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    1.3k repositories

    • depmap-portal

      Public
      Code for the DepMap portal at depmap.org
      Python
      •
      BSD 2-Clause "Simplified" License
      •1•7•0•14•Updated Mar 12, 2025Mar 12, 2025

    • hidive

      Public
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•5•1•Updated Mar 12, 2025Mar 12, 2025

    • dig-dug-portal

      Public
      Vue
      •
      BSD 3-Clause "New" or "Revised" License
      •1•2•1•1•Updated Mar 12, 2025Mar 12, 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 12, 2025Mar 12, 2025

    • monorepo

      Public
      Compendium of tools for the Imaging Platform
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•10•7•0•Updated Mar 12, 2025Mar 12, 2025

    • gatk

      Public
      Official code repository for GATK versions 4 and up
      sciencebioinformaticsgenomicsgenomengssequencingdnasparkgatk
      Java
      •
      Other
      •602•1.8k•1.2k•132•Updated Mar 11, 2025Mar 11, 2025

    • firecloud-orchestration

      Public
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •4•31•0•6•Updated Mar 11, 2025Mar 11, 2025

    • delphy

      Public
      Fast, scalable, accurate and accessible Bayesian phylogenetics
      C++
      •
      Other
      •4•33•0•1•Updated Mar 11, 2025Mar 11, 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•48•Updated Mar 11, 2025Mar 11, 2025

    • starrynight

      Public
      Library and tools to process cell painting images
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•2•23•3•Updated Mar 11, 2025Mar 11, 2025

    • g2p-bis

      Public
      Genomics To Proteins - Bio Integration Suite
      JavaScript
      •
      MIT License
      •0•0•0•0•Updated Mar 11, 2025Mar 11, 2025

    • rawls

      Public
      Rawls service for DSDE
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •4•26•0•13•Updated Mar 11, 2025Mar 11, 2025

    • seqr

      Public
      web-based analysis tool for rare disease genomics
      Python
      •
      GNU Affero General Public License v3.0
      •89•185•49•4•Updated Mar 11, 2025Mar 11, 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•67•0•3•Updated Mar 11, 2025Mar 11, 2025

    • cds-daintree

      Public
      Python
      •0•0•0•1•Updated Mar 11, 2025Mar 11, 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•3•Updated Mar 11, 2025Mar 11, 2025

    • dsp-appsec-infrastructure-apps

      Public
      This repository hosts DSP AppSec internal infrastructure apps deployed in GKE.
      application-securityappsecsecurity-scannersecure-developmentsecurity-automationsecurity-toolsdevsecopssecurity-scanappsecurityappsec-tools
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•6•0•2•Updated Mar 11, 2025Mar 11, 2025

    • warp

      Public
      WDL Analysis Research Pipelines
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •102•210•5•18•Updated Mar 11, 2025Mar 11, 2025

    • BEClust3D

      Public
      Jupyter Notebook
      •
      Other
      •0•0•0•8•Updated Mar 11, 2025Mar 11, 2025

    • picard

      Public
      A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
      Java
      •
      MIT License
      •372•999•203•22•Updated Mar 11, 2025Mar 11, 2025

    • gnomad_local_ancestry

      Public
      Hail batch pipeline and scripts for local ancestry inference
      Python
      •
      MIT License
      •0•5•32•0•Updated Mar 11, 2025Mar 11, 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.
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•8•2•2•Updated Mar 11, 2025Mar 11, 2025

    • gatk-sv

      Public
      A structural variation pipeline for short-read sequencing
      bioinformaticsgenomicsstructural-variationstructural-variants
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •75•182•76•21•Updated Mar 11, 2025Mar 11, 2025

    • viral-references

      Public
      Reference tables for viral genomics
      BSD 2-Clause "Simplified" License
      •1•3•0•0•Updated Mar 11, 2025Mar 11, 2025

    • sam

      Public
      workbench identity and access management
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •12•42•3•30•Updated Mar 11, 2025Mar 11, 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 11, 2025Mar 11, 2025

    • carpenter-singh-lab-standards

      Public
      BSD 3-Clause "New" or "Revised" License
      •0•0•3•0•Updated Mar 11, 2025Mar 11, 2025

    • mitograph

      Public
      Rust
      •0•0•0•0•Updated Mar 11, 2025Mar 11, 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•1•Updated Mar 11, 2025Mar 11, 2025

    • 2024-09-27-python-intro-lesson

      Public
      Based on https://github.com/librarycarpentry/lc-python-intro/
      HTML
      •
      Other
      •1•0•0•2•Updated Mar 11, 2025Mar 11, 2025