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    • agora

      Public
      It's a methods repository!
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •2•11•0•2•Updated Jan 24, 2025Jan 24, 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•745•48•Updated Jan 24, 2025Jan 24, 2025

    • depmap-portal

      Public
      Code for the DepMap portal at depmap.org
      Python
      •
      BSD 2-Clause "Simplified" License
      •1•7•0•12•Updated Jan 24, 2025Jan 24, 2025

    • juniper

      Public
      Java
      •
      BSD 3-Clause "New" or "Revised" License
      •5•9•0•7•Updated Jan 24, 2025Jan 24, 2025

    • dig-dug-portal

      Public
      Vue
      •
      BSD 3-Clause "New" or "Revised" License
      •1•2•0•0•Updated Jan 24, 2025Jan 24, 2025

    • seqr

      Public
      web-based analysis tool for rare disease genomics
      Python
      •
      GNU Affero General Public License v3.0
      •89•180•54•2•Updated Jan 24, 2025Jan 24, 2025

    • gatk

      Public
      Official code repository for GATK versions 4 and up
      sciencebioinformaticsgenomicsgenomengssequencingdnasparkgatk
      Java
      •
      Other
      •597•1.8k•1.2k•137•Updated Jan 24, 2025Jan 24, 2025

    • asari

      Public
      asari, metabolomics data preprocessing
      Python
      •
      Other
      •11•0•0•0•Updated Jan 24, 2025Jan 24, 2025

    • ops-terra-utils

      Public
      Python
      •0•3•0•3•Updated Jan 24, 2025Jan 24, 2025

    • lrma-aou1-panel-creation

      Public
      Pipelines and evaluations covering integration, phasing, and imputation of short and structural variants for the AoU Phase 1 long-reads callset.
      WDL
      •0•1•22•2•Updated Jan 24, 2025Jan 24, 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 Jan 24, 2025Jan 24, 2025

    • seqr-helm

      Public
      Helm charts for the seqr project
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•0•0•Updated Jan 24, 2025Jan 24, 2025

    • gnomad-blog

      Public
      Blog for the gnomAD project
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •0•3•7•3•Updated Jan 24, 2025Jan 24, 2025

    • dcc_pigean_flask

      Public
      Flask server for the Pigean method
      Python
      •1•0•2•0•Updated Jan 24, 2025Jan 24, 2025

    • celldega

      Public
      Spatial omics analysis and visualization library
      Jupyter Notebook
      •
      Other
      •0•4•1•8•Updated Jan 24, 2025Jan 24, 2025

    • warp

      Public
      WDL Analysis Research Pipelines
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •100•207•8•18•Updated Jan 24, 2025Jan 24, 2025

    • gatk-sv

      Public
      A structural variation pipeline for short-read sequencing
      bioinformaticsgenomicsstructural-variationstructural-variants
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •72•176•74•23•Updated Jan 24, 2025Jan 24, 2025

    • rawls

      Public
      Rawls service for DSDE
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •4•26•0•10•Updated Jan 24, 2025Jan 24, 2025

    • T2T-ACE

      Public
      Accurate CNV Evaluation Using Telomere-to-Telomere Assemblies
      Jupyter Notebook
      •
      MIT License
      •0•4•1•1•Updated Jan 24, 2025Jan 24, 2025

    • gnomad-browser

      Public
      Explore gnomAD datasets on the web
      javascriptgenomicsgnomad
      TypeScript
      •
      MIT License
      •45•81•156•13•Updated Jan 24, 2025Jan 24, 2025

    • ddp-study-server

      Public
      Pepper Study Server
      Java
      •
      BSD 3-Clause "New" or "Revised" License
      •5•8•1•3•Updated Jan 24, 2025Jan 24, 2025

    • ddp-angular

      Public
      Angular code for participant-facing pepper studies
      TypeScript
      •4•3•1•32•Updated Jan 24, 2025Jan 24, 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•28•Updated Jan 24, 2025Jan 24, 2025

    • depmap_omics

      Public
      What you need to process the Quarterly DepMap-Omics releases from Terra
      data-sciencecancer-genomicscloud-computingdepmap
      HTML
      •22•114•3•3•Updated Jan 24, 2025Jan 24, 2025

    • gnomad-toolbox

      Public
      This repository provides a set of Python functions to simplify working with gnomAD Hail Tables. It includes tools for data access, filtering, and analysis.
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•0•0•Updated Jan 24, 2025Jan 24, 2025

    • gnomad_methods

      Public
      Hail helper functions for the gnomAD project and Translational Genomics Group
      genomicsgenomesexomeshail
      Python
      •
      MIT License
      •29•92•11•6•Updated Jan 24, 2025Jan 24, 2025

    • ml4h

      Public
      Python
      •
      Other
      •24•126•30•21•Updated Jan 24, 2025Jan 24, 2025

    • viral-pipelines

      Public
      viral-ngs: complete pipelines
      WDL
      •
      Other
      •28•61•23•17•Updated Jan 24, 2025Jan 24, 2025

    • gnomad_qc

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •27•69•7•11•Updated Jan 24, 2025Jan 24, 2025

    • backstage

      Public
      Broad Institute Engineering Portal is an Internal Developer Platform (Spotify Backstage by another name)
      TypeScript
      •0•2•5•4•Updated Jan 24, 2025Jan 24, 2025