Discover hms-dbmi/OncoThreads Open Source project

Workshop on measuring, analyzing, and visualizing the 3D genome with Hi-C data.

273

hic-data-analysis-bootcamp

R package for analyzing single-cell RNA-seq data

189

scde

172

CHIEF

Clinical Histopathology Imaging Evaluation Foundation Model

A minimal Zarr image viewer based on Viv.

130

vizarr

Interactive multiscale visualization for structural variation in human genomes

119

chromoscope

A 3D genome data processing tutorial for ISMB/ECCB 2017

3d-genome-processing-tutorial

MOMA

SPP - R package for analysis of ChIP-seq and other functional sequencing data

spp

C++

upset-altair-notebook

Jupyter Notebooks and other code for Altair-based Interactive UpSet Plots

Redesigning the Patient Portal Experience with SMART on FHIR.

halyos

A Shiny wrapper for the UpSetR R package (https://github.com/hms-dbmi/UpSetR).

UpSetR-shiny

dseqr

single-cell and bulk RNA-seq analyses from counts → pathways → drug candidates.

scw

HSCI/Catalyst Single-cell RNA-Seq Workshop

R package for delineating temporal dataset shifts in Eletronic Health Records

EHRtemporalVariability

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

brainmapr

charm

Interactive visual analytic tool for exploring epigenomics data w/ associated metadata, powered by HiGlass and Gosling

cistrome-explorer

Genomic Visualization Catalog

genocat

An option to spin cost effective EMR clusters in AWS with Hail and JupyterNotebook installed

hail-on-AWS-spot-instances

Shiny app for geno-pheno catalog

GenoPheno-CatalogShiny

breastCaPathologyTranscriptomics

Integrative Transcriptome-Histopathology Analysis for Breast Cancer Classification

Interactive & explainable GNN for drug repurposing

Drug_Explorer

Juptyer Notebooks with Altair Examples

altair_examples

Data and scripts for UpSetR paper.

UpSetR-paper

gehlenborglab-website

Code for Gehlenborg Lab website.

Neural Crest Fate Decisions

crestree

aws-python-utilities

Access-to-Data-using-PIC-SURE-API

A Docker build of the HAPI-FHIR stack

hapi-fhir-docker

Shiny app for EHRtemporalVariability R package

EHRtemporalVariability-shiny

pic-sure

PIC-SURE API

pic-sure-bdc-infrastructure

HCL

avillachlab-jenkins

HCL

pic-sure-hpds

Spatial analysis of genome mutation patterns

spacemut

pic-sure-all-in-one

Hail-on-Google-Cloud

pic-sure-hpds-genotype-load-example

R scatterplot deck.gl widget inspired by vitessce

picker

R package to assess and evaluate longitudinal mHealth sensor data.

mHealthieR

hypatio-app

Adapter library for PIC-SURE HPDS Resources (in R language)

pic-sure-r-adapter-hpds

map-explorer

Use MAP to explore EHR data for individual patients.

decart-2019-data-visualization

Materials for the DeCART 2019 Summer School Data Visualization Course

A Django application to integrate with DBMI services

django-dbmi-client

pic-sure-auth-microapp

Java classes to abstract away i2b2 XML - DEPRECATED, See https://github.com/hms-dbmi/IRCT\

i2b2-Java-API

Repository for tumor evolution visualization back end.

tev-server

Statistical models for finding de novo recurrence and compound heterozygosity across rare disease patient cohorts

RaMeDiES

matrix_storage_benchmark

Hail workshop material for: i2b2tranSMART Foundation Harvard Symposium 2019

hail-workshop-2019

Parse and generate variable-level data to be exposed through the search interface.

pic-sure-metadata-curation

SAS

pic-sure-bdc-frontend

IRCT

Merged IRCT Repository

EMR cluster creation and Hail 0.2 installation

music-ecrf-harmonization

hail-on-EMR

This repository stores Dockerfiles and samples to build Docker images for Avillach Lab hms-dbmi projects.

pklab

Kharchenko Lab Resources

docker-images

Groovy

dbmi-fileservice

pic-sure-core-frontend

fhirquestionnaire

i2b2 to PCORNET CDM Scripts

i2b2-to-PCORNET-CDM

PLSQL

hpds-etl-sbg-cwl

AWS lambda functions to extend SWB functionality

service-workbench-infrastructure-tools

Development of a Histopathology Informatics Pipeline for Classification and Prediction of Clinical Outcome in Subtypes of Renal Cell Carcinoma. Clinical Cancer Research. 2021 Mar 15. doi: 10.1158/1078-0432.CCR-20-4119. Online ahead of print.

rcc_pathology

i2b2v2-webclient

Data Commons Pilot Phase Project

dcppc

Simplified wrapper for react-grid-layout

vitessce-grid

base project to be used as a starter for all your other python projects

pystarter

Guidelines for creating medium-scale visualization software

gehlenborg-lab-best-practices

IRCT-EXT

- DEPRECATED, See https://github.com/hms-dbmi/IRCT

sci-aws-infrastructure

Query and retrieve phenotypics and genotypics data using PIC-SURE API

Rcheesecake

PIC-SURE-resources

PIC-SURE resource configuration files

SQLPL

Rcupcake

dbmisvc-stack

A Python client library for PIC-SURE-HPDS resources

pic-sure-python-adapter-hpds

stack

SciAuth-app-docker

Client library in R for connecting to PIC-SURE resources

pic-sure-r-client

pynxgu

GIC-ontology

ppm-data

pic-sure-bdc-release-control

exposomeDW_public

SciReg-docker

Interactive UpSet plot for DBMI faculty areas of interest.

upset-faculty

A client library for interacting with the PIC-SURE API

pic-sure-python-client

bmi713-visualization-lecture-2018

Dashboard templates for Splunk 8.0

avillachlab-pic-sure-splunk-template

Notesbooks for the 2020 single-cell review paper

single-cell-review-2020

secret-getter

retrieves secrets given a vault_token, and replaces values in files and/or environment variables

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.

A small authorization service

SciAuthZ-app-docker

COPDGene-WGS

A frontend for the PIC-SURE API

sratoolkit

Dockerfile

PIC-SURE-Frontend

Pathology Imaging Characterization with Uncertainty-aware Rapid Evaluation (PICTURE)

100

PICTURE