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    1.3k repositories

    • seqr-helm

      Public
      Helm charts for the seqr project
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•0•2•Updated Nov 30, 2024Nov 30, 2024

    • seqr-loading-pipelines

      Public
      hail-based pipelines for annotating variant callsets and exporting them to elasticsearch
      Python
      •
      MIT License
      •20•22•30•1•Updated Nov 30, 2024Nov 30, 2024

    • CNV-Mag

      Public
      A Tool to Visualize CNV Events in WGS Data
      MIT License
      •0•0•0•0•Updated Nov 30, 2024Nov 30, 2024

    • heimdall

      Public
      Shell
      •0•0•0•0•Updated Nov 30, 2024Nov 30, 2024

    • pyqtl

      Public
      Collection of analysis tools for quantitative trait loci
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •8•41•0•2•Updated Nov 30, 2024Nov 30, 2024

    • pav-wdl

      Public
      Workspace for WDL implementation of PAV
      WDL
      •3•0•0•0•Updated Nov 29, 2024Nov 29, 2024

    • delphy

      Public
      Fast, scalable, accurate and accessible Bayesian phylogenetics
      C++
      •
      Other
      •3•27•0•0•Updated Nov 29, 2024Nov 29, 2024

    • str-analysis

      Public
      Scripts and utilities related to analyzing short tandem repeats (STRs).
      Python
      •
      MIT License
      •8•32•1•0•Updated Nov 29, 2024Nov 29, 2024

    • juniper

      Public
      Java
      •
      BSD 3-Clause "New" or "Revised" License
      •5•8•0•8•Updated Nov 29, 2024Nov 29, 2024

    • hidive

      Public
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•3•2•Updated Nov 28, 2024Nov 28, 2024

    • gnomad_methods

      Public
      Hail helper functions for the gnomAD project and Translational Genomics Group
      genomicsgenomesexomeshail
      Python
      •
      MIT License
      •29•89•10•10•Updated Nov 28, 2024Nov 28, 2024

    • ema

      Public
      Jupyter Notebook
      •
      MIT License
      •0•4•0•0•Updated Nov 28, 2024Nov 28, 2024

    • thurloe

      Public
      A simple service to store arbitrary key/value pairs
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •0•3•0•5•Updated Nov 28, 2024Nov 28, 2024

    • gatk

      Public
      Official code repository for GATK versions 4 and up
      sciencebioinformaticsgenomicsgenomengssequencingdnasparkgatk
      Java
      •
      Other
      •594•1.7k•1.2k•136•Updated Nov 28, 2024Nov 28, 2024

    • depmap-portal

      Public
      Code for the DepMap portal at depmap.org
      Python
      •
      BSD 2-Clause "Simplified" License
      •1•7•0•8•Updated Nov 27, 2024Nov 27, 2024

    • ml4h

      Public
      Python
      •
      Other
      •23•124•30•20•Updated Nov 27, 2024Nov 27, 2024

    • lembic

      Public
      Distilling some data for CFDE
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Nov 27, 2024Nov 27, 2024

    • seqr

      Public
      web-based analysis tool for rare disease genomics
      Python
      •
      GNU Affero General Public License v3.0
      •89•177•48•3•Updated Nov 27, 2024Nov 27, 2024

    • poasta

      Public
      Fast and exact gap-affine partial order alignment
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •2•40•7•2•Updated Nov 27, 2024Nov 27, 2024

    • gatk-sv

      Public
      A structural variation pipeline for short-read sequencing
      bioinformaticsgenomicsstructural-variationstructural-variants
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •70•172•73•22•Updated Nov 27, 2024Nov 27, 2024

    • DBP_Doe

      Public
      files that will be used to train the 3D Unet on CHTC
      Python
      •0•0•0•0•Updated Nov 27, 2024Nov 27, 2024

    • celldega_Xenium_Prime_Human_Skin_FFPE_outs_Cellpose2

      Public
      Jupyter Notebook
      •
      Other
      •1•0•0•0•Updated Nov 27, 2024Nov 27, 2024

    • dig-aggregator-methods

      Public
      Monorepo of methods implemented for the Aggregator
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•1•0•7•Updated Nov 27, 2024Nov 27, 2024

    • ddp-study-server

      Public
      Pepper Study Server
      Java
      •
      BSD 3-Clause "New" or "Revised" License
      •5•8•1•4•Updated Nov 27, 2024Nov 27, 2024

    • mcl_imput

      Public
      WDL Analysis Research Pipelines
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •99•0•0•1•Updated Nov 27, 2024Nov 27, 2024

    • 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
      •360•1k•744•49•Updated Nov 27, 2024Nov 27, 2024

    • rawls

      Public
      Rawls service for DSDE
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •4•26•0•13•Updated Nov 27, 2024Nov 27, 2024

    • 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•63•0•1•Updated Nov 27, 2024Nov 27, 2024

    • dig-dug-portal

      Public
      Vue
      •
      BSD 3-Clause "New" or "Revised" License
      •1•2•0•1•Updated Nov 27, 2024Nov 27, 2024

    • warp

      Public
      WDL Analysis Research Pipelines
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •99•202•7•15•Updated Nov 27, 2024Nov 27, 2024