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    1.4k repositories

    • delphy-2025-paper-data

      Public
      Benchmark data and run results for 2025 Delphy paper
      Python
      •0•0•0•0•Updated Oct 17, 2025Oct 17, 2025

    • Himito

      Public
      Rust
      •
      MIT License
      •0•1•0•0•Updated Oct 17, 2025Oct 17, 2025

    • seqr

      Public
      web-based analysis tool for rare disease genomics
      Python
      •
      GNU Affero General Public License v3.0
      •90•195•53•5•Updated Oct 17, 2025Oct 17, 2025

    • gatk

      Public
      Official code repository for GATK versions 4 and up
      sciencebioinformaticssparkgenomicsgenomengssequencingdnagatk
      Java
      •
      Other
      •616•1.9k•1.3k•141•Updated Oct 17, 2025Oct 17, 2025

    • poolq

      Public
      The Genetic Perturbation Platform's tool for deconvoluting and quantifying the results of pooled screens
      Scala
      •
      Other
      •1•5•8•0•Updated Oct 16, 2025Oct 16, 2025

    • depmap-portal

      Public
      Code for the DepMap portal at depmap.org
      TypeScript
      •
      BSD 2-Clause "Simplified" License
      •1•8•0•7•Updated Oct 16, 2025Oct 16, 2025

    • cromwell

      Public
      Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
      dockerapplicationworkflowcloudbioinformaticsscalaexecutorhpccontainerswdl
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •374•1k•757•55•Updated Oct 16, 2025Oct 16, 2025

    • ml4h

      Public
      Python
      •
      Other
      •27•147•30•25•Updated Oct 16, 2025Oct 16, 2025

    • dig-job-server

      Public
      Vue
      •0•0•0•0•Updated Oct 16, 2025Oct 16, 2025

    • mad4hatter_wdls

      Public
      Repo for conversion of mad4hatter pipelines
      WDL
      •0•0•0•1•Updated Oct 16, 2025Oct 16, 2025

    • warp

      Public
      Warp Analysis Research Pipelines
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •111•216•6•6•Updated Oct 16, 2025Oct 16, 2025

    • dig-pigean

      Public
      PIGEAN method
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Oct 16, 2025Oct 16, 2025

    • gnomad_qc

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •28•68•6•9•Updated Oct 16, 2025Oct 16, 2025

    • gatk-sv

      Public
      A structural variation pipeline for short-read sequencing
      bioinformaticsgenomicsstructural-variationstructural-variants
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •77•194•89•32•Updated Oct 16, 2025Oct 16, 2025

    • data-registry-api

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

    • gnomad-browser

      Public
      Explore gnomAD datasets on the web
      javascriptgenomicsgnomad
      TypeScript
      •
      MIT License
      •49•85•167•8•Updated Oct 16, 2025Oct 16, 2025

    • rawls

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

    • castnet

      Public
      REST-CRUD Bindings for Neo4j in Python
      Python
      •
      MIT License
      •0•1•6•0•Updated Oct 16, 2025Oct 16, 2025

    • seqr-helm

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

    • seqr-loading-pipelines

      Public
      hail-based pipelines for annotating variant callsets and exporting them to elasticsearch
      Python
      •
      MIT License
      •22•23•17•4•Updated Oct 16, 2025Oct 16, 2025

    • stp_celldega_landscape_files

      Public
      Python
      •0•0•0•0•Updated Oct 16, 2025Oct 16, 2025

    • celldega

      Public
      Spatial omics analysis and visualization library
      Jupyter Notebook
      •
      Other
      •1•20•1•46•Updated Oct 16, 2025Oct 16, 2025

    • juniper

      Public
      Java
      •
      BSD 3-Clause "New" or "Revised" License
      •5•9•0•17•Updated Oct 16, 2025Oct 16, 2025

    • ssGSEA2.0

      Public
      Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)
      gene-setsphosphoproteomicsgseapathway-enrichment-analysisptm-seaptm-signaturesptm-siteskseaptm-enrichment-analysis
      R
      •
      Other
      •80•297•10•0•Updated Oct 16, 2025Oct 16, 2025

    • thurloe

      Public
      A simple service to store arbitrary key/value pairs
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •0•3•0•1•Updated Oct 15, 2025Oct 15, 2025

    • terra-terms-of-service

      Public
      A temporary repository to hold Terra Terms of Service before it goes to a more permanent home
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Oct 15, 2025Oct 15, 2025

    • viral-classify

      Public
      viral-ngs: taxonomic identification, classification, and filtering steps
      Python
      •
      Other
      •0•3•3•2•Updated Oct 15, 2025Oct 15, 2025

    • bmxp

      Public
      The tools that constitute a nontargeted LCMS metabolomics data processing pipeline, created and used by the Broad Institute Metabolomics Platform.
      Python
      •
      Other
      •0•13•0•0•Updated Oct 15, 2025Oct 15, 2025

    • viral-pipelines

      Public
      viral-ngs: complete pipelines
      WDL
      •
      Other
      •29•66•24•18•Updated Oct 15, 2025Oct 15, 2025

    • bican-mccarroll-manuscript1

      Public
      Scripts used to process data for the first McCarroll lab BICAN manuscript
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 15, 2025Oct 15, 2025