Repositories list

• long-read-pipelines

  Public
  Long read production pipelines

  pipelineswdlvariant-calling+ 2de-novo-assemblylong-reads

  Jupyter Notebook

  •

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

  •24•143•95•27•Updated Feb 6, 2025Feb 6, 2025

• datarepo-helm

  Public
  A helm repo for Broad Data Science Platforms helm charts

  Mustache

  •1•5•0•3•Updated Feb 6, 2025Feb 6, 2025

• gatk

  Public
  Official code repository for GATK versions 4 and up

  sciencebioinformaticsgenomics+ 6genomengssequencingdnasparkgatk

  Java

  •

  Other

  •597•1.8k•1.2k•136•Updated Feb 6, 2025Feb 6, 2025

• seqr-loading-pipelines

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

  Python

  •

  MIT License

  •20•23•24•3•Updated Feb 6, 2025Feb 6, 2025

• celldega_files_of_ist_benchmarking_paper_data

  Public
  This repo contains a Landscape files for Celldega visualization. The data was originally collected for the paper: Systematic benchmarking of imaging spatial transcriptomics platforms in FFPE tissues.

  0•0•0•0•Updated Feb 6, 2025Feb 6, 2025

• backstage

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

  TypeScript

  •0•2•4•6•Updated Feb 6, 2025Feb 6, 2025

• warp

  Public
  WDL Analysis Research Pipelines

  WDL

  •

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

  •100•207•8•18•Updated Feb 6, 2025Feb 6, 2025

• mitograph

  Public
  Rust

  •0•0•0•0•Updated Feb 6, 2025Feb 6, 2025

• bibt-libraries

  Public
  A small project linking out to our various PyPI projects.

  0•0•0•0•Updated Feb 6, 2025Feb 6, 2025

• depmap_omics

  Public
  What you need to process the Quarterly DepMap-Omics releases from Terra

  data-sciencecancer-genomicscloud-computing+ 1depmap

  HTML

  •22•114•3•4•Updated Feb 6, 2025Feb 6, 2025

• cds-daintree

  Public
  Python

  •0•0•0•1•Updated Feb 6, 2025Feb 6, 2025

• terra-featured-workspace-tests

  Public
  This code is to test that terra featured workspaces are working properly

  Python

  •0•2•0•1•Updated Feb 6, 2025Feb 6, 2025

• BEClust3D

  Public
  Jupyter Notebook

  •

  Other

  •0•0•0•8•Updated Feb 6, 2025Feb 6, 2025

• juniper

  Public
  Java

  •

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

  •5•9•0•4•Updated Feb 6, 2025Feb 6, 2025

• Drop-seq

  Public
  Java tools for analyzing Drop-seq data

  Java

  •

  MIT License

  •35•124•23•1•Updated Feb 5, 2025Feb 5, 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•49•Updated Feb 5, 2025Feb 5, 2025

• depmap-portal

  Public
  Code for the DepMap portal at depmap.org

  Python

  •

  BSD 2-Clause "Simplified" License

  •1•7•0•12•Updated Feb 5, 2025Feb 5, 2025

• exome-results-browsers

  Public
  Results browsers for case-control studies of psychiatric diseases done at the Broad Institute

  JavaScript

  •

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

  •4•11•7•3•Updated Feb 5, 2025Feb 5, 2025

• starrynight

  Public
  Library and tools to process cell painting images

  Python

  •

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

  •0•1•0•3•Updated Feb 5, 2025Feb 5, 2025

• dig-dug-portal

  Public
  Vue

  •

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

  •1•2•0•2•Updated Feb 5, 2025Feb 5, 2025

• celldega

  Public
  Spatial omics analysis and visualization library

  Jupyter Notebook

  •

  Other

  •0•4•1•11•Updated Feb 5, 2025Feb 5, 2025

• ygramul

  Public
  Hierarchical knowledge graph for PIGEAN results

  Rust

  •

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

  •0•0•0•0•Updated Feb 5, 2025Feb 5, 2025

• jump-profiling-recipe

  Public
  Workflow for processing cpg0016-jump profiles

  Python

  •

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

  •7•2•8•1•Updated Feb 5, 2025Feb 5, 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•2•Updated Feb 5, 2025Feb 5, 2025

• anvil_tdr_ingest

  Public
  Resources related to ingesting AnVIL datasets into Terra Data Repository

  Jupyter Notebook

  •2•1•0•1•Updated Feb 5, 2025Feb 5, 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•993•203•20•Updated Feb 5, 2025Feb 5, 2025

• T2T-ACE

  Public
  Accurate CNV Evaluation Using Telomere-to-Telomere Assemblies

  Jupyter Notebook

  •

  MIT License

  •0•4•1•1•Updated Feb 5, 2025Feb 5, 2025

• gnomad_methods

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

  genomicsgenomesexomes+ 1hail

  Python

  •

  MIT License

  •29•92•9•7•Updated Feb 5, 2025Feb 5, 2025

• palantir-workflows

  Public
  Utility workflows for the DSP hydro.gen team (formerly palantir)

  WDL

  •

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

  •8•22•4•5•Updated Feb 5, 2025Feb 5, 2025

• carmen-analysis

  Public
  Python

  •

  MIT License

  •0•4•0•0•Updated Feb 5, 2025Feb 5, 2025