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    1.3k repositories

    • gatk

      Public
      Official code repository for GATK versions 4 and up
      sciencebioinformaticsgenomicsgenomengssequencingdnasparkgatk
      Java
      •
      Other
      •597•1.8k•1.2k•137•Updated Jan 28, 2025Jan 28, 2025

    • 2021_04_07_ProteinKinaseInhibitors_NathanaelGray-analysis

      Public
      Jupyter Notebook
      •1•1•9•0•Updated Jan 28, 2025Jan 28, 2025

    • Xenium_Prime_Ovarian_Cancer_FFPE_XRrun_outs

      Public
      Celldega Landscape files of a public dataset: Xenium_Prime_Ovarian_Cancer_FFPE_XRrun_outs
      1•0•0•0•Updated Jan 28, 2025Jan 28, 2025

    • carmen-analysis

      Public
      Python
      •
      MIT License
      •0•4•0•0•Updated Jan 28, 2025Jan 28, 2025

    • ygramul

      Public
      Hierarchical knowledge graph for PIGEAN results
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Jan 28, 2025Jan 28, 2025

    • depmap-portal

      Public
      Code for the DepMap portal at depmap.org
      Python
      •
      BSD 2-Clause "Simplified" License
      •1•7•0•10•Updated Jan 28, 2025Jan 28, 2025

    • mitograph

      Public
      Rust
      •0•0•0•0•Updated Jan 28, 2025Jan 28, 2025

    • g2p-bis

      Public
      Genomics To Proteins - Bio Integration Suite
      JavaScript
      •
      MIT License
      •0•0•0•1•Updated Jan 28, 2025Jan 28, 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•1•Updated Jan 28, 2025Jan 28, 2025

    • ops-terra-utils

      Public
      Python
      •0•3•0•4•Updated Jan 28, 2025Jan 28, 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•745•48•Updated Jan 28, 2025Jan 28, 2025

    • warp

      Public
      WDL Analysis Research Pipelines
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •100•207•8•17•Updated Jan 28, 2025Jan 28, 2025

    • datarepo-helm

      Public
      A helm repo for Broad Data Science Platforms helm charts
      Mustache
      •1•5•0•3•Updated Jan 28, 2025Jan 28, 2025

    • sam

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

    • juniper

      Public
      Java
      •
      BSD 3-Clause "New" or "Revised" License
      •5•9•0•6•Updated Jan 28, 2025Jan 28, 2025

    • AuSPICES

      Public
      Automated System Processing Infinite Cellpainting Experiments with Step functions
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•6•2•Updated Jan 28, 2025Jan 28, 2025

    • ega_submissions

      Public
      Python
      •0•0•0•1•Updated Jan 28, 2025Jan 28, 2025

    • firecloud-orchestration

      Public
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •4•31•0•2•Updated Jan 28, 2025Jan 28, 2025

    • gnomad_qc

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •27•69•7•11•Updated Jan 28, 2025Jan 28, 2025

    • gatk-sv

      Public
      A structural variation pipeline for short-read sequencing
      bioinformaticsgenomicsstructural-variationstructural-variants
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •72•176•74•23•Updated Jan 28, 2025Jan 28, 2025

    • malaria

      Public
      R
      •
      MIT License
      •0•1•1•0•Updated Jan 28, 2025Jan 28, 2025

    • cellpainting-gallery

      Public
      Cell Painting Gallery
      Other
      •13•75•7•1•Updated Jan 28, 2025Jan 28, 2025

    • gnomad_methods

      Public
      Hail helper functions for the gnomAD project and Translational Genomics Group
      genomicsgenomesexomeshail
      Python
      •
      MIT License
      •29•92•10•7•Updated Jan 28, 2025Jan 28, 2025

    • seqr

      Public
      web-based analysis tool for rare disease genomics
      Python
      •
      GNU Affero General Public License v3.0
      •89•181•55•4•Updated Jan 28, 2025Jan 28, 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 Jan 28, 2025Jan 28, 2025

    • imaging-platform-pipelines

      Public
      Cell Painting and other pipelines from the Imaging Platform
      carpenter-lab
      13•15•2•1•Updated Jan 28, 2025Jan 28, 2025

    • scp-ingest-pipeline

      Public
      File Ingest Pipeline for Single Cell Portal
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•5•0•0•Updated Jan 28, 2025Jan 28, 2025

    • ml4h

      Public
      Python
      •
      Other
      •24•126•30•21•Updated Jan 28, 2025Jan 28, 2025

    • ddp-angular

      Public
      Angular code for participant-facing pepper studies
      TypeScript
      •4•3•1•32•Updated Jan 28, 2025Jan 28, 2025

    • dig-dug-portal

      Public
      Vue
      •
      BSD 3-Clause "New" or "Revised" License
      •1•2•0•0•Updated Jan 28, 2025Jan 28, 2025