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    • 2021_09_01_VarChAMP_CellProfiler_Pipeline

      Public
      Instructions and recipes to run Distributed CellProfiler for processing VarChAMP variant painting images in the CS lab.
      Jupyter Notebook
      •0•0•0•0•Updated Mar 30, 2025Mar 30, 2025

    • seqr-helm

      Public
      Helm charts for the seqr project
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•3•0•0•Updated Mar 29, 2025Mar 29, 2025

    • seqr-loading-pipelines

      Public
      hail-based pipelines for annotating variant callsets and exporting them to elasticsearch
      Python
      •
      MIT License
      •20•23•22•2•Updated Mar 29, 2025Mar 29, 2025

    • jati

      Public
      DSL support library for Rust
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Mar 29, 2025Mar 29, 2025

    • epi-SHARE-seq-pipeline

      Public
      Epigenomics Program pipeline to analyze SHARE-seq data.
      WDL
      •
      MIT License
      •3•20•28•0•Updated Mar 29, 2025Mar 29, 2025

    • viral-core

      Public
      viral-ngs: read QC, barcode metrics, spike-in metrics, Illumina metrics and demux
      Python
      •
      Other
      •1•4•10•1•Updated Mar 29, 2025Mar 29, 2025

    • jump_hub

      Public
      The one-stop-shop for Morphological Profiling and JUMP Cell-Painting
      compbioprofiling
      Python
      •
      Creative Commons Zero v1.0 Universal
      •1•4•7•0•Updated Mar 29, 2025Mar 29, 2025

    • gatk-sv

      Public
      A structural variation pipeline for short-read sequencing
      bioinformaticsgenomicsstructural-variationstructural-variants
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •75•185•79•23•Updated Mar 29, 2025Mar 29, 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•5•Updated Mar 29, 2025Mar 29, 2025

    • starrynight

      Public
      Library and tools to process optical pooled screening datasets
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•2•27•2•Updated Mar 29, 2025Mar 29, 2025

    • viral-pipelines

      Public
      viral-ngs: complete pipelines
      WDL
      •
      Other
      •28•61•24•18•Updated Mar 29, 2025Mar 29, 2025

    • ml4h

      Public
      Python
      •
      Other
      •25•130•30•21•Updated Mar 29, 2025Mar 29, 2025

    • depmap-portal

      Public
      Code for the DepMap portal at depmap.org
      Python
      •
      BSD 2-Clause "Simplified" License
      •1•7•0•8•Updated Mar 29, 2025Mar 29, 2025

    • viral-workshops

      Public
      Documentation for viral analysis workshops
      HTML
      •
      BSD 2-Clause "Simplified" License
      •0•3•0•1•Updated Mar 29, 2025Mar 29, 2025

    • gatk

      Public
      Official code repository for GATK versions 4 and up
      sciencebioinformaticsgenomicsgenomengssequencingdnasparkgatk
      Java
      •
      Other
      •603•1.8k•1.2k•139•Updated Mar 28, 2025Mar 28, 2025

    • wdl-ide

      Public
      Rich IDE support for Workflow Description Language
      vscodetheiadockeridewdlcromwelllspwdl-devtools
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •9•42•12•1•Updated Mar 28, 2025Mar 28, 2025

    • firecloud-orchestration

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

    • rawls

      Public
      Rawls service for DSDE
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •4•26•0•14•Updated Mar 28, 2025Mar 28, 2025

    • GeneTEA

      Public
      Gene-Term Enrichment Analysis (GeneTEA)
      Jupyter Notebook
      •0•0•0•6•Updated Mar 28, 2025Mar 28, 2025

    • thurloe

      Public
      A simple service to store arbitrary key/value pairs
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •0•3•0•5•Updated Mar 28, 2025Mar 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 Mar 28, 2025Mar 28, 2025

    • depmap_omics

      Public
      What you need to process the Quarterly DepMap-Omics releases from Terra
      data-sciencecancer-genomicscloud-computingdepmap
      HTML
      •22•114•3•7•Updated Mar 28, 2025Mar 28, 2025

    • 2025_Grigoryan_Proteomics

      Public
      Repo for analysis of the Nomic Bio proteomics pilot data, collected as part of the OASIS Consortium
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •2•0•4•0•Updated Mar 28, 2025Mar 28, 2025

    • modal

      Public
      Ontology for biological nature of information from an experimental activity, independent of method.
      Creative Commons Zero v1.0 Universal
      •0•0•0•0•Updated Mar 28, 2025Mar 28, 2025

    • uger-instructions

      Public
      0•0•0•0•Updated Mar 28, 2025Mar 28, 2025

    • TAG-public

      Public
      Official workflows published by the Broad Institute's Genomics Platform Translation Analysis Group (TAG)
      WDL
      •3•5•1•16•Updated Mar 28, 2025Mar 28, 2025

    • agora

      Public
      It's a methods repository!
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •2•11•0•1•Updated Mar 28, 2025Mar 28, 2025

    • juniper

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

    • python-sudoers

      Public
      Python library for parsing a Linux sudoers file
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •7•7•2•0•Updated Mar 28, 2025Mar 28, 2025

    • PANOPLY

      Public
      Repository for the Broad Institute Proteogenomic Data Analysis Center (PGDAC) established by the NIH Clinical Proteomics Tumor Analysis Consortium (CPTAC)
      R
      •
      Other
      •15•34•0•1•Updated Mar 28, 2025Mar 28, 2025