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    1.3k repositories

    • viral-pipelines

      Public
      viral-ngs: complete pipelines
      WDL
      •
      Other
      •28•61•23•18•Updated Jan 23, 2025Jan 23, 2025

    • seqr

      Public
      web-based analysis tool for rare disease genomics
      Python
      •
      GNU Affero General Public License v3.0
      •89•180•55•4•Updated Jan 23, 2025Jan 23, 2025

    • firecloud-orchestration

      Public
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •4•31•0•1•Updated Jan 23, 2025Jan 23, 2025

    • depmap-portal

      Public
      Code for the DepMap portal at depmap.org
      Python
      •
      BSD 2-Clause "Simplified" License
      •1•7•0•8•Updated Jan 23, 2025Jan 23, 2025

    • 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 Jan 23, 2025Jan 23, 2025

    • warp

      Public
      WDL Analysis Research Pipelines
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •100•207•8•17•Updated Jan 23, 2025Jan 23, 2025

    • cellpainting-gallery

      Public
      Cell Painting Gallery
      Other
      •12•75•7•1•Updated Jan 23, 2025Jan 23, 2025

    • gnomad_methods

      Public
      Hail helper functions for the gnomAD project and Translational Genomics Group
      genomicsgenomesexomeshail
      Python
      •
      MIT License
      •29•92•10•5•Updated Jan 23, 2025Jan 23, 2025

    • ddp-study-server

      Public
      Pepper Study Server
      Java
      •
      BSD 3-Clause "New" or "Revised" License
      •5•8•1•4•Updated Jan 23, 2025Jan 23, 2025

    • juniper

      Public
      Java
      •
      BSD 3-Clause "New" or "Revised" License
      •5•9•0•7•Updated Jan 23, 2025Jan 23, 2025

    • submissions

      Public
      Python
      •0•1•0•0•Updated Jan 23, 2025Jan 23, 2025

    • rawls

      Public
      Rawls service for DSDE
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •4•26•0•10•Updated Jan 23, 2025Jan 23, 2025

    • sam

      Public
      workbench identity and access management
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •12•42•3•29•Updated Jan 23, 2025Jan 23, 2025

    • viral-phylo

      Public
      viral-ngs: phylogenetics, annotation, intrahost variants
      Python
      •
      Other
      •0•2•8•2•Updated Jan 23, 2025Jan 23, 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 23, 2025Jan 23, 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•65•0•0•Updated Jan 23, 2025Jan 23, 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 23, 2025Jan 23, 2025

    • ml4h

      Public
      Python
      •
      Other
      •24•126•30•21•Updated Jan 23, 2025Jan 23, 2025

    • dsp-reusable-workflows

      Public
      publicly available reusable workflows
      Python
      •0•1•0•3•Updated Jan 23, 2025Jan 23, 2025

    • ddp-angular

      Public
      Angular code for participant-facing pepper studies
      TypeScript
      •4•3•1•32•Updated Jan 23, 2025Jan 23, 2025

    • exome-results-browsers

      Public
      Results browsers for case-control studies of psychiatric diseases done at the Broad Institute
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •4•11•7•4•Updated Jan 23, 2025Jan 23, 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 23, 2025Jan 23, 2025

    • gatk

      Public
      Official code repository for GATK versions 4 and up
      sciencebioinformaticsgenomicsgenomengssequencingdnasparkgatk
      Java
      •
      Other
      •597•1.8k•1.2k•137•Updated Jan 23, 2025Jan 23, 2025

    • thurloe

      Public
      A simple service to store arbitrary key/value pairs
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •0•3•0•4•Updated Jan 23, 2025Jan 23, 2025

    • orsp-pub

      Public
      Public ORSP Compliance Portal
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •0•3•0•25•Updated Jan 23, 2025Jan 23, 2025

    • monorepo

      Public
      Compendium of tools for the Imaging Platform
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•9•9•0•Updated Jan 23, 2025Jan 23, 2025

    • BEClust3D

      Public
      Jupyter Notebook
      •
      Other
      •0•0•0•8•Updated Jan 23, 2025Jan 23, 2025

    • dsp-appsec-infrastructure-apps

      Public
      This repository hosts DSP AppSec internal infrastructure apps deployed in GKE.
      application-securityappsecsecurity-scannersecure-developmentsecurity-automationsecurity-toolsdevsecopssecurity-scanappsecurityappsec-tools
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•6•0•4•Updated Jan 23, 2025Jan 23, 2025

    • dig-aws

      Public
      Amazon Web Services support for DIG projects
      Scala
      •0•0•0•0•Updated Jan 22, 2025Jan 22, 2025

    • genetic-prevalence-estimator

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•47•5•Updated Jan 22, 2025Jan 22, 2025