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    1.3k repositories

    • rawls

      Public
      Rawls service for DSDE
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •4•26•0•13•Updated Feb 21, 2025Feb 21, 2025

    • warp

      Public
      WDL Analysis Research Pipelines
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •101•208•4•18•Updated Feb 21, 2025Feb 21, 2025

    • gnomad-browser

      Public
      Explore gnomAD datasets on the web
      javascriptgenomicsgnomad
      TypeScript
      •
      MIT License
      •46•81•163•14•Updated Feb 21, 2025Feb 21, 2025

    • hidive

      Public
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•5•1•Updated Feb 21, 2025Feb 21, 2025

    • bmxp

      Public
      The tools that constitute a nontargeted LCMS metabolomics data processing pipeline, created and used by the Broad Institute Metabolomics Platform.
      Python
      •
      Other
      •0•6•0•0•Updated Feb 21, 2025Feb 21, 2025

    • long-read-pipelines

      Public
      Long read production pipelines
      pipelineswdlvariant-callingde-novo-assemblylong-reads
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •24•144•95•26•Updated Feb 21, 2025Feb 21, 2025

    • celldega

      Public
      Spatial omics analysis and visualization library
      Jupyter Notebook
      •
      Other
      •0•5•1•12•Updated Feb 21, 2025Feb 21, 2025

    • depmap-portal

      Public
      Code for the DepMap portal at depmap.org
      Python
      •
      BSD 2-Clause "Simplified" License
      •1•7•0•5•Updated Feb 21, 2025Feb 21, 2025

    • datarepo-helm

      Public
      A helm repo for Broad Data Science Platforms helm charts
      Mustache
      •1•5•0•3•Updated Feb 21, 2025Feb 21, 2025

    • juniper

      Public
      Java
      •
      BSD 3-Clause "New" or "Revised" License
      •5•9•0•8•Updated Feb 21, 2025Feb 21, 2025

    • jump-profiling-recipe

      Public
      Workflow for processing cpg0016-jump profiles
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •8•3•9•2•Updated Feb 21, 2025Feb 21, 2025

    • anvil_tdr_ingest

      Public
      Resources related to ingesting AnVIL datasets into Terra Data Repository
      Jupyter Notebook
      •2•1•0•1•Updated Feb 21, 2025Feb 21, 2025

    • gnomad_qc

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •27•69•6•13•Updated Feb 21, 2025Feb 21, 2025

    • seqr-loading-pipelines

      Public
      hail-based pipelines for annotating variant callsets and exporting them to elasticsearch
      Python
      •
      MIT License
      •20•23•21•7•Updated Feb 21, 2025Feb 21, 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
      •360•1k•744•48•Updated Feb 21, 2025Feb 21, 2025

    • gnomad_methods

      Public
      Hail helper functions for the gnomAD project and Translational Genomics Group
      genomicsgenomesexomeshail
      Python
      •
      MIT License
      •29•93•7•8•Updated Feb 21, 2025Feb 21, 2025

    • seqr

      Public
      web-based analysis tool for rare disease genomics
      Python
      •
      GNU Affero General Public License v3.0
      •89•183•52•5•Updated Feb 21, 2025Feb 21, 2025

    • shibboleth-service-provider

      Public
      A generic Shibboleth service provider service for use in Shibboleth authentication schemes.
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •2•2•0•4•Updated Feb 21, 2025Feb 21, 2025

    • pattern-storybook

      Public
      data-visualizationstorybookjscomponents-library
      Vue
      •0•1•0•0•Updated Feb 21, 2025Feb 21, 2025

    • sam

      Public
      workbench identity and access management
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •12•42•3•28•Updated Feb 21, 2025Feb 21, 2025

    • dig-dug-portal

      Public
      Vue
      •
      BSD 3-Clause "New" or "Revised" License
      •1•2•0•0•Updated Feb 21, 2025Feb 21, 2025

    • orsp-pub

      Public
      Public ORSP Compliance Portal
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •0•3•0•25•Updated Feb 21, 2025Feb 21, 2025

    • ABC-Enhancer-Gene-Prediction

      Public
      Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)
      Python
      •
      MIT License
      •64•213•8•0•Updated Feb 21, 2025Feb 21, 2025

    • BCL-Examples

      Public
      Storehouse of Scripts to share with our API customers to assist with their interactions with BCL Orders
      Python
      •0•1•0•2•Updated Feb 21, 2025Feb 21, 2025

    • gatk

      Public
      Official code repository for GATK versions 4 and up
      sciencebioinformaticsgenomicsgenomengssequencingdnasparkgatk
      Java
      •
      Other
      •601•1.8k•1.2k•139•Updated Feb 20, 2025Feb 20, 2025

    • gatk-sv

      Public
      A structural variation pipeline for short-read sequencing
      bioinformaticsgenomicsstructural-variationstructural-variants
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •73•180•76•21•Updated Feb 20, 2025Feb 20, 2025

    • toob

      Public
      Data munging
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Feb 20, 2025Feb 20, 2025

    • single_cell_portal_core

      Public
      Rails/Docker application for the Broad Institute's single cell RNA-seq data portal
      rna-seq-analysissingle-cell-genomicshuman-cell-atlas
      Ruby
      •
      BSD 3-Clause "New" or "Revised" License
      •26•67•0•2•Updated Feb 20, 2025Feb 20, 2025

    • dsp-reusable-workflows

      Public
      publicly available reusable workflows
      Python
      •0•1•0•3•Updated Feb 20, 2025Feb 20, 2025

    • DropSift

      Public
      cell caller for sn/snRNA sequence data
      R
      •
      Other
      •0•0•0•0•Updated Feb 20, 2025Feb 20, 2025