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Broad Institute

Login: broadinstitute

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Location: Cambridge, MA

email: github@broadinstitute.org

Blog: http://www.broadinstitute.org/

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Repositories

2017_05_10_neutrophile_inhibitor: null
2018_04_25_Rosetta: The�Rosetta�project:�translating�data�across�single�-cell technologies�to�define�human�cell�types
3dmutvis: null
adam: A genomics processing engine and specialized file format built using Apache Avro, Apache Spark and Parquet. Apache 2 licensed.
agora: It's a methods repository!
akka-statsd: Statsd client using an Akka actor
anorm221: Our local fork of Anorm 2.2.1
antryg: Scala lib to access SQL or Cassandra without knowing the schema in advance
aou-api-prototype-java7: null
aou-researcher-webui-react-prototype: Web UI for All of Us researchers.
aou-ui-angular-prototype: null
apache2-onehealth: This is the OneHealth Apache 2.4 fork of the original Opscode apache2 cookbook
atestrepo: A Test Repo
aurora: Mirror of Apache Aurora
aws-backend: null
barclay: Command line argument parser and online documentation generation utilities for java command line programs.
BARD: BioAssay Research Database
baseimage: Broad Institute BaseImage
bdg-formats: null
bdg-services: Utility classes for wrapping services or other interfaces around a Spark/ADAM cluster.
beacon-of-beacons: Beacon of beacons.
beast-beagle-cuda: BEAST with BEAGLE compiled via NVIDIA CUDA
beast-beagle-pocl: BEAST with BEAGLE compiled via portable OpenCL
bioscala: Bioinformatics for the Scala programming language
BipolarCell2016: null
bits-chef-repo: BITS Chef Repository
broadinstitute.github.io: Broad Institute GitHub Page
broad-translator: Component of the Broad-based gray team to the NCATS Biomedical translator
BTL-EntryCreator: null
btl_firecloud: null
btl_firecloud_gatk: null
BTL-MdReport: null
BTL-Parsomatic: null
BTL-tracker: null
busyflow.pivotal: Pivotal API Client library
cakephp: CakePHP: The Rapid Development Framework for PHP - Official Repository
cakephp-mongodb: MongoDB database driver for CakePHP
catch: A package for designing compact and comprehensive probe sets.
CEGS_single_cell_tx_workshop_Sept2017: CEGS Single cell transcriptomics workshop @ Broad Institute, Sept 2017, leveraging Seurat
cellpainting_RareDiseases: null
centaur: Cromwell integration testing environment
ces-incipient: CES Incipient
cfn-pyplates: Amazon Web Services CloudFormation templates, generated with Python!
chef-docker: Chef Cookbook for Docker
chef-shibboleth_idp: Chef cookbook to install and configure the Shibboleth SAML IdP
clio: null
cmi-cas-rest-client: A RestClient for integrating with applications protected by CAS Single-Sign-On (http://www.jasig.org/cas)
cms: Composite of Multiple Signals: tests for selection in meiotically recombinant populations
consensus_svs: firecloud tasks to make consensus SV lists (VCF and txt) using Breakpointer
cosi2: Fast coalescent simulator with selection
cotton: A library of useful functions for managing deployments with Fabric.
CromIAM: The Workbench proxy to Cromwell for IAM
cromshell: shell script for interacting with cromwell servers
cromstream: POC Implementation(s) of a PubSub -> Metadata writing service
cromwell: Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
cromwell-accountant: A script to calculate estimated cost of a Cromwell workflow on Google Cloud
cromwell-backend: Cromwell Backend Repository
cromwell-tools: null
crowd-jaas: JAAS LoginModule for Crowd
ctc_firehose: Directions and upload scripts for connecting LIMS to Firehose (CTC QC and analysis)
cwl-proto: Reading and writing Common Workflow Language to Protocol Buffers. I.e. CWL <-> Protobuf
cxowrapper: Wrapper for Python's cx_Oracle database API that returns results in a slightly more sane format.
cytominer_scripts: Scripts for processing morphological profiling data using cytominer
dalmatian: dalmatian is a collection of high-level companion functions for Firecloud and FISS.
datacentred-ldap: OpenLDAP module for Puppet
deepometry: Image classification for imaging flow cytometry.
