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    • Drop-seq-wdl

      Public
      WDL
      •
      MIT License
      •0•0•0•0•Updated Feb 2, 2025Feb 2, 2025

    • tensorqtl

      Public
      Ultrafast GPU-enabled QTL mapper
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •53•168•35•2•Updated Feb 1, 2025Feb 1, 2025

    • infercnv

      Public
      Inferring CNV from Single-Cell RNA-Seq
      R
      •
      Other
      •170•589•214•4•Updated Feb 1, 2025Feb 1, 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
      •359•1k•744•50•Updated Feb 1, 2025Feb 1, 2025

    • dig-dug-portal

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

    • monorepo

      Public
      Compendium of tools for the Imaging Platform
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•9•9•0•Updated Feb 1, 2025Feb 1, 2025

    • depmap-portal

      Public
      Code for the DepMap portal at depmap.org
      Python
      •
      BSD 2-Clause "Simplified" License
      •1•7•0•9•Updated Jan 31, 2025Jan 31, 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•0•Updated Jan 31, 2025Jan 31, 2025

    • gatk-sv

      Public
      A structural variation pipeline for short-read sequencing
      bioinformaticsgenomicsstructural-variationstructural-variants
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •72•177•74•23•Updated Jan 31, 2025Jan 31, 2025

    • depmap-omics-long-read-rna

      Public
      Python
      •0•0•0•0•Updated Jan 31, 2025Jan 31, 2025

    • viral-pipelines

      Public
      viral-ngs: complete pipelines
      WDL
      •
      Other
      •28•61•23•16•Updated Jan 31, 2025Jan 31, 2025

    • backstage

      Public
      Broad Institute Engineering Portal is an Internal Developer Platform (Spotify Backstage by another name)
      TypeScript
      •0•2•5•4•Updated Jan 31, 2025Jan 31, 2025

    • gatk

      Public
      Official code repository for GATK versions 4 and up
      sciencebioinformaticsgenomicsgenomengssequencingdnasparkgatk
      Java
      •
      Other
      •597•1.8k•1.2k•137•Updated Jan 31, 2025Jan 31, 2025

    • sam

      Public
      workbench identity and access management
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •12•42•3•28•Updated Jan 31, 2025Jan 31, 2025

    • juniper

      Public
      Java
      •
      BSD 3-Clause "New" or "Revised" License
      •5•9•0•8•Updated Jan 31, 2025Jan 31, 2025

    • ops-terra-utils

      Public
      Python
      •0•3•0•3•Updated Jan 31, 2025Jan 31, 2025

    • firecloud-orchestration

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

    • seqr-helm

      Public
      Helm charts for the seqr project
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•3•0•0•Updated Jan 31, 2025Jan 31, 2025

    • warp

      Public
      WDL Analysis Research Pipelines
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •100•207•8•18•Updated Jan 31, 2025Jan 31, 2025

    • cookiecutter-bits-pypi

      Public
      Cookiecutter template for a BITS repo for a Python package
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Jan 31, 2025Jan 31, 2025

    • kpt-packages

      Public
      A Catalog of Kpt packages and Blueprints
      MIT License
      •0•1•0•0•Updated Jan 31, 2025Jan 31, 2025

    • seqr-loading-pipelines

      Public
      hail-based pipelines for annotating variant callsets and exporting them to elasticsearch
      Python
      •
      MIT License
      •20•23•24•1•Updated Jan 31, 2025Jan 31, 2025

    • gnomad_methods

      Public
      Hail helper functions for the gnomAD project and Translational Genomics Group
      genomicsgenomesexomeshail
      Python
      •
      MIT License
      •29•92•9•8•Updated Jan 31, 2025Jan 31, 2025

    • ABC-Enhancer-Gene-Prediction

      Public
      Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)
      Python
      •
      MIT License
      •64•212•7•0•Updated Jan 31, 2025Jan 31, 2025

    • celldega

      Public
      Spatial omics analysis and visualization library
      Jupyter Notebook
      •
      Other
      •0•4•1•11•Updated Jan 31, 2025Jan 31, 2025

    • palantir-workflows

      Public
      Utility workflows for the DSP hydro.gen team (formerly palantir)
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •8•22•4•5•Updated Jan 31, 2025Jan 31, 2025

    • agora

      Public
      It's a methods repository!
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •2•11•0•2•Updated Jan 31, 2025Jan 31, 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•65•0•3•Updated Jan 31, 2025Jan 31, 2025

    • viral-phylo

      Public
      viral-ngs: phylogenetics, annotation, intrahost variants
      Python
      •
      Other
      •0•3•8•2•Updated Jan 31, 2025Jan 31, 2025