from segmentation file
      0•0•0•0•Updated Jun 25, 2025Jun 25, 2025

    • INCLUDE-Ch21-Variant-Calling-Dev

      Public
      Common Workflow Language
      •
      Apache License 2.0
      •0•0•0•0•Updated Jun 3, 2025Jun 3, 2025

    • hope-cohort-analysis

      Public
      Analysis for HOPE cohort
      HTML
      •1•3•1•1•Updated May 9, 2025May 9, 2025

    • fw-captk-preproc-zscore-norm

      Public
      Flywheel gear implementing CaPTk's Preprocessing Z-score Normalization
      Shell
      •0•0•0•0•Updated Apr 15, 2025Apr 15, 2025

    • fw-gear-extract-slide-metadata

      Public
      Flywheel gear to extract pathology slide metadata using OpenSlide
      Python
      •0•0•1•0•Updated Apr 11, 2025Apr 11, 2025

    • d3b-tiru-flywheel-code-repo

      Public
      Flywheel SDK example scripts
      Python
      •0•0•0•0•Updated Apr 7, 2025Apr 7, 2025

    • D3b-Pathogenicity-Preprocessing

      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
      •1•0•0•0•Updated Apr 2, 2025Apr 2, 2025

    • nextflow-pilot

      Public
      Nextflow
      •0•0•0•1•Updated Mar 31, 2025Mar 31, 2025

    • fw-prov-gigapath-extract-tile-embeds

      Public
      Flywheel gear to extract tile embeddings using pretrained Prov-Gigapath model (H&E slides)
      Jupyter Notebook
      •0•0•0•0•Updated Mar 20, 2025Mar 20, 2025

    • d3b-api-client-cli

      Public
      👨🏻‍💻 CLI client for APIs frequently used in D3b
      Python
      •
      Apache License 2.0
      •0•0•7•0•Updated Mar 3, 2025Mar 3, 2025

    • d3b-dff-cli

      Public
      the command line tool code base for d3b data file foundation
      Python
      •
      Apache License 2.0
      •0•0•1•1•Updated Feb 27, 2025Feb 27, 2025

    • peds-brain-auto-skull-strip

      Public
      Docker for automated skull stripping for pediatric brain tumor subjects
      Other
      •0•0•1•0•Updated Feb 26, 2025Feb 26, 2025

    • peds-brain-auto-seg-public

      Public
      D3b PedsBrainAutoSeg tool (public realease)
      Other
      •0•7•0•0•Updated Feb 26, 2025Feb 26, 2025

    • peds-brain-seg-pipeline-public

      Public
      Preprocessing and automatic tumor segmentation for pediatric brain tumor subjects
      Other
      •1•4•0•0•Updated Feb 26, 2025Feb 26, 2025

    • d3b-warehouse-redcap

      Public
      🏭 D3b Warehouse Pipeline for REDCap
      Python
      •0•0•1•0•Updated Feb 25, 2025Feb 25, 2025

    • d3b-release-maker

      Public
      🛠 Tool to generate GitHub-based software releases with semantic versioning tags
      Python
      •
      Apache License 2.0
      •1•0•1•1•Updated Jan 17, 2025Jan 17, 2025