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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•2•Updated Nov 28, 2024Nov 28, 2024

    • seqr-loading-pipelines

      Public
      hail-based pipelines for annotating variant callsets and exporting them to elasticsearch
      Python
      •
      MIT License
      •20•22•30•1•Updated Nov 28, 2024Nov 28, 2024

    • juniper

      Public
      Java
      •
      BSD 3-Clause "New" or "Revised" License
      •5•8•0•7•Updated Nov 28, 2024Nov 28, 2024

    • depmap-portal

      Public
      Code for the DepMap portal at depmap.org
      Python
      •
      BSD 2-Clause "Simplified" License
      •1•7•0•8•Updated Nov 27, 2024Nov 27, 2024

    • ml4h

      Public
      Python
      •
      Other
      •23•123•30•20•Updated Nov 27, 2024Nov 27, 2024

    • lembic

      Public
      Distilling some data for CFDE
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Nov 27, 2024Nov 27, 2024

    • seqr

      Public
      web-based analysis tool for rare disease genomics
      Python
      •
      GNU Affero General Public License v3.0
      •89•177•47•3•Updated Nov 27, 2024Nov 27, 2024

    • poasta

      Public
      Fast and exact gap-affine partial order alignment
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •2•40•7•2•Updated Nov 27, 2024Nov 27, 2024

    • gatk-sv

      Public
      A structural variation pipeline for short-read sequencing
      bioinformaticsgenomicsstructural-variationstructural-variants
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •70•172•73•22•Updated Nov 27, 2024Nov 27, 2024

    • DBP_Doe

      Public
      files that will be used to train the 3D Unet on CHTC
      Python
      •0•0•0•0•Updated Nov 27, 2024Nov 27, 2024

    • gatk

      Public
      Official code repository for GATK versions 4 and up
      sciencebioinformaticsgenomicsgenomengssequencingdnasparkgatk
      Java
      •
      Other
      •594•1.7k•1.2k•136•Updated Nov 27, 2024Nov 27, 2024

    • celldega_Xenium_Prime_Human_Skin_FFPE_outs_Cellpose2

      Public
      Jupyter Notebook
      •
      Other
      •1•0•0•0•Updated Nov 27, 2024Nov 27, 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 27, 2024Nov 27, 2024

    • ddp-study-server

      Public
      Pepper Study Server
      Java
      •
      BSD 3-Clause "New" or "Revised" License
      •5•8•1•4•Updated Nov 27, 2024Nov 27, 2024

    • mcl_imput

      Public
      WDL Analysis Research Pipelines
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •99•0•0•1•Updated Nov 27, 2024Nov 27, 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
      •360•999•744•49•Updated Nov 27, 2024Nov 27, 2024

    • rawls

      Public
      Rawls service for DSDE
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •4•26•0•13•Updated Nov 27, 2024Nov 27, 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 27, 2024Nov 27, 2024

    • dig-dug-portal

      Public
      Vue
      •
      BSD 3-Clause "New" or "Revised" License
      •1•2•0•1•Updated Nov 27, 2024Nov 27, 2024

    • warp

      Public
      WDL Analysis Research Pipelines
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •99•202•7•15•Updated Nov 27, 2024Nov 27, 2024

    • hidive

      Public
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•3•2•Updated Nov 27, 2024Nov 27, 2024

    • terra-featured-workspace-tests

      Public
      This code is to test that terra featured workspaces are working properly
      Python
      •0•2•0•1•Updated Nov 27, 2024Nov 27, 2024

    • orsp-pub

      Public
      Public ORSP Compliance Portal
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •0•3•0•25•Updated Nov 27, 2024Nov 27, 2024

    • heimdall

      Public
      Shell
      •0•0•0•0•Updated Nov 27, 2024Nov 27, 2024

    • juniper0

      Public
      Preliminary Version of JUNIPER: Large-Scale Outbreak Reconstruction
      R
      •
      MIT License
      •0•2•0•0•Updated Nov 27, 2024Nov 27, 2024

    • monorepo

      Public
      Compendium of tools for the Imaging Platform
      Python
      •1•9•7•1•Updated Nov 27, 2024Nov 27, 2024

    • ops-terra-utils

      Public
      Python
      •0•3•0•0•Updated Nov 26, 2024Nov 26, 2024

    • datarepo-helm

      Public
      A helm repo for Broad Data Science Platforms helm charts
      Mustache
      •1•5•0•5•Updated Nov 26, 2024Nov 26, 2024

    • backstage

      Public
      Broad Institute Engineering Portal is an Internal Developer Platform (Spotify Backstage by another name)
      TypeScript
      •0•2•0•4•Updated Nov 26, 2024Nov 26, 2024

    • firecloud-orchestration

      Public
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •4•31•0•3•Updated Nov 26, 2024Nov 26, 2024