DeepProfiler: Morphological profiling using deep learning
DeepProfiler: Morphological profiling using deep learning
denimcoat: NCATS Translator Indigo Team GUI
deTiN: DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated matched control.
dig-diabetes-portal: Diabetes portal for the Medical Population Genetics department at the Broad Institute
DLBCL_Nat_Med_April_2018: null
docker-buckettest: Docker image to test web buckets
docker-clojure-node: Docker image with clojure and node.
docker-cloudsqlproxy: Google CloudSQL proxy service
docker-consul: Dockerized Consul Agent
docker-consul-server: Docker image for a Consul server
docker-elasticsearch: null
docker-flyway: Dockerized mysql flyway tool
docker-gam: Docker container for Dito GAM
docker-gcds: Google Cloud Directory Sync
docker-gradle: Dockerized gradle build environment
docker-hastebin: a docker container for hastebin server
docker-liquibase: Dockerfile and built utility for creating Liquibase utility in a docker container
docker-mongo: Repo to build our own version of mongo docker containers
docker-nedi: Docker container image for the NeDi Network Discovery service
docker-orientdb: Docker container for OrientDB
docker-pyplates: Docker container for the cfn-pyplates Python library
docker-scala: Build a docker image for Scala, SBT
docker-sentry-github: Sentry Docker image with GitHub authentication support
docker-slapd: Docker image for a basic OpenLDAP server
docker-terraform: Docker container for running the Terraform application
docker-timefix: Docker image to fix time on Docker for Mac
docker-vaultcli: null
docker-vault-server: Docker image for a Vault server
DropSeq_utility: null
dropviz: Shiny app for visualization, exploration of mouse brain single cell gene expression
dsde-deep-learning: DSDE Deep Learning Club
ebola-imc-public: Prognosis models and apps derived from the Ebola IMC dataset
ebola-predictor: Prediction pipeline to generate prognosis predictors for Ebola Virus Disease
elba: Gatling load-testing scripts for the cromwell project
epi-wdl-script: null
eroc: ELN Reporter -- make sure those experiments get witnessed!
evangalion: Firecloud instrumentation service
fcgdctools: Python utilities and command line tools for integration of FireCloud (Broad's NCI Cancer Genomics Cloud Pilot) and the NIH/NCI Genomics Data Commons
fiabftw: Firecloud in a Box for the World
firecloud-bucket-log-shipper: A quick Cloud Function to send bucket audit logs from Google to Logit.
firecloud-cli: null
firecloud_developer_toolkit: Utilities to help algorithm developers dockerize new tasks, debug them, and put them into Firecloud.
firecloud-explorer: Firecloud Tool to handle file downloads, uploads and transfers
firecloud-orchestration: null
firecloud_sugar: Wrapper functions for importing / exporting metadata from Firecloud
firecloud-tools: Tools for use with FireCloud
firecloud-ui: FireCloud user interface for web browsers.
firecloud-ui-browser-tests: null
firepony: Efficient base quality score recalibrator for NGS data
fiss: FireCloud Service Selector (FISS) -- Python bindings and CLI for FireCloud execution engine
forseti-security: Security tools for visibility, detection, and policy enforcement on Google Cloud Platform
funnel: funnel executes tasks on a cluster.
gamgee: A C++14 library for NGS data formats
Gap2Seq: Customization of Gap2Seq, a gap filling and insertion genotyping tool, for use with broadinstitute/viral-ngs; NOT the official Gap2Seq repo. .
