CD2H gitForager

Harvard Medical School - Department of Biomedical Informatics

Login: hms-dbmi

Company: null

Location: Boston

email:

Blog: http://dbmi.hms.harvard.edu/

Members

Repositories

3d-genome-processing-tutorial: A 3D genome data processing tutorial for ISMB/ECCB 2017
4DN_dcic-website: Havard/MIT 4D Nucleome Data Coordination and Integration Center website.
4DN_dcic-website-redirect: A repo to enable redirect from 4dn-dcic.hms.harvard.edu to dcic.4dnucleome.org
4dn-dcic-workflow-codes: CWL codes
4DN_matrix_view_tile_generator: null
Autism_code: null
aws-python-utilities: null
BAM-MD5-DBGAP: null
BD2K-PIC-SURE-EXAMPLES: null
bd2k-picsure.hms.harvard.edu: null
BMI-703: null
brainmapr: R package to infer spatial location of neuronal subpopulations within the developing mouse brain by integrating single-cell RNA-seq data with in situ RNA patterns from the Allen Developing Mouse Brain Atlas
cistrome-higlass-demo: null
clodius: Clodius is a tool for breaking up large data sets into smaller tiles that can subsequently be displayed using an appropriate viewer.
dbmi-r-java-docker: null
django-session-security: A little javascript and middleware work together to ensure that the user was active during the past X minutes in any tab he has open. Otherwise, display a warning leaving a couple of minutes to show any kind of activity like moving the mouse. Otherwise, logout the user.
docker-commons-plugin: null
docker-images: This repository stores Dockerfiles and samples to build Docker images for hms-dbmi projects.
dockerspawner: Spawns JupyterHub user servers in Docker containers
dropEst: Pipeline for initial analysis of droplet-based single-cell RNA-seq data
exac_browser: Browser for ExAC consortium data
exac.hms.harvard.edu: A repository that includes the HTML for the exac.hms.harvard.edu website
exposomeDW_public: null
halyos: Redesigning the Patient Portal Experience with SMART on FHIR.
halyos: Redesigning the Patient Portal Experience with SMART on FHIR.
gatk-docker: Docker source file for duplexa/gatk_env:v1 on hub.docker.com
gehlenborg-lab-best-practices: Guidelines for creating medium-scale visualization software
gehlenborglab-website: Code for Gehlenborg Lab website.
hackathon-Sept2017: null
halyos: Redesigning the Patient Portal Experience with SMART on FHIR.
halyos: Redesigning the Patient Portal Experience with SMART on FHIR.
hic-data-analysis-bootcamp: Workshop on measuring, analyzing, and visualizing the 3D genome with Hi-C data.
higlass: Fast contact matrix visualization for the web.
higlass-app: HiGlass App: a fully featured application for viewing, exploring, and annotating 1D and 2D genomic data
higlass-docker: Builds a docker container wrapping higlass-server and higlass-client in nginx
higlass-docs: null
higlass-multivec: Multivec Tracks for Higlass
higlass-register: Helper tool to register pluggable tracks
higlass-server: null
higlass-website: HiGlass Project Website
HMS-DBMI-transmartApp: Public facing tranSMART Application repository of Harvard Medical School's Department of Biomedical Informatics
HMS-DBMI-transmartETL: Public facing tranSMART ETL repository of Harvard Medical School's Department of Biomedical Informatics
hypatio-app: null
hypatio-app-docker: null
i2b2-authn-proxy: Proxy Service to allow usernames to be transferred from an authenticating service and an i2b2 XML message.
i2b2-Java-API: Java classes to abstract away i2b2 XML
i2b2-to-PCORNET-CDM: i2b2 to PCORNET CDM Scripts
idstore-app: null
idstore-app-docker: null
IRCT: Merged IRCT Repository
IRCT-API: PIC-SURE Inline Query Engine
IRCT-CL: PIC-SURE Resource Interface
IRCT-DB-SCHEMA: null
IRCT-EXT: null
IRCT-RI: null
JenkinsTestRepository: This repo is only used to test Jenkins build workflow and integration with Confluence
jwt-creator: A simple utility to create JWT tokens for development purposes. Feel free to extend if you need more claims or something.
mallet_time: null
matrix_storage_benchmark: null
mc4c-sample-data: null
metadataproxy: A proxy for AWS's metadata service that gives out scoped IAM credentials from STS
mHealthieR: R package to assess and evaluate longitudinal mHealth sensor data.
mod_auth_openidc: OpenID Connect Relying Party and OAuth 2.0 Resource Server for Apache HTTP Server 2.x
oauthenticator: GitHub OAuth + JupyterHub Authenticator = OAuthenticator
OncoThreads: OncoThreads longitudinal cancer genomics visualization project.
