Repositories list

• ddp-study-server

  Public
  Pepper Study Server

  Java

  •

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

  •6•8•1•3•Updated Aug 11, 2025Aug 11, 2025

• bican-mccarroll-manuscript1

  Public
  Scripts used to process data for the first McCarroll lab BICAN manuscript

  Python

  •

  MIT License

  •0•0•0•1•Updated Aug 11, 2025Aug 11, 2025

• nf-pooled-cellpainting-infra

  Public
  Python

  •0•0•0•0•Updated Aug 11, 2025Aug 11, 2025

• celldega

  Public
  Spatial omics analysis and visualization library

  Jupyter Notebook

  •

  Other

  •1•12•1•46•Updated Aug 11, 2025Aug 11, 2025

• depmap-portal

  Public
  Code for the DepMap portal at depmap.org

  Python

  •

  BSD 2-Clause "Simplified" License

  •1•8•0•10•Updated Aug 11, 2025Aug 11, 2025

• nf-pooled-cellpainting-assets

  Public
  0•0•0•0•Updated Aug 11, 2025Aug 11, 2025

• NewCpdAnalysis

  Public
  new "https://github.com/broadinstitute/cellprofiler-on-Terra/blob/v0.3.0/pipelines/cellpainting/cpd_analysis_pipeline.wdl" with runcellpose module enabled

  WDL

  •0•0•0•0•Updated Aug 11, 2025Aug 11, 2025

• seqr-helm

  Public
  Helm charts for the seqr project

  Python

  •

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

  •2•3•2•0•Updated Aug 11, 2025Aug 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

  •27•68•0•1•Updated Aug 11, 2025Aug 11, 2025

• warp

  Public
  Warp Analysis Research Pipelines

  WDL

  •

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

  •109•215•5•11•Updated Aug 11, 2025Aug 11, 2025

• thelma

  Public
  Go

  •

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

  •1•0•0•10•Updated Aug 11, 2025Aug 11, 2025

• pyqtl

  Public
  Collection of analysis tools for quantitative trait loci

  Python

  •

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

  •11•57•0•2•Updated Aug 11, 2025Aug 11, 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

  •373•1k•755•55•Updated Aug 11, 2025Aug 11, 2025

• depmap_omics

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

  data-sciencecancer-genomicscloud-computing+ 1depmap

  HTML

  •23•119•3•3•Updated Aug 11, 2025Aug 11, 2025

• warp-tools

  Public
  This repository contains all containers that WARP uses.

  Python

  •

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

  •2•10•1•12•Updated Aug 11, 2025Aug 11, 2025

• seqr

  Public
  web-based analysis tool for rare disease genomics

  Python

  •

  GNU Affero General Public License v3.0

  •90•192•55•1•Updated Aug 11, 2025Aug 11, 2025

• firecloud-orchestration

  Public
  Scala

  •

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

  •4•31•0•1•Updated Aug 11, 2025Aug 11, 2025

• gatk-sv

  Public
  A structural variation pipeline for short-read sequencing

  bioinformaticsgenomicsstructural-variation+ 1structural-variants

  Python

  •

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

  •77•191•87•27•Updated Aug 11, 2025Aug 11, 2025

• rawls

  Public
  Rawls service for DSDE

  Scala

  •

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

  •4•25•0•5•Updated Aug 11, 2025Aug 11, 2025

• dig-aggregator-methods

  Public
  Monorepo of methods implemented for the Aggregator

  Python

  •

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

  •2•1•0•8•Updated Aug 11, 2025Aug 11, 2025

• glama

  Public
  Genomic long-read analysis modules and applications

  Rust

  •

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

  •0•0•0•2•Updated Aug 11, 2025Aug 11, 2025

• carpenter-singh-lab-guide

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

  •0•1•1•1•Updated Aug 11, 2025Aug 11, 2025

• jump-profiling-recipe

  Public
  Workflow for processing cpg0016-jump profiles

  Python

  •

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

  •8•4•12•2•Updated Aug 11, 2025Aug 11, 2025

• gnomad_qc

  Public
  Jupyter Notebook

  •

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

  •27•68•6•13•Updated Aug 11, 2025Aug 11, 2025

• juniper

  Public
  Java

  •

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

  •5•9•0•18•Updated Aug 11, 2025Aug 11, 2025

• dsp-appsec-trivy-action

  Public
  DSP Appsec team action, which checks if a Dockerfile is using our base "blessed" image, if yes, no scan is needed, otherwise this action will build image and scan it with Trivy tool.

  2•2•0•1•Updated Aug 11, 2025Aug 11, 2025

• celldega_Xenium_Prime_Ovarian_Cancer_FFPE_XRrun_outs_v3

  Public
  Include cell types

  1•0•0•0•Updated Aug 11, 2025Aug 11, 2025

• data-registry-api

  Public
  Python

  •

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

  •1•1•0•1•Updated Aug 11, 2025Aug 11, 2025

• dig-dug-portal

  Public
  Vue

  •

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

  •2•2•1•0•Updated Aug 11, 2025Aug 11, 2025

• gatk

  Public
  Official code repository for GATK versions 4 and up

  sciencebioinformaticsgenomics+ 6genomengssequencingdnasparkgatk

  Java

  •

  Other

  •608•1.8k•1.3k•140•Updated Aug 11, 2025Aug 11, 2025