garethr-docker: Puppet module for managing docker
gatk: Official code repository for GATK versions 4 and up
gatk3-4-rnaseq-germline-snps-indels: Workflows for processing RNA data for germline short variant discovery with GATK (v3+v4) and related tools
gatk4-data-processing: Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools
gatk-bwamem-jni: JNI code for bwa mem
gatk-dataflow: Development dataflow
gatk-evaluation: null
gatk-fermilite-jni: JNI code for fermi lite.
gatk-native-bindings: GATK Native Bindings Repository
gatk-protected: Obsolete/Legacy GATK repository -- go to https://github.com/broadinstitute/gatk instead
gdata-cli: tool to manipulate Google App domains from the command line
gdctools: Python and UNIX CLI utilities to simplify interaction with the NIH/NCI Genomics Data Commons
gene-mashup: Mashup information about genes
genomespace_dot_org: null
GitDescribe-Maven-Plugin: Sets the maven attribute 'describe' to the current git describe output. Currently directly executes git describe, no JGit implementation yet.
GoogleBillingDashboard: A utility for consuming and reporting Google Cloud billing metrics
google-cloud-auto-snapshot: Auto snapshot GCE disks. From:
google-cloud-java: Google Cloud Client Library for Java
gpalloc: Allocates Google projects
GpUnit: Testing framework for GenePattern modules
graphite-experiment: Setting up Graphite inside of Vagrant.
gsalib: R package of utility functions for GATK
gtex-ashg2017-workshop: null
gtex-pipeline: GTEx Consortium data production and analysis pipelines
gtex-public: null
gtex-tutorials: null
hdf5-java-bindings: java bindings for hdf5
herc: null
homebrew-core: :beers: Core formulae for the Homebrew package manager
honeypot: Honeypot repo
hostinfo: Old code to get some host information with bash/python
htsjdk: A Java API for high-throughput sequencing data (HTS) formats.
htslib: C library for high-throughput sequencing data formats. This is the repository for any necessary gamgee-specific changes.
HydrantFC: Repository for the FireCloud version of Hydrant (currently in alpha testing)
ichorCNA: Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.
identify: null
imaging-backup-scripts: Scripts to backup data
imaging_metric_comparison: null
imaging-platform-pipelines: Cell Painting and other pipelines from the Imaging Platform
imaging-platform-terraform: Software to use Terraform and CellProfiler together to process images on cloud-computing platforms.
inferCNV: Inferring CNV from Single-Cell RNA-Seq
inferCNV_examples: additional examples for use with inferCNV
java: Development repository for Opscode Cookbook java
java-baseimage: Base docker image for Java 8 applications
Jira_Google_Integration: Random code for integrating Jira Cloud and Google Apps
jSnap: null
kdux-rails-baseimage: Dockerfile and support libraries for kdux-rails-baseimage docker image
keras-imaging: A Keras package for biological and medical imaging
keras-rcnn: Keras package for region-based convolutional neural networks
keras-resnet: Keras package for deep residual networks
KrumlovSingleCellTx2018: single cell transcriptome workshop in Krumlov, Jan 2018
kryo: Java serialization and cloning: fast, efficient, automatic
kubeque: null
labs-on-cloud: Automated Computational Biology Analysis Infrastructure on the Cloud
language-wdl: WDL Language Support For Atom
lassa-isth-code: null
lenthall: null
Loggly-Puppet: null
lxc: Linux Containers via Chef
martha: Google Cloud Function for Blue Box/GUID resolution
metabaron: OIDC access_token userinfo endpoint for multiple Providers
MPG-Hack_2: MPG Hackathon 2016 project 2
mutect: MuTect -- Accurate and sensitive cancer mutation detection
MuTest: A prototype database for storing somatic variants.
