Broad Institute

Repositories

• covid19-testing

  COVID-19 Diagnostic Processing Dashboard
  HTML MIT 2 15 2 0 Updated Dec 2, 2020

• datarepo-helm-definitions

  Helm deployment specific values and definitions for Dev, Integration and Prod
  Shell 0 0 0 3 Updated Dec 1, 2020

• picard

  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 299 627 160 26 Updated Dec 2, 2020

• single_cell_portal_core

  Rails/Docker application for the Broad Institute's single cell RNA-seq data portal

  rna-seq-analysis single-cell-genomics human-cell-atlas
  Ruby BSD-3-Clause 19 33 0 3 Updated Dec 1, 2020

• gatk-sv
  wdl BSD-3-Clause 6 30 34 4 Updated Dec 1, 2020

• ml4h
  1 package Python 1 3 31 (1 issue needs help) 9 Updated Dec 1, 2020

• rawls

  Rawls service for DSDE
  Scala 2 13 0 11 Updated Dec 2, 2020

• puppet-ssh

  Forked from xaque208/puppet-ssh

  An SSH module from the Puppet Labs Ops team
  Puppet 3 0 0 0 Updated Dec 1, 2020

• firecloud-orchestration
  Scala BSD-3-Clause 1 21 0 4 Updated Dec 1, 2020

• terra-helm

  A helm repo for Terra from Broad Data Science Platforms Group
  Smarty 1 2 0 6 Updated Dec 1, 2020

• datarepo-actions
  Shell 1 0 0 2 Updated Dec 1, 2020

• cromwell

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

  docker application workflow cloud bioinformatics scala executor
  Scala 224 617 668 66 Updated Dec 1, 2020

• wfl

  WorkFlow Launcher (née Zero)
  Clojure BSD-3-Clause 0 5 0 4 Updated Dec 1, 2020

• ddp-angular

  Angular code for participant-facing pepper studies
  TypeScript 0 1 0 10 Updated Dec 1, 2020

• ddp-study-server

  Pepper Study Server
  Java BSD-3-Clause 0 4 0 15 Updated Dec 1, 2020

• terra-helm-definitions

  This repository contains Helm files for every kernel-style Terra deployment
  0 0 0 0 Updated Dec 1, 2020

• sam

  workbench identity and access management
  Scala BSD-3-Clause 5 17 2 4 Updated Dec 1, 2020

• getzlab-SignatureAnalyzer

  Updated SignatureAnalyzer-GPU with mutational spectra & RNA expression compatibility.
  Python MIT 4 21 8 1 Updated Dec 1, 2020

• workbench-libs

  Workbench utility libraries
  Scala 2 4 0 5 Updated Dec 1, 2020

• terraform-terra
  HCL 1 4 0 3 Updated Dec 1, 2020

• adapt

  A package for designing activity-informed nucleic acid diagnostics for viruses.

  science bioinformatics genomics dna diagnostics viral
  Python MIT 0 6 0 2 Updated Dec 1, 2020

• carrot-publish-github-action

  A GitHub action for publishing a test to be run in CARROT via a PR comment
  JavaScript MIT 0 0 0 4 Updated Dec 1, 2020

• leonardo-cron-jobs
  Scala 0 0 0 3 Updated Dec 1, 2020

• dig-loam-stream

  dig-loam-stream
  Scala 0 1 18 1 Updated Dec 1, 2020

• ddp-study-manager

  Pepper Study Manager
  3 packages Java BSD-3-Clause 1 2 0 7 Updated Dec 1, 2020

• tgg-viewer

  A free, open-source web app for visualizing splice junctions, expression, and other sequencing data genome-wide using IGV.js
  JavaScript MIT 0 2 0 1 Updated Dec 1, 2020

• warp

  WDL Analysis Research Pipelines
  wdl BSD-3-Clause 10 15 5 6 Updated Dec 1, 2020

• terraform-shared

  Reusable Terraform modules
  HCL 1 2 1 2 Updated Dec 1, 2020

• cda-helm-definitions
  0 0 0 0 Updated Dec 1, 2020

• cda-helm

  helm charts for cda
  Smarty 0 0 0 0 Updated Dec 1, 2020