Repositories list

• BEClust3D

  Public
  Jupyter Notebook

  •

  Other

  •0•0•0•8•Updated Feb 11, 2025Feb 11, 2025

• gatk

  Public
  Official code repository for GATK versions 4 and up

  sciencebioinformaticsgenomics+ 6genomengssequencingdnasparkgatk

  Java

  •

  Other

  •596•1.8k•1.2k•137•Updated Feb 11, 2025Feb 11, 2025

• 2024-09-27-python-intro-lesson

  Public
  Based on https://github.com/librarycarpentry/lc-python-intro/

  HTML

  •

  Other

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

• 2024-09-20-unix-shell-lesson

  Public
  Based on https://github.com/datacarpentry/shell-genomics/

  R

  •

  Other

  •0•0•0•0•Updated Feb 11, 2025Feb 11, 2025

• rawls

  Public
  Rawls service for DSDE

  Scala

  •

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

  •4•26•0•12•Updated Feb 11, 2025Feb 11, 2025

• carmen-analysis

  Public
  Python

  •

  MIT License

  •0•4•0•0•Updated Feb 10, 2025Feb 10, 2025

• puppet-sentinelone_agent

  Public
  Puppet module to manage the SentinelOne agent

  Ruby

  •

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

  •2•1•1•1•Updated Feb 10, 2025Feb 10, 2025

• SpliceAI-lookup

  Public
  Website for checking SpliceAI and Pangolin scores:

  pangolinspliceai

  HTML

  •

  MIT License

  •7•20•3•0•Updated Feb 10, 2025Feb 10, 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 10, 2025Feb 10, 2025

• depmap-portal

  Public
  Code for the DepMap portal at depmap.org

  Python

  •

  BSD 2-Clause "Simplified" License

  •1•7•0•9•Updated Feb 10, 2025Feb 10, 2025

• seqr-loading-pipelines

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

  Python

  •

  MIT License

  •20•23•24•6•Updated Feb 10, 2025Feb 10, 2025

• dig-dug-portal

  Public
  Vue

  •

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

  •1•2•0•0•Updated Feb 10, 2025Feb 10, 2025

• backstage

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

  TypeScript

  •0•2•4•5•Updated Feb 10, 2025Feb 10, 2025

• 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 10, 2025Feb 10, 2025

• gnomad_methods

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

  genomicsgenomesexomes+ 1hail

  Python

  •

  MIT License

  •29•92•8•7•Updated Feb 10, 2025Feb 10, 2025

• firecloud-orchestration

  Public
  Scala

  •

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

  •4•31•0•5•Updated Feb 10, 2025Feb 10, 2025

• sam

  Public
  workbench identity and access management

  Scala

  •

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

  •12•42•3•30•Updated Feb 10, 2025Feb 10, 2025

• workbench-libs

  Public
  Workbench utility libraries

  Scala

  •

  Other

  •4•9•0•2•Updated Feb 10, 2025Feb 10, 2025

• gnomad-browser

  Public
  Explore gnomAD datasets on the web

  javascriptgenomicsgnomad

  TypeScript

  •

  MIT License

  •45•81•162•14•Updated Feb 10, 2025Feb 10, 2025

• warp

  Public
  WDL Analysis Research Pipelines

  WDL

  •

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

  •100•208•7•17•Updated Feb 10, 2025Feb 10, 2025

• celldega

  Public
  Spatial omics analysis and visualization library

  Jupyter Notebook

  •

  Other

  •0•4•1•12•Updated Feb 10, 2025Feb 10, 2025

• datarepo-helm

  Public
  A helm repo for Broad Data Science Platforms helm charts

  Mustache

  •1•5•0•3•Updated Feb 10, 2025Feb 10, 2025

• gatk-sv

  Public
  A structural variation pipeline for short-read sequencing

  bioinformaticsgenomicsstructural-variation+ 1structural-variants

  Python

  •

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

  •72•178•74•21•Updated Feb 10, 2025Feb 10, 2025

• ops-terra-utils

  Public
  Python

  •0•4•0•4•Updated Feb 10, 2025Feb 10, 2025

• shared-workflows

  Public
  GitHub Action workflows that can be shared by multiple repositories

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

  •1•0•3•0•Updated Feb 10, 2025Feb 10, 2025

• juniper

  Public
  Java

  •

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

  •5•9•0•16•Updated Feb 10, 2025Feb 10, 2025

• glama

  Public
  Genomic long-read analysis modules and applications

  Rust

  •

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

  •0•0•0•2•Updated Feb 10, 2025Feb 10, 2025

• jump-profiling-recipe

  Public
  Workflow for processing cpg0016-jump profiles

  Python

  •

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

  •7•2•8•2•Updated Feb 10, 2025Feb 10, 2025

• carpenter-singh-lab-standards

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

  •0•0•3•1•Updated Feb 10, 2025Feb 10, 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•65•0•3•Updated Feb 10, 2025Feb 10, 2025