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    1.3k repositories

    • depmap-portal

      Public
      Code for the DepMap portal at depmap.org
      Python
      •
      BSD 2-Clause "Simplified" License
      •1•7•0•4•Updated Nov 7, 2024Nov 7, 2024

    • ddp-study-server

      Public
      Pepper Study Server
      Java
      •
      BSD 3-Clause "New" or "Revised" License
      •5•8•1•4•Updated Nov 7, 2024Nov 7, 2024

    • stp_segmentation_wdl

      Public
      WDL
      •0•0•0•0•Updated Nov 7, 2024Nov 7, 2024

    • long-read-pipelines

      Public
      Long read production pipelines
      pipelineswdlvariant-callingde-novo-assemblylong-reads
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •25•141•95•26•Updated Nov 7, 2024Nov 7, 2024

    • gatk

      Public
      Official code repository for GATK versions 4 and up
      sciencebioinformaticsgenomicsgenomengssequencingdnasparkgatk
      Java
      •
      Other
      •591•1.7k•1.2k•141•Updated Nov 7, 2024Nov 7, 2024

    • seqr

      Public
      web-based analysis tool for rare disease genomics
      Python
      •
      GNU Affero General Public License v3.0
      •89•176•49•4•Updated Nov 6, 2024Nov 6, 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 6, 2024Nov 6, 2024

    • thurloe

      Public
      A simple service to store arbitrary key/value pairs
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •0•3•0•23•Updated Nov 6, 2024Nov 6, 2024

    • sam

      Public
      workbench identity and access management
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •12•42•3•46•Updated Nov 6, 2024Nov 6, 2024

    • firecloud-orchestration

      Public
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •4•31•0•1•Updated Nov 6, 2024Nov 6, 2024

    • carpenter-singh-lab-standards

      Public
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•1•Updated Nov 6, 2024Nov 6, 2024

    • viral-pipelines

      Public
      viral-ngs: complete pipelines
      WDL
      •
      Other
      •28•60•23•15•Updated Nov 6, 2024Nov 6, 2024

    • epi-SHARE-seq-pipeline

      Public
      Epigenomics Program pipeline to analyze SHARE-seq data.
      WDL
      •
      MIT License
      •3•17•28•1•Updated Nov 6, 2024Nov 6, 2024

    • warp

      Public
      WDL Analysis Research Pipelines
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •96•202•6•24•Updated Nov 6, 2024Nov 6, 2024

    • ops-terra-utils

      Public
      Python
      •0•2•0•1•Updated Nov 6, 2024Nov 6, 2024

    • rawls

      Public
      Rawls service for DSDE
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •4•26•0•23•Updated Nov 6, 2024Nov 6, 2024

    • submissions

      Public
      Python
      •0•1•0•1•Updated Nov 6, 2024Nov 6, 2024

    • juniper

      Public
      Java
      •
      BSD 3-Clause "New" or "Revised" License
      •5•8•0•7•Updated Nov 6, 2024Nov 6, 2024

    • seqr-loading-pipelines

      Public
      hail-based pipelines for annotating variant callsets and exporting them to elasticsearch
      Python
      •
      MIT License
      •20•22•31•2•Updated Nov 6, 2024Nov 6, 2024

    • backstage

      Public
      Broad Institute Engineering Portal is an Internal Developer Platform (Spotify Backstage by another name)
      TypeScript
      •0•2•0•4•Updated Nov 6, 2024Nov 6, 2024

    • dsp-reusable-workflows

      Public
      publicly available reusable workflows
      Python
      •0•0•0•3•Updated Nov 6, 2024Nov 6, 2024

    • g2papi

      Public
      Python
      •
      MIT License
      •0•3•1•0•Updated Nov 6, 2024Nov 6, 2024

    • monorepo

      Public
      Compendium of tools for the Imaging Platform
      Python
      •1•9•6•2•Updated Nov 6, 2024Nov 6, 2024

    • 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•62•0•1•Updated Nov 6, 2024Nov 6, 2024

    • scp-ingest-pipeline

      Public
      File Ingest Pipeline for Single Cell Portal
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•5•0•0•Updated Nov 6, 2024Nov 6, 2024

    • seqr-helm

      Public
      Helm charts for the seqr project
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•0•2•Updated Nov 6, 2024Nov 6, 2024

    • SpliceAI-lookup

      Public
      Website for checking SpliceAI and Pangolin scores:
      pangolinspliceai
      Python
      •
      MIT License
      •7•19•2•0•Updated Nov 6, 2024Nov 6, 2024

    • workbench-libs

      Public
      Workbench utility libraries
      Scala
      •
      Other
      •4•8•0•2•Updated Nov 6, 2024Nov 6, 2024

    • puppet-qualys_agent

      Public
      Puppet module for installing and configuring the Qualys Cloud Agent
      Ruby
      •
      BSD 3-Clause "New" or "Revised" License
      •9•3•2•0•Updated Nov 6, 2024Nov 6, 2024

    • genetic-prevalence-estimator

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•46•1•Updated Nov 6, 2024Nov 6, 2024