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    • seqr

      Public
      web-based analysis tool for rare disease genomics
      Python
      •
      GNU Affero General Public License v3.0
      •89•176•53•2•Updated Nov 22, 2024Nov 22, 2024

    • gatk

      Public
      Official code repository for GATK versions 4 and up
      sciencebioinformaticsgenomicsgenomengssequencingdnasparkgatk
      Java
      •
      Other
      •594•1.7k•1.2k•137•Updated Nov 22, 2024Nov 22, 2024

    • seqr-helm

      Public
      Helm charts for the seqr project
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•0•1•Updated Nov 22, 2024Nov 22, 2024

    • seqr-loading-pipelines

      Public
      hail-based pipelines for annotating variant callsets and exporting them to elasticsearch
      Python
      •
      MIT License
      •20•22•31•4•Updated Nov 22, 2024Nov 22, 2024

    • juniper

      Public
      Java
      •
      BSD 3-Clause "New" or "Revised" License
      •5•8•0•8•Updated Nov 22, 2024Nov 22, 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•998•744•48•Updated Nov 22, 2024Nov 22, 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 22, 2024Nov 22, 2024

    • rawls

      Public
      Rawls service for DSDE
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •4•26•0•13•Updated Nov 22, 2024Nov 22, 2024

    • depmap-portal

      Public
      Code for the DepMap portal at depmap.org
      Python
      •
      BSD 2-Clause "Simplified" License
      •1•7•0•6•Updated Nov 22, 2024Nov 22, 2024

    • ops-terra-utils

      Public
      Python
      •0•3•0•2•Updated Nov 22, 2024Nov 22, 2024

    • sam

      Public
      workbench identity and access management
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •12•42•3•29•Updated Nov 22, 2024Nov 22, 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 22, 2024Nov 22, 2024

    • dig-dug-portal

      Public
      Vue
      •
      BSD 3-Clause "New" or "Revised" License
      •1•2•0•0•Updated Nov 22, 2024Nov 22, 2024

    • gnomad-browser

      Public
      Explore gnomAD datasets on the web
      javascriptgenomicsgnomad
      TypeScript
      •
      MIT License
      •44•80•160•13•Updated Nov 22, 2024Nov 22, 2024

    • gnomad-blog

      Public
      Blog for the gnomAD project
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •0•3•7•2•Updated Nov 22, 2024Nov 22, 2024

    • ist_benchmarking

      Public
      Jupyter Notebook
      •0•0•0•1•Updated Nov 22, 2024Nov 22, 2024

    • ddp-study-server

      Public
      Pepper Study Server
      Java
      •
      BSD 3-Clause "New" or "Revised" License
      •5•8•1•3•Updated Nov 22, 2024Nov 22, 2024

    • gatk-sv

      Public
      A structural variation pipeline for short-read sequencing
      bioinformaticsgenomicsstructural-variationstructural-variants
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •71•172•73•22•Updated Nov 22, 2024Nov 22, 2024

    • delphy

      Public
      Fast, scalable, accurate and accessible Bayesian phylogenetics
      C++
      •
      Other
      •3•27•0•0•Updated Nov 22, 2024Nov 22, 2024

    • warp

      Public
      WDL Analysis Research Pipelines
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •96•202•7•13•Updated Nov 22, 2024Nov 22, 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•63•0•1•Updated Nov 22, 2024Nov 22, 2024

    • orsp-pub

      Public
      Public ORSP Compliance Portal
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •0•3•0•25•Updated Nov 22, 2024Nov 22, 2024

    • juniper0

      Public
      Preliminary Version of JUNIPER: Large-Scale Outbreak Reconstruction
      R
      •
      MIT License
      •0•2•0•0•Updated Nov 22, 2024Nov 22, 2024

    • heimdall

      Public
      Shell
      •0•0•0•0•Updated Nov 22, 2024Nov 22, 2024

    • data-registry

      Public
      Vue
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•9•Updated Nov 22, 2024Nov 22, 2024

    • data-registry-api

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•0•0•Updated Nov 22, 2024Nov 22, 2024

    • molecular-data-provider

      Public
      Molecular Data Provider
      Python
      •
      MIT License
      •8•11•3•5•Updated Nov 22, 2024Nov 22, 2024

    • viral-pipelines

      Public
      viral-ngs: complete pipelines
      WDL
      •
      Other
      •27•62•23•16•Updated Nov 22, 2024Nov 22, 2024

    • cms2-work

      Public
      Gather in one place various repos and files related to CMS2.0 work.
      Python
      •
      Apache License 2.0
      •3•1•0•0•Updated Nov 21, 2024Nov 21, 2024

    • kpt-packages

      Public
      A Catalog of Kpt packages and Blueprints
      MIT License
      •0•1•0•0•Updated Nov 21, 2024Nov 21, 2024