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    1.3k repositories

    • seqr-helm

      Public
      Helm charts for the seqr project
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•0•0•Updated Jan 14, 2025Jan 14, 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•6•3•Updated Jan 14, 2025Jan 14, 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
      •360•1k•745•50•Updated Jan 14, 2025Jan 14, 2025

    • seqr-loading-pipelines

      Public
      hail-based pipelines for annotating variant callsets and exporting them to elasticsearch
      Python
      •
      MIT License
      •20•22•25•2•Updated Jan 14, 2025Jan 14, 2025

    • kinnex-preliminary-processing

      Public
      Python
      •0•0•0•0•Updated Jan 14, 2025Jan 14, 2025

    • warp

      Public
      WDL Analysis Research Pipelines
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •100•207•7•18•Updated Jan 14, 2025Jan 14, 2025

    • tgg_methods

      Public
      Repo for miscellaneous methods developed by the methods group that don't fit anywhere else
      Python
      •
      MIT License
      •0•4•5•4•Updated Jan 14, 2025Jan 14, 2025

    • sam

      Public
      workbench identity and access management
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •12•42•3•29•Updated Jan 14, 2025Jan 14, 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•64•0•1•Updated Jan 14, 2025Jan 14, 2025

    • juniper

      Public
      Java
      •
      BSD 3-Clause "New" or "Revised" License
      •5•9•0•5•Updated Jan 14, 2025Jan 14, 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.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•5•Updated Jan 14, 2025Jan 14, 2025

    • juniper0

      Public
      Preliminary Version of JUNIPER: Large-Scale Outbreak Reconstruction
      R
      •
      MIT License
      •0•3•0•0•Updated Jan 14, 2025Jan 14, 2025

    • gnomad-browser

      Public
      Explore gnomAD datasets on the web
      javascriptgenomicsgnomad
      TypeScript
      •
      MIT License
      •45•81•157•19•Updated Jan 14, 2025Jan 14, 2025

    • broad-epi-repeats-analysis

      Public
      Workflow to quantify transposable elements expression.
      WDL
      •0•0•0•0•Updated Jan 14, 2025Jan 14, 2025

    • mitograph

      Public
      Rust
      •0•0•0•0•Updated Jan 14, 2025Jan 14, 2025

    • celldega

      Public
      Spatial omics analysis and visualization library
      Jupyter Notebook
      •
      Other
      •0•4•1•6•Updated Jan 14, 2025Jan 14, 2025

    • ddp-study-server

      Public
      Pepper Study Server
      Java
      •
      BSD 3-Clause "New" or "Revised" License
      •5•8•1•3•Updated Jan 14, 2025Jan 14, 2025

    • ml4h

      Public
      Python
      •
      Other
      •24•128•30•21•Updated Jan 14, 2025Jan 14, 2025

    • submissions

      Public
      Python
      •0•1•0•1•Updated Jan 14, 2025Jan 14, 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 14, 2025Jan 14, 2025

    • gnomad-blog

      Public
      Blog for the gnomAD project
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •0•3•7•3•Updated Jan 14, 2025Jan 14, 2025

    • thelma

      Public
      Go
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•10•Updated Jan 14, 2025Jan 14, 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 14, 2025Jan 14, 2025

    • dagster-utils

      Public
      Utilities and reusable patterns for using Dagster for Broad pipeline orchestration
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•4•0•0•Updated Jan 14, 2025Jan 14, 2025

    • seqr

      Public
      web-based analysis tool for rare disease genomics
      Python
      •
      GNU Affero General Public License v3.0
      •89•179•46•3•Updated Jan 14, 2025Jan 14, 2025

    • gatk

      Public
      Official code repository for GATK versions 4 and up
      sciencebioinformaticsgenomicsgenomengssequencingdnasparkgatk
      Java
      •
      Other
      •596•1.7k•1.2k•136•Updated Jan 14, 2025Jan 14, 2025

    • datarepo-helm

      Public
      A helm repo for Broad Data Science Platforms helm charts
      Mustache
      •1•5•0•3•Updated Jan 14, 2025Jan 14, 2025

    • viral-pipelines

      Public
      viral-ngs: complete pipelines
      WDL
      •
      Other
      •28•61•23•17•Updated Jan 14, 2025Jan 14, 2025

    • TAG-public

      Public
      Official workflows published by the Broad Institute's Genomics Platform Translation Analysis Group (TAG)
      WDL
      •3•5•1•17•Updated Jan 14, 2025Jan 14, 2025

    • CNV-Mag

      Public
      A Tool to Visualize CNV Events in WGS Data
      Python
      •
      MIT License
      •0•1•0•0•Updated Jan 14, 2025Jan 14, 2025