OncoThreads: OncoThreads longitudinal cancer genomics visualization project.
OncoThreads: OncoThreads longitudinal cancer genomics visualization project.
OncoThreads: OncoThreads longitudinal cancer genomics visualization project.
OpenClinica: OpenClinica is the world's first commercial open source clinical trial software for Electronic Data Capture (EDC) Clinical Data Management (CDM).
pagoda2: R package for analyzing and interactively exploring large single-cell RNA-seq datasets
phenotips: PhenoTips provides an easy-to-use Web interface and standardized database back-end for collecting clinical findings observed in patients with possible genetic disorders.
picsuRe: null
PIC-SURE-resources: PIC-SURE resource configuration files
pklab: Kharchenko Lab Resources
ppmtest: null
public-data-deployments: null
py-auth0-jwt: null
py-auth0-jwt-rest: null
pyencoded-tools: null
pynxgu: null
pystarter: base project to be used as a starter for all your other python projects
Rcheesecake: Query and retrieve phenotypics and genotypics data using PIC-SURE API
Rcupcake: null
Rcupcake-case-studies: null
r-datascience-notebook: null
R-IRCT: null
Rmodules-1: A R statistical analysis module plugin for tranSMART
Rstarter: Template for creating an R package
r_testing: Example repo of how to properly test an R package
samplestore: This app uses Django Rest Framework to expose an API for managing a collection of data about samples from subjects that participate in a research project.
sandboxR: Helps to search, explore, extract and transform phenotypics datasets from dbGap studies
scalable-jupyter-hosting: DBMI Hackathon project to provide some scaling functionality to the existing Jupyterhub architecture
scde: R package for analyzing single-cell RNA-seq data
SciAuth: null
SciAuth-app-docker: null
SciAuthZ: null
SciAuthZ-app-docker: A small authorization service
sci-aws-infrastructure: null
SciDB-Java: Java wrapper for SciDB queries
sci-logging: null
SciReg: null
SciReg-docker: null
sci-services: null
scw: HSCI/Catalyst Single-cell RNA-Seq Workshop
secret-getter: retrieves secrets given a vault_token, and replaces values in files and/or environment variables
secret-getter: retrieves secrets given a vault_token, and replaces values in files and/or environment variables
smart-fhir-drill: Test performance of FHIR API implementations. ?
spp: SPP - R package for analysis of ChIP-seq and other functional sequencing data
stack: null
tentacle: tentacles of the mother brain to suck in all knowledge of works products
tev-server: Repository for tumor evolution visualization back end.
tibanna: Tibanna is the gas mined in Cloud City that makes Hyperdrives zoom. It's also the pipeline running in the cloud that ensure data is properly processed for 4dn.
transmartApp-1: tranSMART is a knowledge management platform that enables scientists to develop and refine research hypotheses by investigating correlations between genetic and phenotypic data, and assessing their analytical results in the context of published literature and other work.
transmart-core: Core components and documentation of the tranSMART platform.
transmart-core-api: null
transmart-core-db: TranSMART Core
transmart-data: Tools for managing tranSMART's database
transmartDB: null
transmart-docker: null
tranSMART-Documentation: null
tranSMART-ETL: tranSMART ETL pipelines and configurations
transmart-gwas-plugin: The transmart (and grails) plugin that contains the GWAS elements.
transmart-i2b2-plugin: null
transmart-legacy-db: Contains the Grails domain declarations of the legacy transmart schema
transmart-rest-api: HTTP available tranSMART RESTful API
tranSMART-R-Scripts: null
udngateway_codepipeline_lambda: null
udngateway-database-docker: null
udngateway-etl-docker: null
upload-preprocessing-service-docker: null
UpSetR: An R implementation of the UpSet set visualization technique published by Lex, Gehlenborg, et al..
UpSetR-orthologs: Shiny app to compute and visualize ortholog intersections across multiple species using UpSetR.
UpSetR-paper: Data and scripts for UpSetR paper.
UpSetR-shiny: A Shiny wrapper for the UpSetR R package (https://github.com/hms-dbmi/UpSetR).
secret-getter: retrieves secrets given a vault_token, and replaces values in files and/or environment variables
secret-getter: retrieves secrets given a vault_token, and replaces values in files and/or environment variables
VisSV: null
zaklabcore: null

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.