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    1.3k repositories

    • gatk

      Public
      Official code repository for GATK versions 4 and up
      sciencebioinformaticsgenomicsgenomengssequencingdnasparkgatk
      Java
      •
      Other
      •596•1.7k•1.2k•136•Updated Jan 10, 2025Jan 10, 2025

    • gatk-sv

      Public
      A structural variation pipeline for short-read sequencing
      bioinformaticsgenomicsstructural-variationstructural-variants
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •71•175•74•26•Updated Jan 10, 2025Jan 10, 2025

    • genetic-prevalence-estimator

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•49•3•Updated Jan 10, 2025Jan 10, 2025

    • str-analysis

      Public
      Scripts and utilities related to analyzing short tandem repeats (STRs).
      Python
      •
      MIT License
      •8•32•1•0•Updated Jan 10, 2025Jan 10, 2025

    • seqr-loading-pipelines

      Public
      hail-based pipelines for annotating variant callsets and exporting them to elasticsearch
      Python
      •
      MIT License
      •20•22•26•4•Updated Jan 10, 2025Jan 10, 2025

    • seqr

      Public
      web-based analysis tool for rare disease genomics
      Python
      •
      GNU Affero General Public License v3.0
      •89•179•48•5•Updated Jan 9, 2025Jan 9, 2025

    • gnomad-browser

      Public
      Explore gnomAD datasets on the web
      javascriptgenomicsgnomad
      TypeScript
      •
      MIT License
      •45•81•157•18•Updated Jan 9, 2025Jan 9, 2025

    • sam

      Public
      workbench identity and access management
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •12•42•3•29•Updated Jan 9, 2025Jan 9, 2025

    • dig-dug-portal

      Public
      Vue
      •
      BSD 3-Clause "New" or "Revised" License
      •1•2•0•0•Updated Jan 9, 2025Jan 9, 2025

    • mitograph

      Public
      Rust
      •0•0•0•0•Updated Jan 9, 2025Jan 9, 2025

    • carmen-analysis

      Public
      Python
      •
      MIT License
      •0•3•0•0•Updated Jan 9, 2025Jan 9, 2025

    • depmap-portal

      Public
      Code for the DepMap portal at depmap.org
      Python
      •
      BSD 2-Clause "Simplified" License
      •1•7•0•5•Updated Jan 9, 2025Jan 9, 2025

    • celldega

      Public
      Spatial omics analysis and visualization library
      Jupyter Notebook
      •
      Other
      •0•3•1•5•Updated Jan 9, 2025Jan 9, 2025

    • juniper

      Public
      Java
      •
      BSD 3-Clause "New" or "Revised" License
      •5•9•0•12•Updated Jan 9, 2025Jan 9, 2025

    • datarepo-helm

      Public
      A helm repo for Broad Data Science Platforms helm charts
      Mustache
      •1•5•0•3•Updated Jan 9, 2025Jan 9, 2025

    • PANOPLY

      Public
      Repository for the Broad Institute Proteogenomic Data Analysis Center (PGDAC) established by the NIH Clinical Proteomics Tumor Analysis Consortium (CPTAC)
      R
      •
      Other
      •15•33•0•1•Updated Jan 9, 2025Jan 9, 2025

    • pangenome-pipelines

      Public
      Terra WDL pipelines using the Human Pangenome Reference Graph
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Jan 9, 2025Jan 9, 2025

    • datarepo-helm-definitions

      Public
      Helm deployment specific values and definitions for Dev, Integration and Prod
      1•3•0•10•Updated Jan 9, 2025Jan 9, 2025

    • ddp-study-server

      Public
      Pepper Study Server
      Java
      •
      BSD 3-Clause "New" or "Revised" License
      •5•8•1•4•Updated Jan 9, 2025Jan 9, 2025

    • warp

      Public
      WDL Analysis Research Pipelines
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •99•207•7•17•Updated Jan 9, 2025Jan 9, 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•63•0•2•Updated Jan 9, 2025Jan 9, 2025

    • viral-pipelines

      Public
      viral-ngs: complete pipelines
      WDL
      •
      Other
      •28•61•23•15•Updated Jan 9, 2025Jan 9, 2025

    • dig-aggregator-methods

      Public
      Monorepo of methods implemented for the Aggregator
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•1•0•7•Updated Jan 9, 2025Jan 9, 2025

    • gnomad_qc

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •27•69•7•10•Updated Jan 9, 2025Jan 9, 2025

    • backstage

      Public
      Broad Institute Engineering Portal is an Internal Developer Platform (Spotify Backstage by another name)
      TypeScript
      •0•2•1•1•Updated Jan 9, 2025Jan 9, 2025

    • gnomad_methods

      Public
      Hail helper functions for the gnomAD project and Translational Genomics Group
      genomicsgenomesexomeshail
      Python
      •
      MIT License
      •29•91•10•8•Updated Jan 9, 2025Jan 9, 2025

    • ml4h

      Public
      Python
      •
      Other
      •24•127•30•21•Updated Jan 9, 2025Jan 9, 2025

    • BEClust3D

      Public
      Jupyter Notebook
      •
      Other
      •0•0•0•8•Updated Jan 9, 2025Jan 9, 2025

    • dsp-reusable-workflows

      Public
      publicly available reusable workflows
      Python
      •0•1•0•4•Updated Jan 9, 2025Jan 9, 2025

    • kinnex-preliminary-processing

      Public
      Python
      •0•0•0•0•Updated Jan 9, 2025Jan 9, 2025