Broad Institute

Repositories

• covid19-testing

  COVID-19 Diagnostic Processing Dashboard
  HTML MIT 0 6 0 0 Updated Jun 13, 2020

• ABC-Enhancer-Gene-Prediction

  Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)
  Python MIT 4 37 3 3 Updated Jun 13, 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 201 557 632 10 Updated Jun 13, 2020

• tensorqtl

  Ultrafast GPU-based QTL mapper
  Python BSD-3-Clause 14 44 5 0 Updated Jun 13, 2020

• rawls

  Rawls service for DSDE
  Scala 2 13 0 6 Updated Jun 12, 2020

• agora

  It's a methods repository!
  Scala 1 9 0 0 Updated Jun 13, 2020

• gatk

  Official code repository for GATK versions 4 and up

  science bioinformatics spark genomics genome ngs sequencing
  Java BSD-3-Clause 344 831 880 (8 issues need help) 77 Updated Jun 12, 2020

• thurloe

  A simple service to store arbitrary key/value pairs
  Scala BSD-3-Clause 1 3 0 2 Updated Jun 12, 2020

• firecloud-orchestration
  Scala BSD-3-Clause 1 21 0 3 Updated Jun 12, 2020

• sam

  workbench identity and access management
  Scala BSD-3-Clause 5 16 2 0 Updated Jun 12, 2020

• ddp-study-server

  Pepper Study Server
  Java BSD-3-Clause 0 3 0 8 Updated Jun 12, 2020

• scp-ingest-pipeline

  File Ingest Pipeline for Single Cell Portal
  Python BSD-3-Clause 0 2 0 0 Updated Jun 12, 2020

• lunaris

  Lunaris reads and munges data from block-gzipped, location-sorted, tabix-indexed files on Google Cloud.
  Scala BSD-3-Clause 1 0 1 1 Updated Jun 12, 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 31 0 3 Updated Jun 12, 2020

• catch

  A package for designing compact and comprehensive capture probe sets.

  science bioinformatics genomics genome ngs sequencing metagenomics
  Python MIT 8 35 0 0 Updated Jun 12, 2020

• orsp-pub

  Public ORSP Compliance Portal
  JavaScript BSD-3-Clause 0 2 0 20 Updated Jun 12, 2020

• terraform-shared

  Reusable Terraform modules
  HCL 1 2 1 4 Updated Jun 12, 2020

• horsefish
  Python 0 0 0 1 Updated Jun 12, 2020

• viral-ngs-staging

  CI staging area between github.com/broadinstitute/viral-pipelines and Dockstore (via Travis)
  wdl BSD-3-Clause 1 0 0 0 Updated Jun 12, 2020

• dockstore-tool-cosi2

  Forked from notestaff/dockstore-tool-cosi2

  Dockstore wrapper for cosi2
  wdl Apache-2.0 1 0 0 0 Updated Jun 12, 2020

• PhylogicNDT
  HTML 15 22 12 1 Updated Jun 12, 2020

• viral-pipelines

  viral-ngs: complete pipelines
  wdl 7 8 7 2 Updated Jun 12, 2020

• push-to-cloud-service

  This is the repo for the WorkFlow Launcher's PTC server
  Clojure BSD-3-Clause 0 1 0 1 Updated Jun 12, 2020

• docker-devnull-vscode-puppet

  Docker image for a VS Code Remote-Containers image for Puppet development
  Dockerfile 0 0 0 0 Updated Jun 12, 2020

• gpalloc

  Allocates Google projects
  Scala 0 1 4 0 Updated Jun 12, 2020

• APSGhistory

  Import of APSG subversion repository
  PHP 0 0 0 0 Updated Jun 12, 2020

• cosi2

  Fast coalescent simulator with selection
  C++ GPL-3.0 0 2 3 0 Updated Jun 12, 2020

• ddp-angular

  Angular code for participant-facing pepper studies
  TypeScript 0 1 0 6 Updated Jun 12, 2020

• terra-helm

  A helm repo for Terra from Broad Data Science Platforms Group
  Python 1 0 0 1 Updated Jun 12, 2020

• terra-incident-response

  Collect metrics around incident response times to production Terra
  Python 0 0 0 0 Updated Jun 12, 2020