Repositories list

• jump-profiling-recipe

  Public
  Workflow for processing cpg0016-jump profiles

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •8•3•10•3•Updated Mar 13, 2025Mar 13, 2025

• rawls

  Public
  Rawls service for DSDE

  Scala

  •

  BSD 3-Clause "New" or "Revised" License

  •4•26•0•12•Updated Mar 13, 2025Mar 13, 2025

• mitograph

  Public
  Rust

  •0•0•0•0•Updated Mar 13, 2025Mar 13, 2025

• scp-rails-baseimage

  Public
  Docker image builder repository to build Phusion/Passenger & Single Cell Portal docker images using managed GCR Ubuntu base image

  Shell

  •0•2•0•0•Updated Mar 13, 2025Mar 13, 2025

• dsp-appsec-infrastructure-apps

  Public
  This repository hosts DSP AppSec internal infrastructure apps deployed in GKE.

  application-securityappsecsecurity-scanner+ 10secure-developmentsecurity-automationsecurity-toolsdevsecopssecurity-scanappsecurityappsec-tools+ 3

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •2•6•0•3•Updated Mar 13, 2025Mar 13, 2025

• depmap-portal

  Public
  Code for the DepMap portal at depmap.org

  Python

  •

  BSD 2-Clause "Simplified" License

  •1•7•0•12•Updated Mar 13, 2025Mar 13, 2025

• dig-bioindex

  Public
  BIO index for genetic records stored in S3 and FastAPI server.

  ot2od036440

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •6•6•0•3•Updated Mar 13, 2025Mar 13, 2025

• juniper

  Public
  Java

  •

  BSD 3-Clause "New" or "Revised" License

  •5•9•0•7•Updated Mar 13, 2025Mar 13, 2025

• cromwell

  Public
  Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

  dockerapplicationcloud+ 10bioinformaticsscalaexecutorhpccontainerswdlga4gh+ 3

  Scala

  •

  BSD 3-Clause "New" or "Revised" License

  •359•1k•744•47•Updated Mar 13, 2025Mar 13, 2025

• gatk

  Public
  Official code repository for GATK versions 4 and up

  sciencebioinformaticsgenomics+ 6genomengssequencingdnasparkgatk

  Java

  •

  Other

  •602•1.8k•1.2k•133•Updated Mar 13, 2025Mar 13, 2025

• scp-ingest-pipeline

  Public
  File Ingest Pipeline for Single Cell Portal

  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •0•5•0•0•Updated Mar 13, 2025Mar 13, 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•1•Updated Mar 13, 2025Mar 13, 2025

• gnomad_qc

  Public
  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •27•69•6•14•Updated Mar 13, 2025Mar 13, 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 13, 2025Mar 13, 2025

• kage-lite-development

  Public
  Python

  •0•0•10•0•Updated Mar 13, 2025Mar 13, 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 13, 2025Mar 13, 2025

• gnomad_methods

  Public
  Hail helper functions for the gnomAD project and Translational Genomics Group

  genomicsgenomesexomes+ 1hail

  Python

  •

  MIT License

  •29•93•8•9•Updated Mar 13, 2025Mar 13, 2025

• gnomad-constraint

  Public
  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•5•0•0•Updated Mar 13, 2025Mar 13, 2025

• viral-pipelines

  Public
  viral-ngs: complete pipelines

  WDL

  •

  Other

  •28•61•24•18•Updated Mar 13, 2025Mar 13, 2025

• seqr-loading-pipelines

  Public
  hail-based pipelines for annotating variant callsets and exporting them to elasticsearch

  Python

  •

  MIT License

  •20•23•23•8•Updated Mar 13, 2025Mar 13, 2025

• gatk-sv

  Public
  A structural variation pipeline for short-read sequencing

  bioinformaticsgenomicsstructural-variation+ 1structural-variants

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •75•182•78•22•Updated Mar 13, 2025Mar 13, 2025

• celldega

  Public
  Spatial omics analysis and visualization library

  Jupyter Notebook

  •

  Other

  •0•5•1•14•Updated Mar 13, 2025Mar 13, 2025

• SpliceAI-lookup

  Public
  Website for checking SpliceAI and Pangolin scores:

  pangolinspliceai

  HTML

  •

  MIT License

  •7•22•2•0•Updated Mar 13, 2025Mar 13, 2025

• starrynight

  Public
  Library and tools to process cell painting images

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•2•20•3•Updated Mar 13, 2025Mar 13, 2025

• sherlock

  Public
  DSP DevOps's deployment source-of-truth service

  golangpostgresgorm

  Go

  •

  BSD 3-Clause "New" or "Revised" License

  •0•1•0•11•Updated Mar 13, 2025Mar 13, 2025

• BEClust3D

  Public
  Jupyter Notebook

  •

  Other

  •0•0•0•8•Updated Mar 12, 2025Mar 12, 2025

• firecloud-orchestration

  Public
  Scala

  •

  BSD 3-Clause "New" or "Revised" License

  •4•31•0•6•Updated Mar 12, 2025Mar 12, 2025

• jati

  Public
  DSL support library for Rust

  Rust

  •

  BSD 3-Clause "New" or "Revised" License

  •0•1•0•0•Updated Mar 12, 2025Mar 12, 2025

• gnomad-browser

  Public
  Explore gnomAD datasets on the web

  javascriptgenomicsgnomad

  TypeScript

  •

  MIT License

  •47•81•165•12•Updated Mar 12, 2025Mar 12, 2025

• backstage

  Public
  Broad Institute Engineering Portal is an Internal Developer Platform (Spotify Backstage by another name)

  TypeScript

  •0•2•3•8•Updated Mar 12, 2025Mar 12, 2025