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    1.4k repositories

    • str-truth-set

      Public
      Genome-wide tandem repeat (TR) truth set based on the Synthetic Diploid Benchmark [Li et al. 2018]
      Python
      •
      MIT License
      •0•6•0•1•Updated Apr 17, 2025Apr 17, 2025

    • palantir-workflows

      Public
      Utility workflows for the DSP hydro.gen team (formerly palantir)
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •8•23•4•3•Updated Apr 17, 2025Apr 17, 2025

    • gatk

      Public
      Official code repository for GATK versions 4 and up
      sciencebioinformaticsgenomicsgenomengssequencingdnasparkgatk
      Java
      •
      Other
      •604•1.8k•1.2k•139•Updated Apr 17, 2025Apr 17, 2025

    • mitograph

      Public
      Rust
      •0•0•0•0•Updated Apr 17, 2025Apr 17, 2025

    • str-truth-set-v2

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Apr 17, 2025Apr 17, 2025

    • seqr-loading-pipelines

      Public
      hail-based pipelines for annotating variant callsets and exporting them to elasticsearch
      Python
      •
      MIT License
      •20•23•27•4•Updated Apr 16, 2025Apr 16, 2025

    • rawls

      Public
      Rawls service for DSDE
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •4•25•0•2•Updated Apr 16, 2025Apr 16, 2025

    • celldega

      Public
      Spatial omics analysis and visualization library
      Jupyter Notebook
      •
      Other
      •0•5•1•14•Updated Apr 16, 2025Apr 16, 2025

    • depmap-portal

      Public
      Code for the DepMap portal at depmap.org
      Python
      •
      BSD 2-Clause "Simplified" License
      •1•8•0•9•Updated Apr 16, 2025Apr 16, 2025

    • workbench-libs

      Public
      Workbench utility libraries
      Scala
      •
      Other
      •4•9•0•3•Updated Apr 16, 2025Apr 16, 2025

    • tandem-repeat-explorer

      Public
      An online portal for exploring genome-wide TR catalogs
      HTML
      •
      MIT License
      •0•0•0•0•Updated Apr 16, 2025Apr 16, 2025

    • sam

      Public
      workbench identity and access management
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •12•41•3•31•Updated Apr 16, 2025Apr 16, 2025

    • malaria

      Public
      R
      •
      MIT License
      •0•1•2•2•Updated Apr 16, 2025Apr 16, 2025

    • 2025_04_13_OASIS_CellPainting

      Public
      Repo for OASIS Cell Painting data
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•1•0•Updated Apr 16, 2025Apr 16, 2025

    • hca-ingest-migration

      Public
      Working Repo for migration of HCA ingest from Dagster 0.12 to Dagster 1.8 (or 1.9)
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•0•0•1•Updated Apr 16, 2025Apr 16, 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
      •361•1k•746•49•Updated Apr 16, 2025Apr 16, 2025

    • backstage

      Public
      Broad Institute Engineering Portal is an Internal Developer Platform (Spotify Backstage by another name)
      TypeScript
      •0•2•0•2•Updated Apr 16, 2025Apr 16, 2025

    • idmp-fungal-pipelines

      Public
      WDL
      •
      GNU General Public License v3.0
      •0•0•0•1•Updated Apr 16, 2025Apr 16, 2025

    • Drop-seq

      Public
      Java tools for analyzing Drop-seq data
      Java
      •
      MIT License
      •35•125•22•0•Updated Apr 16, 2025Apr 16, 2025

    • warp

      Public
      WDL Analysis Research Pipelines
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •102•211•5•12•Updated Apr 16, 2025Apr 16, 2025

    • pyops-service-toolkit

      Public
      Shared Python utilities that help with interacting with Terra, TDR, BigQuery, and GCP to name a few.
      Python
      •0•1•0•0•Updated Apr 16, 2025Apr 16, 2025

    • dig-dug-portal

      Public
      Vue
      •
      BSD 3-Clause "New" or "Revised" License
      •1•2•1•0•Updated Apr 16, 2025Apr 16, 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•1•Updated Apr 16, 2025Apr 16, 2025

    • ml4h

      Public
      Python
      •
      Other
      •25•132•30•21•Updated Apr 16, 2025Apr 16, 2025

    • ddp-angular

      Public
      Angular code for participant-facing pepper studies
      TypeScript
      •4•3•1•34•Updated Apr 16, 2025Apr 16, 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•67•0•3•Updated Apr 16, 2025Apr 16, 2025

    • monorepo

      Public
      Compendium of tools for the Imaging Platform
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•11•8•0•Updated Apr 16, 2025Apr 16, 2025

    • seqr-helm

      Public
      Helm charts for the seqr project
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•3•0•0•Updated Apr 16, 2025Apr 16, 2025

    • firecloud-orchestration

      Public
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •4•31•0•2•Updated Apr 16, 2025Apr 16, 2025

    • gumbo_client

      Public
      python client for DepMap Gumbo database
      Python
      •0•5•1•0•Updated Apr 16, 2025Apr 16, 2025