mvicuna: The mvicuna tool for the analysis of viral NGS data
mysql: Development repository for Opscode Cookbook mysql
ohai: Ohai profiles your system and emits JSON
oncotator: null
ontology-service: Ontology Matching and Storage Service
openldap: Development repository for Opscode Cookbook openldap
OptionsMenu: Material design style popover options menu
ORFCall: null
orsp-api: ORSP Compliance Portal API
orsp-ci: Compliance CI
ossec-puppet: Puppet module for OSSEC
password-alert: A Chrome Extension to help protect against phishing attacks.
pcawg_public: null
pcull: kill or renice processes that are overusing resources
pe2loaddata: Script to parse a Phenix metadata XML file and generate a .CSV for CellProfiler's loaddata module
PEHaplo: Custom fork of chjiao/PEHaplo for use with broadinstitute/viral-ngs.
phlock: used to publish a tool called "phlock" which is used for submitting R/python jobs to job queues and tracking the status
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.
pilon: Pilon is an automated genome assembly improvement and variant detection tool
plinkdocker: null
policyscanner: null
proteomics: Repository for proteomics code and projects
puppet-amavisd: Puppet module for installing and configuring amavis-new
puppet-avamar: Puppet Avamar Class - https://forge.puppetlabs.com/Ramorous/avamar
puppet-certs: SSL Certificate File Management for Puppet
puppet-clamav: Puppet Module for managing ClamAV
puppet-dell: dell specific installations (openmanage and others)
puppet-dhcp: Puppet module for deploying dhcp
puppet-dovecot: Puppet Dovecot Module for Dovecot 2+
puppet-fail2ban: Puppet module to manage fail2ban
puppet-fluentd: Manage fluentd installation with Puppet
puppet-foreman_proxy: Puppet module for Foreman Smart Proxy
puppet-freeradius: Puppet module to install and configure FreeRADIUS
puppet-gcloudsdk: null
puppet-google_cloud_sdk: Puppet module for installing and configuring Google's Cloud SDK
puppetlabs-firewall: Puppet Firewall Module
puppetlabs-puppetdb: A puppet module for installing and managing puppetdb
puppet-logrotate: Puppet logrotate module
puppet-module-epel: Setup/configure EPEL (extra repository for enterprise linux) with Puppet
puppet-module-nrpe: Puppet module for NRPE
puppet-mongodb: mongodb installation
puppet-nsswitch: Puppet module to control /etc/nsswitch.conf file.
puppet-openam: OpenAM Puppet module
puppet-opendj: OpenDJ Puppet module
puppet-openssl: Puppet OpenSSL module
puppet-php: A puppet module for php. According to Example42 NextGen spec.
puppet-portmap: Puppet Module for managing the RPC port mapper
puppet-postfix: Puppet Postfix module
puppet-qpage: Puppet module for controlling the qpage service
puppet-rssh: Puppet module for rssh
puppet-rsyslog: Manage rsyslog through puppet
puppet-saslauthd: Puppet saslauthd module
puppet-snmp: Puppet module to manage Net-SNMP.
puppet-stackdriver-agent: Puppet module for stackdriver-agent
PyGithub: Python library implementing the GitHub API v3
pywdl: Python bindings for WDL
qbsub: qsub replacement to make it behave more similarly to bsub
rawls: Rawls service for DSDE
react-broad: React components written and maintained by the Broad Institute
react-broad-bootstrap: null
react-cljs-modal: Modal UI Component in React CLJS
react-cljs-nav: URL navigation and routing for React CLJS single-page applications
reasoner: Reasoner
rigerj: Java implementation of RIGER and other gene enrichment methods, useful for RNAi and CRISPR screen analysis.
