Repositories list

• palantir-workflows

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

  WDL

  •

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

  •8•19•4•4•Updated Nov 19, 2024Nov 19, 2024

• stp_space_ranger

  Public
  WDL

  •0•0•0•0•Updated Nov 19, 2024Nov 19, 2024

• 2024-09-27-python-intro-lesson

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

  HTML

  •

  Other

  •1•0•0•1•Updated Nov 19, 2024Nov 19, 2024

• 2024-09-20-unix-shell-lesson

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

  R

  •

  Other

  •0•0•0•0•Updated Nov 19, 2024Nov 19, 2024

• seqr-loading-pipelines

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

  Python

  •

  MIT License

  •20•22•32•4•Updated Nov 19, 2024Nov 19, 2024

• depmap-portal

  Public
  Code for the DepMap portal at depmap.org

  Python

  •

  BSD 2-Clause "Simplified" License

  •1•7•0•6•Updated Nov 19, 2024Nov 19, 2024

• gatk

  Public
  Official code repository for GATK versions 4 and up

  sciencebioinformaticsgenomics+ 6genomengssequencingdnasparkgatk

  Java

  •

  Other

  •592•1.7k•1.2k•137•Updated Nov 19, 2024Nov 19, 2024

• 2024-06-24-python-novice-lesson

  Public
  based on https://swcarpentry.github.io/python-novice-inflammation/

  Jupyter Notebook

  •

  Other

  •0•0•0•0•Updated Nov 19, 2024Nov 19, 2024

• seqr

  Public
  web-based analysis tool for rare disease genomics

  Python

  •

  GNU Affero General Public License v3.0

  •89•176•56•3•Updated Nov 18, 2024Nov 18, 2024

• hca-ingest-migration

  Public
  Working Repo for migration of HCA ingest from Dagster 0.12 to Dagster 1.8 (or 1.9)

  Python

  •

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

  •2•0•0•1•Updated Nov 18, 2024Nov 18, 2024

• penyu

  Public
  Write some RDF as Turtle

  Rust

  •

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

  •0•0•0•0•Updated Nov 18, 2024Nov 18, 2024

• seqr-helm

  Public
  Helm charts for the seqr project

  Python

  •

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

  •1•1•0•3•Updated Nov 18, 2024Nov 18, 2024

• gnomad-browser

  Public
  Explore gnomAD datasets on the web

  javascriptgenomicsgnomad

  TypeScript

  •

  MIT License

  •44•81•160•13•Updated Nov 18, 2024Nov 18, 2024

• tgg-terraform-modules

  Public
  HCL

  •2•0•4•1•Updated Nov 18, 2024Nov 18, 2024

• ops-terra-utils

  Public
  Python

  •0•3•0•1•Updated Nov 18, 2024Nov 18, 2024

• warp

  Public
  WDL Analysis Research Pipelines

  WDL

  •

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

  •97•202•7•12•Updated Nov 18, 2024Nov 18, 2024

• backstage

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

  TypeScript

  •0•2•0•2•Updated Nov 18, 2024Nov 18, 2024

• ddp-study-server

  Public
  Pepper Study Server

  Java

  •

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

  •5•8•1•3•Updated Nov 18, 2024Nov 18, 2024

• juniper

  Public
  Java

  •

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

  •5•8•0•8•Updated Nov 18, 2024Nov 18, 2024

• 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•7•Updated Nov 18, 2024Nov 18, 2024

• gnomad-deployments

  Public
  kustomizations for current gnomad project kubernetes deployments

  0•0•0•2•Updated Nov 18, 2024Nov 18, 2024

• dig-dug-portal

  Public
  Vue

  •

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

  •1•2•0•0•Updated Nov 18, 2024Nov 18, 2024

• rawls

  Public
  Rawls service for DSDE

  Scala

  •

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

  •4•26•0•14•Updated Nov 18, 2024Nov 18, 2024

• data-registry-api

  Public
  Python

  •

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

  •1•1•0•0•Updated Nov 18, 2024Nov 18, 2024

• datarepo-helm

  Public
  A helm repo for Broad Data Science Platforms helm charts

  Mustache

  •1•5•0•5•Updated Nov 18, 2024Nov 18, 2024

• molecular-data-provider

  Public
  Molecular Data Provider

  Python

  •

  MIT License

  •8•11•3•5•Updated Nov 18, 2024Nov 18, 2024

• DBP_Doe

  Public
  files that will be used to train the 3D Unet on CHTC

  Python

  •0•0•0•0•Updated Nov 18, 2024Nov 18, 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 18, 2024Nov 18, 2024

• pe2loaddata

  Public
  Script to parse a Phenix metadata XML file and generate a .CSV for CellProfiler's loaddata module

  carpenter-lab

  Python

  •

  BSD 2-Clause "Simplified" License

  •7•2•11•3•Updated Nov 18, 2024Nov 18, 2024

• warp-tools

  Public
  This repository contains all containers that WARP uses.

  Python

  •

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

  •2•8•1•11•Updated Nov 18, 2024Nov 18, 2024