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    1.3k repositories

    • pipecraft

      Public
      Library and tools to build and execute pipelines
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•2•0•1•Updated Jan 4, 2025Jan 4, 2025

    • depmap-portal

      Public
      Code for the DepMap portal at depmap.org
      Python
      •
      BSD 2-Clause "Simplified" License
      •1•7•0•7•Updated Jan 4, 2025Jan 4, 2025

    • juniper

      Public
      Java
      •
      BSD 3-Clause "New" or "Revised" License
      •5•9•0•16•Updated Jan 4, 2025Jan 4, 2025

    • jump_hub

      Public
      Collection of JUMP documentation and projects for internal and public consumption
      compbioprofiling
      Python
      •1•2•6•2•Updated Jan 3, 2025Jan 3, 2025

    • starrynight

      Public
      Library and tools to process cell painting images
      TypeScript
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•2•Updated Jan 3, 2025Jan 3, 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 3, 2025Jan 3, 2025

    • ygramul

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

    • long-read-pipelines

      Public
      Long read production pipelines
      pipelineswdlvariant-callingde-novo-assemblylong-reads
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •24•142•95•27•Updated Jan 3, 2025Jan 3, 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•49•Updated Jan 3, 2025Jan 3, 2025

    • warp

      Public
      WDL Analysis Research Pipelines
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •98•207•7•22•Updated Jan 3, 2025Jan 3, 2025

    • gatk-sv

      Public
      A structural variation pipeline for short-read sequencing
      bioinformaticsgenomicsstructural-variationstructural-variants
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •71•174•74•27•Updated Jan 3, 2025Jan 3, 2025

    • python-sudoers

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

    • firecloud-orchestration

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

    • celldega

      Public
      Jupyter Notebook
      •
      Other
      •0•0•1•6•Updated Jan 3, 2025Jan 3, 2025

    • gnomad-toolbox

      Public
      This repository provides a set of Python functions to simplify working with gnomAD Hail Tables. It includes tools for data access, filtering, and analysis.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•2•Updated Jan 3, 2025Jan 3, 2025

    • seqr

      Public
      web-based analysis tool for rare disease genomics
      Python
      •
      GNU Affero General Public License v3.0
      •89•179•47•6•Updated Jan 3, 2025Jan 3, 2025

    • sam

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

    • dig-dug-portal

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

    • bits-appengine

      Public
      BITS AppEngine Python Package
      Python
      •0•0•0•0•Updated Jan 3, 2025Jan 3, 2025

    • 2021_09_01_VarChAMP

      Public
      Jupyter Notebook
      •
      MIT License
      •4•0•13•0•Updated Jan 3, 2025Jan 3, 2025

    • 2021_09_01_VarChAMP-data

      Public
      Image analysis profiles for VarChAMP project
      BSD 3-Clause "New" or "Revised" License
      •2•0•0•0•Updated Jan 3, 2025Jan 3, 2025

    • carpenter-singh-lab-standards

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

    • cellpainting-gallery

      Public
      Cell Painting Gallery
      Other
      •12•74•6•0•Updated Jan 3, 2025Jan 3, 2025

    • cpg

      Public
      Cell painting gallery
      TypeScript
      •
      BSD 3-Clause "New" or "Revised" License
      •3•2•14•8•Updated Jan 3, 2025Jan 3, 2025

    • cytoskel

      Public
      Cloud infrastrcuture abstraction
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•0•1•1•Updated Jan 3, 2025Jan 3, 2025

    • deepometry

      Public
      Image classification for imaging flow cytometry.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •7•27•3•3•Updated Jan 3, 2025Jan 3, 2025

    • jump-profiling-recipe

      Public
      Workflow for processing cpg0016-jump profiles
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •6•2•6•2•Updated Jan 3, 2025Jan 3, 2025

    • NeuroPainting

      Public
      Pilot experiments for establishing a neuronal Cell Painting protocol
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Jan 3, 2025Jan 3, 2025

    • pe2loaddata

      Public
      Script to parse a Phenix metadata XML file and generate a .CSV for CellProfiler's loaddata module
      carpenter-lab
      Python
      •
      BSD 2-Clause "Simplified" License
      •7•2•10•3•Updated Jan 3, 2025Jan 3, 2025

    • ml4h

      Public
      Python
      •
      Other
      •24•126•30•21•Updated Jan 3, 2025Jan 3, 2025