Broad Institute

Repositories

• covid19-testing

  COVID-19 Diagnostic Processing Dashboard
  HTML MIT 2 15 2 0 Updated Jan 29, 2021

• ddp-study-manager-ui

  Pepper Study Manager UI
  TypeScript BSD-3-Clause 0 1 0 1 Updated Jan 29, 2021

• ddp-angular

  Angular code for participant-facing pepper studies
  TypeScript 0 1 0 24 Updated Jan 29, 2021

• ddp-study-manager

  Pepper Study Manager
  3 packages Java BSD-3-Clause 1 2 0 16 Updated Jan 29, 2021

• annmas

  Annotation and segmentation of MAS-seq data
  Python BSD-3-Clause 0 0 0 0 Updated Jan 29, 2021

• str-callers

  tools for comparing existing tools for calling short tandem repeats (STRs)
  Jupyter Notebook MIT 0 0 0 0 Updated Jan 29, 2021

• rawls

  Rawls service for DSDE
  Scala 2 13 0 10 Updated Jan 29, 2021

• ml4h
  1 package Python 1 4 30 (1 issue needs help) 10 Updated Jan 29, 2021

• gatk

  Official code repository for GATK versions 4 and up

  science bioinformatics spark genomics genome ngs sequencing
  Java BSD-3-Clause 387 968 942 (8 issues need help) 83 Updated Jan 29, 2021

• dig-loam-stream

  dig-loam-stream
  Scala 0 1 18 1 Updated Jan 29, 2021

• ABC-Enhancer-Gene-Prediction

  Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)
  Python MIT 12 59 11 4 Updated Jan 29, 2021

• taigapy

  Library for reading from taiga in python
  Python 0 0 1 1 Updated Jan 29, 2021

• wfl

  WorkFlow Launcher (née Zero)
  Clojure BSD-3-Clause 0 6 0 4 Updated Jan 29, 2021

• ddp-study-server

  Pepper Study Server
  Java BSD-3-Clause 0 4 0 15 Updated Jan 28, 2021

• gnomad_methods

  Hail helper functions for gnomAD/MacArthur lab

  genomics genomes exomes hail
  Python MIT 13 29 19 4 Updated Jan 28, 2021

• infra20
  HCL 0 0 17 1 Updated Jan 28, 2021

• lincs-profiling-comparison

  Analyzing and comparing signal found in different profiling technologies
  Jupyter Notebook BSD-3-Clause 2 0 3 1 Updated Jan 28, 2021

• viral-core

  viral-ngs: read QC, barcode metrics, spike-in metrics, Illumina metrics and demux
  Python 0 1 2 1 Updated Jan 28, 2021

• terra-helm

  A helm repo for Terra from Broad Data Science Platforms Group
  Smarty BSD-3-Clause 1 4 0 3 Updated Jan 28, 2021

• lunaris

  Lunaris reads and munges data from block-gzipped, location-sorted, tabix-indexed files on Google Cloud.
  Scala BSD-3-Clause 1 1 1 1 Updated Jan 28, 2021

• GATK-for-Microbes
  wdl 1 1 7 0 Updated Jan 28, 2021

• docker-terraform

  Docker container for running the Terraform application
  Shell 40 49 1 0 Updated Jan 28, 2021

• seqr

  web-based analysis tool for rare disease genomics
  Python AGPL-3.0 49 100 53 7 Updated Jan 28, 2021

• 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 229 640 673 20 Updated Jan 28, 2021

• 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 303 640 166 25 Updated Jan 28, 2021

• warp

  WDL Analysis Research Pipelines
  wdl BSD-3-Clause 12 22 3 10 Updated Jan 28, 2021

• datarepo-helm-definitions

  Helm deployment specific values and definitions for Dev, Integration and Prod
  Shell 0 1 0 5 Updated Jan 28, 2021

• viral-pipelines

  viral-ngs: complete pipelines
  wdl 10 18 11 3 Updated Jan 28, 2021

• gatk-sv
  wdl BSD-3-Clause 10 37 31 2 Updated Jan 28, 2021

• monster-deploy

  Infrastructure-as-code for Monster team's "core" environments
  HCL BSD-3-Clause 0 2 0 1 Updated Jan 28, 2021