Broad Institute

Repositories

• ml4h
  1 package Python 2 7 30 (1 issue needs help) 10 Updated Feb 19, 2021

• covid19-testing

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

• terra-helm

  A helm repo for Terra from Broad Data Science Platforms Group
  Smarty BSD-3-Clause 1 4 0 2 Updated Feb 19, 2021

• ddp-angular

  Angular code for participant-facing pepper studies
  TypeScript 0 1 0 9 Updated Feb 19, 2021

• annmas

  Annotation and segmentation of MAS-seq data
  Python BSD-3-Clause 0 0 2 1 Updated Feb 19, 2021

• long-read-pipelines

  Long read production pipelines

  pipelines wdl variant-calling de-novo-assembly long-reads
  Jupyter Notebook BSD-3-Clause 2 37 31 (4 issues need help) 1 Updated Feb 19, 2021

• 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 35 0 2 Updated Feb 19, 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 232 644 678 16 Updated Feb 19, 2021

• warp

  WDL Analysis Research Pipelines
  wdl BSD-3-Clause 13 25 3 12 Updated Feb 19, 2021

• nextstrain-builds

  Nextstrain build definitions
  MIT 0 0 0 0 Updated Feb 19, 2021

• seqr

  web-based analysis tool for rare disease genomics
  Python AGPL-3.0 50 101 48 1 Updated Feb 19, 2021

• wfl

  WorkFlow Launcher (née Zero)
  Clojure BSD-3-Clause 0 6 0 2 Updated Feb 19, 2021

• agora

  It's a methods repository!
  Scala 1 9 0 1 Updated Feb 18, 2021

• gatk

  Official code repository for GATK versions 4 and up

  java science bioinformatics spark genomics genome cluster
  Java BSD-3-Clause 394 983 941 (8 issues need help) 78 Updated Feb 18, 2021

• GpUnit

  Testing framework for GenePattern modules
  JavaScript 2 3 0 0 Updated Feb 18, 2021

• ccle_processing

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

  data-science cancer-genomics cloud-computing depmap
  Jupyter Notebook 4 16 0 2 Updated Feb 19, 2021

• sam

  workbench identity and access management
  Scala BSD-3-Clause 5 17 2 4 Updated Feb 18, 2021

• ddp-study-server

  Pepper Study Server
  Java BSD-3-Clause 0 4 0 13 Updated Feb 18, 2021

• terraform-ap-modules

  DSP Analysis Platform Terraform Modules
  HCL BSD-3-Clause 0 0 0 4 Updated Feb 18, 2021

• rawls

  Rawls service for DSDE
  Scala 2 13 0 6 Updated Feb 19, 2021

• gatk-sv
  wdl BSD-3-Clause 12 41 33 2 Updated Feb 18, 2021

• grit-benchmark

  Benchmarking a metric used to evaluate a perturbation strength
  Jupyter Notebook BSD-3-Clause 2 1 5 0 Updated Feb 18, 2021

• genepy

  Forked from jkobject/JKBio

  Genepy is an open source utils package covering a range of useful functions for large scale genomics data analysis in python
  Python Apache-2.0 1 1 0 2 Updated Feb 18, 2021

• gnomad-blog

  Blog for the gnomAD project
  JavaScript 0 0 4 0 Updated Feb 18, 2021

• workbench-libs

  Workbench utility libraries
  Scala 2 4 0 4 Updated Feb 18, 2021

• bibtutils

  Functionality often used by BITS Blue Team. Open-source.
  Python MIT 0 1 0 0 Updated Feb 18, 2021

• taigapy

  Library for reading from taiga in python
  Python 0 0 1 0 Updated Feb 18, 2021

• datarepo-helm

  A helm repo for Broad Data Science Platforms helm charts
  Mustache 1 0 0 2 Updated Feb 18, 2021

• gnomad_methods

  Hail helper functions for gnomAD/MacArthur lab

  genomics genomes exomes hail
  Python MIT 15 30 24 4 Updated Feb 18, 2021

• pooled-cell-painting-image-processing

  pooled-cell-painting
  Python BSD-3-Clause 0 3 2 0 Updated Feb 18, 2021