RNA_MUTECT_1.0-1: null
RNA-SeQC: null
sabeti-dhis2-clinical-express: Express version of the sabeti-dhis2-clinical
sabetilab-remote-config: configuration files for systems deployed at our African field sites (Ansible, route53, autossh)
sails-mongo: MongoDB adapter for Sails.js
sam: workbench identity and access management
SamplyzeR: null
scala-baseimage: Base image for Scala programs and services
scalable_analytics: Public collaboration of Scalable Single Cell Analytics
scalacache: Simple caching in Scala
sc_analysis_portal: null
scientific-python-2.7: scientific python 2.7 with intel MKL built into virtual machines. Docker, AMI, Virtualbox, Vmware, KVM and more
security_monkey: Security Monkey
sensu-chef: Sensu Chef cookbook.
sensu-community-plugins: Sensu community plugins & handlers, sharing is good.
seqr: null
servicenow-powershell: This PowerShell module provides a series of cmdlets for interacting with the ServiceNow REST API
shibboleth-service-provider: A generic Shibboleth service provider service for use in Shibboleth authentication schemes.
single_cell_analysis: Documents used for workshops on single cell analysis
single_cell_portal: null
single_cell_portal_core: Rails/Docker application for the Regev lab's single cell RNA-seq data portal
skopy: null
snakemake-broad-uger: Snakemake profile to execute workflows on the Broad Institute UGER cluster
snoop: null
SnowmanSV: Structural variation and indel detection using rolling local string graph assembly
soerenbe-syslog_ng: syslogng puppet module
somatic-benchmark: Tools for comparing somatic variant calling tools.
spames: spam an elasticsearch with a zillion concurrent updates
sparklespray: Easy batch submission of adhoc jobs onto GCP
Squeryl: A Scala DSL for talking with databases with minimum verbosity and maximum type safety
ssl-cert-test: null
stxxl: STXXL: Standard Template Library for Extra Large Data Sets
taiga: Taiga for Dataset management
tango: Taxonomic identification of unaligned reads
terraform: Terraform is a tool for building, changing, and combining infrastructure safely and efficiently.
TestArsen2: null
thrift: Rebasing py3 support
thurloe: A simple service to store arbitrary key/value pairs
tmpnb: Creates temporary Jupyter Notebook servers using Docker containers.
toil: Toil is a Python-based workflow engine for clusters that makes running recursive and dynamically scheduled computations straightforward. So far works with Azure, EC2, Mesos, GridEngine and Parasol.
toothpick: null
trinityrnaseq: Trinity RNA-Seq de novo transcriptome assembly
TSCA_firecloud_WDLS: Collection of WDLs for CCLF's TSCA Pipeline
uploader: A CakePHP plugin for file uploading and validating.
vagrant: null
VariantBam: Filtering and profiling of next-generational sequencing data using region-specific rules
vault: A tool for managing secrets.
vault-api: Vault Orchestration Service
vault-boss: Public repo for BOSS
vault-common: null
vault-datamanagement: null
vectors4s: A vector library for Scala.
vim-wdl: Vim syntax highlighting for WDL
viral-baseimage: Broad Viral Genomics base docker image
viral-ngs: Viral genomics analysis pipelines
viral-ngs-deploy: Deployment files related to https://github.com/broadinstitute/viral-ngs
vlad: LD for variants
v-phaser2: The v-phaser tool for the analysis of viral NGS data
wdl: Workflow Description Language - Specification and Implementations
wdl4s: Scala bindings for WDL
wdl-sublime-syntax-highlighter: null
wdl-syntax-highlighting: Syntax Highlighting for WDL files
wdltool: null
wes2cromwell: Shim accepting WES REST requests and translating to/from Cromwell REST requests
widdler: A command-line tool for executing, managing, and querying WDL workflows on Cromwell servers.
winstanley: An IntelliJ Plug-in for WDL
wordpress-crowd-plugin: Crowd Authentication Plugin for Wordpress
workbench-libs: Workbench utility libraries
wot: Optimal transport for time-course single cell data
xtermcolor: Python library for terminal color support (including 256-color support)

This work is supported by the National Institutes of Health's National Center for Advancing Translational Sciences, Grant Number U24TR002306. This work is solely the responsibility of the creators and does not necessarily represent the official views of the National Institutes of Health.