Broad Institute

Repositories

• covid19-testing

  COVID-19 Diagnostic Processing Dashboard
  HTML MIT 1 8 0 0 Updated Jul 18, 2020

• pyqtl

  Collection of analysis tools for quantitative trait loci
  Python BSD-3-Clause 0 3 0 0 Updated Jul 18, 2020

• sdarq_survey

  Security requirements for new services
  Python 0 1 0 4 Updated Jul 18, 2020

• pyfrost

  Python bindings for Bifrost with a NetworkX compatible API
  C++ BSD-3-Clause 0 2 2 0 Updated Jul 18, 2020

• gatk

  Official code repository for GATK versions 4 and up

  science bioinformatics spark genomics genome ngs sequencing
  Java BSD-3-Clause 350 843 880 (8 issues need help) 77 Updated Jul 17, 2020

• ddp-angular

  Angular code for participant-facing pepper studies
  TypeScript 0 1 0 10 Updated Jul 17, 2020

• ddp-study-server

  Pepper Study Server
  Java BSD-3-Clause 0 4 0 12 Updated Jul 17, 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 203 564 635 8 Updated Jul 17, 2020

• fiss

  FireCloud Service Selector (FISS) -- Python bindings and CLI for FireCloud execution engine
  Python BSD-3-Clause 13 12 44 0 Updated Jul 17, 2020

• terra-helm-definitions

  This repository contains Helm files for every kernel-style Terra deployment
  0 0 0 0 Updated Jul 17, 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 Jul 17, 2020

• pooled-cell-painting-profiling-recipe

  👩‍🍳 Recipe repository for image-based profiling of Pooled Cell Painting experiments

  data-science recipe pooled-screen cell-painting carpenter-lab pooled-cell-painting in-situ-sequencing
  Python BSD-3-Clause 2 1 11 (1 issue needs help) 3 Updated Jul 17, 2020

• terra-helm

  A helm repo for Terra from Broad Data Science Platforms Group
  Smarty 1 1 0 1 Updated Jul 17, 2020

• terra-tools

  scripts for use with Terra
  Python 0 0 0 0 Updated Jul 17, 2020

• martha

  Google Cloud Function for Blue Box/GUID resolution
  JavaScript BSD-3-Clause 2 2 2 3 Updated Jul 17, 2020

• firecloud-ui

  FireCloud user interface for web browsers.
  Clojure BSD-3-Clause 7 18 3 8 Updated Jul 17, 2020

• SpliceAI-lookup

  web app for checking SpliceAI scores for any variant
  HTML MIT 0 0 0 0 Updated Jul 17, 2020

• gatk-sv
  wdl 2 11 16 2 Updated Jul 17, 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 293 581 150 24 Updated Jul 17, 2020

• comparing-moa-representations

  A systematic comparison of perturbation screening approaches to capture mechanisms-of-action (MOA) representations
  0 0 1 0 Updated Jul 17, 2020

• wfl

  WorkFlow Launcher (née Zero)
  Clojure BSD-3-Clause 0 4 0 2 Updated Jul 17, 2020

• scp-ingest-pipeline

  File Ingest Pipeline for Single Cell Portal
  Python BSD-3-Clause 0 2 0 2 Updated Jul 17, 2020

• palantir-workflows

  Utility workflows for the DSP palantir team
  wdl BSD-3-Clause 0 4 0 2 Updated Jul 17, 2020

• dockstore-tool-cosi2

  Forked from notestaff/dockstore-tool-cosi2

  Dockstore wrapper for cosi2
  Python Apache-2.0 1 0 0 0 Updated Jul 17, 2020

• gnomad_methods

  Hail helper functions for gnomAD/MacArthur lab

  genomics genomes exomes hail
  Python MIT 10 25 12 2 Updated Jul 17, 2020

• AutoTrain

  Using RL to solve overfitting in neural networks
  Jupyter Notebook 0 0 4 0 Updated Jul 17, 2020

• rawls

  Rawls service for DSDE
  Scala 2 13 0 5 Updated Jul 17, 2020

• push-to-cloud-service

  This is the repo for the WorkFlow Launcher's PTC server
  Clojure BSD-3-Clause 0 2 0 3 Updated Jul 17, 2020

• datarepo-helm-definitions

  Helm deployment specific values and definitions for Dev, Integration and Prod
  Shell 0 0 0 1 Updated Jul 17, 2020

• dockerized_mts
  R 0 0 0 0 Updated Jul 17, 2020