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    140 repositories

    • d3b-data-transfer-pipeline

      Public
      💡 Evaluate current data transfer pipeline. Propose improvements here
      HCL
      •
      Apache License 2.0
      •0•0•8•0•Updated Nov 15, 2024Nov 15, 2024

    • OpenPedCan-analysis

      Public archive
      The analysis repository for the Open Pediatric Cancer Project
      HTML
      •
      Other
      •67•18•0•0•Updated Nov 11, 2024Nov 11, 2024

    • d3b-cli-igor

      Public
      All-purpose CLI tool for D3b Center and partner orgs
      Python
      •0•0•1•0•Updated Nov 11, 2024Nov 11, 2024

    • fw-deepliif-predict

      Public
      Flywheel gear to implement DeepLIIF for IHC images
      Python
      •0•0•0•0•Updated Nov 9, 2024Nov 9, 2024

    • d3b-tiru-flywheel-code-repo

      Public
      Flywheel SDK example scripts
      Python
      •0•0•0•0•Updated Nov 9, 2024Nov 9, 2024

    • hope-cohort-analysis

      Public
      Analysis for HOPE cohort
      HTML
      •1•3•0•0•Updated Oct 28, 2024Oct 28, 2024

    • pLGG-immune-clinicoradiomics

      Public
      Jupyter Notebook
      •
      Apache License 2.0
      •0•0•0•0•Updated Oct 28, 2024Oct 28, 2024

    • 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 Oct 24, 2024Oct 24, 2024

    • d3b-dff-cli

      Public
      the command line tool code base for d3b data file foundation
      Python
      •
      Apache License 2.0
      •0•0•0•1•Updated Oct 23, 2024Oct 23, 2024

    • peds-brain-seg-pipeline-public

      Public
      Preprocessing and automatic tumor segmentation for pediatric brain tumor subjects
      Other
      •1•2•0•1•Updated Oct 15, 2024Oct 15, 2024

    • AlleleCouNT

      Public
      Development repo for LOH
      Python
      •
      Apache License 2.0
      •0•1•1•0•Updated Oct 11, 2024Oct 11, 2024

    • d3b_cbtn_summit

      Public
      R
      •
      Apache License 2.0
      •0•0•0•0•Updated Oct 9, 2024Oct 9, 2024

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

    • fw-histoqc

      Public
      Flywheel gear that implements HistoQC package
      Python
      •0•0•0•0•Updated Oct 7, 2024Oct 7, 2024

    • Playbook-Workflow-Builder

      Public
      A repository for the Playbook Workflow Builder project.
      TypeScript
      •
      Other
      •18•0•0•2•Updated Oct 3, 2024Oct 3, 2024

    • fw-brats2024-peds-tumor-seg

      Public
      Flywheel gear to implement BraTS 2024 pediatric tumor segmentation model via AWS SageMaker endpoint
      0•0•0•0•Updated Oct 2, 2024Oct 2, 2024

    • pediatric-auto-defacer-public

      Public
      Release of pretrained pediatric de-facing model for MRI file de-identification
      Other
      •0•1•0•0•Updated Oct 2, 2024Oct 2, 2024

    • pbta-ancestry

      Public archive
      HTML
      •
      BSD 2-Clause "Simplified" License
      •1•1•0•0•Updated Oct 2, 2024Oct 2, 2024

    • pbta-tumor-evolution

      Public archive
      HTML
      •
      BSD 2-Clause "Simplified" License
      •1•0•6•2•Updated Oct 2, 2024Oct 2, 2024

    • pbta-splicing

      Public
      Splicing analysis across the PBTA
      HTML
      •1•1•1•0•Updated Oct 1, 2024Oct 1, 2024

    • annoFuse

      Public
      Filter and prioritize fusion calls
      R
      •
      Other
      •3•20•11•0•Updated Sep 30, 2024Sep 30, 2024

    • 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•2•22•0•Updated Sep 26, 2024Sep 26, 2024

    • d3b-dev-rnaseq-snv

      Public
      RNAseq SNV Calling Workflow (beta). This workflow follows the COV-IRT NASA-developed pipeline, with the exception of joint genotyping-specific params and steps.
      bioinformaticsrna-seq-pipeline
      Jupyter Notebook
      •
      Apache License 2.0
      •2•0•0•1•Updated Sep 24, 2024Sep 24, 2024

    • d3b-flywheel-warehousing

      Public
      Warehousing from flywheel
      Python
      •0•0•0•0•Updated Sep 4, 2024Sep 4, 2024

    • bixtools

      Public
      🐳 Dockerfiles for bioinformatics tools
      bioinformaticsbixdocker
      Dockerfile
      •4•15•0•0•Updated Aug 26, 2024Aug 26, 2024

    • d3b-flywheel-routine-missing-classifications

      Public
      routine QC job for data hosted on Flywheel
      Python
      •0•0•0•0•Updated Aug 21, 2024Aug 21, 2024

    • annoFuseData

      Public
      R
      •
      Other
      •0•0•0•0•Updated Aug 2, 2024Aug 2, 2024

    • fw-fsl-fast

      Public
      Flywheel gear to implement FSL's FAST tool
      Shell
      •0•0•0•0•Updated Aug 2, 2024Aug 2, 2024

    • fw-captk-preproc-zscore-norm

      Public
      Flywheel gear implementing CaPTk's Preprocessing Z-score Normalization
      Shell
      •0•0•0•0•Updated Jul 31, 2024Jul 31, 2024

    • fw-geojson2image

      Public
      Flywheel gear to create a labeled image from a QuPath GeoJSON
      Python
      •0•0•0•0•Updated Jul 31, 2024Jul 31, 2024