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    1.4k repositories

    • celldega

      Public
      Spatial omics analysis and visualization library
      Jupyter Notebook
      •
      Other
      •1•21•1•59•Updated Nov 23, 2025Nov 23, 2025

    • palantir-workflows

      Public
      Utility workflows for the DSP hydro.gen team (formerly palantir)
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •10•26•4•2•Updated Nov 23, 2025Nov 23, 2025

    • gatk

      Public
      Official code repository for GATK versions 4 and up
      sciencebioinformaticssparkgenomicsgenomengssequencingdnagatk
      Java
      •
      Other
      •619•1.9k•1.3k•143•Updated Nov 23, 2025Nov 23, 2025

    • poolq

      Public
      The Genetic Perturbation Platform's tool for deconvoluting and quantifying the results of pooled screens
      Scala
      •
      Other
      •1•5•8•1•Updated Nov 22, 2025Nov 22, 2025

    • DropSift

      Public
      cell caller for sn/snRNA sequence data
      R
      •
      Other
      •0•1•0•0•Updated Nov 22, 2025Nov 22, 2025

    • gatk-sv

      Public
      A structural variation pipeline for short-read sequencing
      bioinformaticsgenomicsstructural-variationstructural-variants
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •75•196•93•28•Updated Nov 22, 2025Nov 22, 2025

    • warp

      Public
      Warp Analysis Research Pipelines
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •111•220•6•11•Updated Nov 21, 2025Nov 21, 2025

    • dig-dug-portal

      Public
      Vue
      •
      BSD 3-Clause "New" or "Revised" License
      •2•2•1•0•Updated Nov 21, 2025Nov 21, 2025

    • cromwell

      Public
      Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
      dockerapplicationworkflowcloudbioinformaticsscalaexecutorhpccontainerswdl
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •375•1k•757•52•Updated Nov 21, 2025Nov 21, 2025

    • warp-tools

      Public
      This repository contains all containers that WARP uses.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•12•1•3•Updated Nov 21, 2025Nov 21, 2025

    • lrma-aou1-panel-creation

      Public
      Pipelines and evaluations covering integration, phasing, and imputation of short and structural variants for the AoU Phase 1 long-reads callset.
      WDL
      •2•1•22•2•Updated Nov 21, 2025Nov 21, 2025

    • depmap-portal

      Public
      Code for the DepMap portal at depmap.org
      TypeScript
      •
      BSD 2-Clause "Simplified" License
      •1•8•1•12•Updated Nov 21, 2025Nov 21, 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
      •27•68•0•1•Updated Nov 21, 2025Nov 21, 2025

    • dig-aggregator-methods

      Public
      Monorepo of methods implemented for the Aggregator
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•1•0•8•Updated Nov 21, 2025Nov 21, 2025

    • gnomad-browser

      Public
      Explore gnomAD datasets on the web
      javascriptgenomicsgnomad
      TypeScript
      •
      MIT License
      •49•85•165•10•Updated Nov 21, 2025Nov 21, 2025

    • gnomad_qc

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •28•68•6•11•Updated Nov 21, 2025Nov 21, 2025

    • ddp-angular

      Public
      Angular code for participant-facing pepper studies
      TypeScript
      •6•3•1•36•Updated Nov 21, 2025Nov 21, 2025

    • broad-epi-workflows-collection

      Public
      This repo contains WDL workflows written by the Epigenomics program.
      Jupyter Notebook
      •
      MIT License
      •1•1•0•0•Updated Nov 21, 2025Nov 21, 2025

    • sparklespray

      Public
      Easy batch submission of adhoc jobs onto GCP
      Go
      •3•13•1•9•Updated Nov 21, 2025Nov 21, 2025

    • dig-job-server

      Public
      Vue
      •0•0•0•1•Updated Nov 21, 2025Nov 21, 2025

    • backstage

      Public
      Broad Institute Engineering Portal is an Internal Developer Platform (Spotify Backstage by another name)
      TypeScript
      •0•2•2•0•Updated Nov 21, 2025Nov 21, 2025

    • data-registry

      Public
      Vue
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•10•Updated Nov 21, 2025Nov 21, 2025

    • bmxp

      Public
      The tools that constitute a nontargeted LCMS metabolomics data processing pipeline, created and used by the Broad Institute Metabolomics Platform.
      Python
      •
      Other
      •0•13•0•0•Updated Nov 21, 2025Nov 21, 2025

    • long-read-pipelines

      Public
      Long read production pipelines
      pipelineswdlvariant-callingde-novo-assemblylong-reads
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •25•150•95•25•Updated Nov 21, 2025Nov 21, 2025

    • trexplorer-catalog

      Public
      Genome-wide TR catalog and variation clusters described in [Weisburd, Dolzhenko, et al. 2024]
      Python
      •
      MIT License
      •1•17•0•0•Updated Nov 21, 2025Nov 21, 2025

    • seqr

      Public
      web-based analysis tool for rare disease genomics
      Python
      •
      GNU Affero General Public License v3.0
      •91•195•51•10•Updated Nov 21, 2025Nov 21, 2025

    • Himito

      Public
      Rust
      •
      MIT License
      •0•4•0•0•Updated Nov 21, 2025Nov 21, 2025

    • ml4h

      Public
      Python
      •
      GNU General Public License v3.0
      •27•155•32•26•Updated Nov 21, 2025Nov 21, 2025

    • dig-bioindex

      Public
      BIO index for genetic records stored in S3 and FastAPI server.
      ot2od036440
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •6•6•0•3•Updated Nov 20, 2025Nov 20, 2025

    • str-analysis

      Public
      Scripts and utilities related to analyzing tandem repeats (TRs).
      Python
      •
      MIT License
      •10•41•0•0•Updated Nov 20, 2025Nov 20, 2025