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    1.3k repositories

    • hca-ingest-migration

      Public
      Working Repo for migration of HCA ingest from Dagster 0.12 to Dagster 1.8 (or 1.9)
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•0•0•1•Updated Feb 4, 2025Feb 4, 2025

    • cromwell

      Public
      Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
      dockerapplicationcloudbioinformaticsscalaexecutorhpccontainerswdlga4gh
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •359•1k•744•52•Updated Feb 4, 2025Feb 4, 2025

    • depmap-omics-long-read-rna

      Public
      Python
      •0•0•0•0•Updated Feb 4, 2025Feb 4, 2025

    • mitograph

      Public
      Rust
      •0•0•0•0•Updated Feb 4, 2025Feb 4, 2025

    • juniper

      Public
      Java
      •
      BSD 3-Clause "New" or "Revised" License
      •5•9•0•7•Updated Feb 4, 2025Feb 4, 2025

    • exome-results-browsers

      Public
      Results browsers for case-control studies of psychiatric diseases done at the Broad Institute
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •4•11•7•3•Updated Feb 4, 2025Feb 4, 2025

    • ops-terra-utils

      Public
      Python
      •0•4•0•4•Updated Feb 4, 2025Feb 4, 2025

    • gnomad_qc

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •27•69•6•13•Updated Feb 4, 2025Feb 4, 2025

    • stp_segmentation_wdl

      Public
      WDL
      •0•0•0•0•Updated Feb 4, 2025Feb 4, 2025

    • celldega

      Public
      Spatial omics analysis and visualization library
      Jupyter Notebook
      •
      Other
      •0•4•1•12•Updated Feb 4, 2025Feb 4, 2025

    • palantir-workflows

      Public
      Utility workflows for the DSP hydro.gen team (formerly palantir)
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •8•22•4•6•Updated Feb 4, 2025Feb 4, 2025

    • warp

      Public
      WDL Analysis Research Pipelines
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •100•207•8•18•Updated Feb 4, 2025Feb 4, 2025

    • depmap-portal

      Public
      Code for the DepMap portal at depmap.org
      Python
      •
      BSD 2-Clause "Simplified" License
      •1•7•0•10•Updated Feb 4, 2025Feb 4, 2025

    • long-read-pipelines

      Public
      Long read production pipelines
      pipelineswdlvariant-callingde-novo-assemblylong-reads
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •24•143•95•27•Updated Feb 4, 2025Feb 4, 2025

    • shared-workflows

      Public
      GitHub Action workflows that can be shared by multiple repositories
      BSD 3-Clause "New" or "Revised" License
      •1•0•3•0•Updated Feb 4, 2025Feb 4, 2025

    • igv.js

      Public
      Embeddable genomic visualization component based on the Integrative Genomics Viewer
      HTML
      •
      MIT License
      •232•0•0•0•Updated Feb 4, 2025Feb 4, 2025

    • BEClust3D

      Public
      Jupyter Notebook
      •
      Other
      •0•0•0•8•Updated Feb 4, 2025Feb 4, 2025

    • seqr-helm

      Public
      Helm charts for the seqr project
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•3•0•0•Updated Feb 4, 2025Feb 4, 2025

    • seqr

      Public
      web-based analysis tool for rare disease genomics
      Python
      •
      GNU Affero General Public License v3.0
      •89•182•55•4•Updated Feb 4, 2025Feb 4, 2025

    • datarepo-helm

      Public
      A helm repo for Broad Data Science Platforms helm charts
      Mustache
      •1•5•0•3•Updated Feb 4, 2025Feb 4, 2025

    • nebelung

      Public
      Python wrapper for the Firecloud API
      Python
      •0•2•0•0•Updated Feb 4, 2025Feb 4, 2025

    • dig-dug-portal

      Public
      Vue
      •
      BSD 3-Clause "New" or "Revised" License
      •1•2•0•1•Updated Feb 4, 2025Feb 4, 2025

    • gatk

      Public
      Official code repository for GATK versions 4 and up
      sciencebioinformaticsgenomicsgenomengssequencingdnasparkgatk
      Java
      •
      Other
      •597•1.8k•1.2k•137•Updated Feb 4, 2025Feb 4, 2025

    • monorepo

      Public
      Compendium of tools for the Imaging Platform
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•9•10•0•Updated Feb 4, 2025Feb 4, 2025

    • PTA_Analysis

      Public
      WDL
      •0•0•0•0•Updated Feb 4, 2025Feb 4, 2025

    • variant-curation-portal

      Public
      Web application for curating loss of function variants
      Python
      •
      MIT License
      •1•4•46•2•Updated Feb 4, 2025Feb 4, 2025

    • gatk-sv

      Public
      A structural variation pipeline for short-read sequencing
      bioinformaticsgenomicsstructural-variationstructural-variants
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •72•177•73•21•Updated Feb 4, 2025Feb 4, 2025

    • dig-bioindex

      Public
      BIO index for genetic records stored in S3 and FastAPI server.
      ot2od036440
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •6•6•0•2•Updated Feb 4, 2025Feb 4, 2025

    • tgg_methods

      Public
      Repo for miscellaneous methods developed by the methods group that don't fit anywhere else
      Python
      •
      MIT License
      •0•4•5•5•Updated Feb 4, 2025Feb 4, 2025

    • gatk-native-bindings

      Public
      GATK Native Bindings Repository
      Java
      •
      BSD 3-Clause "New" or "Revised" License
      •2•3•0•0•Updated Feb 4, 2025Feb 4, 2025