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    1.3k repositories

    • gatk

      Public
      Official code repository for GATK versions 4 and up
      sciencebioinformaticsgenomicsgenomengssequencingdnasparkgatk
      Java
      •
      Other
      •593•1.7k•1.2k•136•Updated Nov 19, 2024Nov 19, 2024

    • 2023_12_JUMP_data_only_vignettes

      Public
      Collection of JUMP documentation and projects for internal and public consumption
      compbioprofiling
      Python
      •1•1•11•0•Updated Nov 19, 2024Nov 19, 2024

    • dig-dug-portal

      Public
      Vue
      •
      BSD 3-Clause "New" or "Revised" License
      •1•2•0•1•Updated Nov 19, 2024Nov 19, 2024

    • depmap-portal

      Public
      Code for the DepMap portal at depmap.org
      Python
      •
      BSD 2-Clause "Simplified" License
      •1•7•0•7•Updated Nov 19, 2024Nov 19, 2024

    • depmap_omics

      Public
      What you need to process the Quarterly DepMap-Omics releases from Terra
      data-sciencecancer-genomicscloud-computingdepmap
      HTML
      •22•110•3•3•Updated Nov 19, 2024Nov 19, 2024

    • cromwell-develop

      Public
      Repository for Broad specific cromwell **configs**. For the cromwell software, see https://github.com/broadinstitute/cromwell
      Shell
      •0•1•0•1•Updated Nov 19, 2024Nov 19, 2024

    • wfl

      Public
      WorkFlow Launcher (née Zero)
      Clojure
      •
      BSD 3-Clause "New" or "Revised" License
      •0•7•0•5•Updated Nov 19, 2024Nov 19, 2024

    • juniper0

      Public
      Preliminary Version of JUNIPER: Large-Scale Outbreak Reconstruction
      R
      •
      MIT License
      •0•2•0•0•Updated Nov 19, 2024Nov 19, 2024

    • bibt-slack

      Public
      Broad Institute BITS Blue Team repository for bibt-slack PyPI library.
      Python
      •
      MIT License
      •0•0•0•8•Updated Nov 19, 2024Nov 19, 2024

    • juniper

      Public
      Java
      •
      BSD 3-Clause "New" or "Revised" License
      •5•8•0•11•Updated Nov 19, 2024Nov 19, 2024

    • 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
      •361•997•743•49•Updated Nov 19, 2024Nov 19, 2024

    • dig-aggregator-methods

      Public
      Monorepo of methods implemented for the Aggregator
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•1•0•7•Updated Nov 19, 2024Nov 19, 2024

    • datarepo-helm

      Public
      A helm repo for Broad Data Science Platforms helm charts
      Mustache
      •1•5•0•5•Updated Nov 19, 2024Nov 19, 2024

    • penyu

      Public
      Write some RDF as Turtle
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Nov 19, 2024Nov 19, 2024

    • palantir-workflows

      Public
      Utility workflows for the DSP hydro.gen team (formerly palantir)
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •8•19•4•4•Updated Nov 19, 2024Nov 19, 2024

    • sam

      Public
      workbench identity and access management
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •12•42•3•29•Updated Nov 19, 2024Nov 19, 2024

    • rawls

      Public
      Rawls service for DSDE
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •4•26•0•13•Updated Nov 19, 2024Nov 19, 2024

    • seqr

      Public
      web-based analysis tool for rare disease genomics
      Python
      •
      GNU Affero General Public License v3.0
      •89•176•57•2•Updated Nov 19, 2024Nov 19, 2024

    • gnomad-browser

      Public
      Explore gnomAD datasets on the web
      javascriptgenomicsgnomad
      TypeScript
      •
      MIT License
      •44•81•159•12•Updated Nov 19, 2024Nov 19, 2024

    • cytoskel

      Public
      Cloud infrastrcuture abstraction
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•0•1•1•Updated Nov 19, 2024Nov 19, 2024

    • picard

      Public
      A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
      Java
      •
      MIT License
      •368•984•200•17•Updated Nov 19, 2024Nov 19, 2024

    • warp

      Public
      WDL Analysis Research Pipelines
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •97•202•7•14•Updated Nov 19, 2024Nov 19, 2024

    • sherlock

      Public
      DSP DevOps's deployment source-of-truth service
      golangpostgresgorm
      Go
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•4•Updated Nov 19, 2024Nov 19, 2024

    • beehive

      Public
      Beehive is a web UI for interacting with Sherlock, DSP DevOps's deployment source-of-truth service
      remixreacttypescripttailwindcss
      TypeScript
      •
      BSD 3-Clause "New" or "Revised" License
      •1•2•0•7•Updated Nov 19, 2024Nov 19, 2024

    • seqr-loading-pipelines

      Public
      hail-based pipelines for annotating variant callsets and exporting them to elasticsearch
      Python
      •
      MIT License
      •20•22•32•3•Updated Nov 19, 2024Nov 19, 2024

    • 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•1•4•Updated Nov 19, 2024Nov 19, 2024

    • warp-tools

      Public
      This repository contains all containers that WARP uses.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•8•1•11•Updated Nov 19, 2024Nov 19, 2024

    • genetic-prevalence-estimator

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•48•0•Updated Nov 19, 2024Nov 19, 2024

    • molecular-data-provider

      Public
      Molecular Data Provider
      Python
      •
      MIT License
      •8•11•3•5•Updated Nov 19, 2024Nov 19, 2024

    • cellpainting-gallery

      Public
      Cell Painting Gallery
      MIT License
      •11•68•6•1•Updated Nov 19, 2024Nov 19, 2024