hms-dbmi/samplestore

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hms-dbmi/samplestore

hms-dbmi

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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.

UpSetR

An R implementation of the UpSet set visualization technique published by Lex, Gehlenborg, et al..

viv

Library for multiscale visualization of high-resolution multiplexed bioimaging data on the web. Directly renders Zarr and OME-TIFF.

hic-data-analysis-bootcamp

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

Jupyter Notebook

scde

R package for analyzing single-cell RNA-seq data

CHIEF

Clinical Histopathology Imaging Evaluation Foundation Model

vizarr

A minimal Zarr image viewer based on Viv.

chromoscope

Interactive multiscale visualization for structural variation in human genomes

3d-genome-processing-tutorial

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

Jupyter Notebook

MOMA

spp

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

upset-altair-notebook

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

Jupyter Notebook

halyos

Redesigning the Patient Portal Experience with SMART on FHIR.

UpSetR-shiny

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

dseqr

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

scw

HSCI/Catalyst Single-cell RNA-Seq Workshop

EHRtemporalVariability

R package for delineating temporal dataset shifts in Eletronic Health Records

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

charm

cistrome-explorer

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

Jupyter Notebook

genocat

Genomic Visualization Catalog

hail-on-AWS-spot-instances

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

GenoPheno-CatalogShiny

Shiny app for geno-pheno catalog

OncoThreads

OncoThreads longitudinal cancer genomics visualization project.

breastCaPathologyTranscriptomics

Integrative Transcriptome-Histopathology Analysis for Breast Cancer Classification

Drug_Explorer

Interactive & explainable GNN for drug repurposing

altair_examples

Juptyer Notebooks with Altair Examples

Jupyter Notebook

UpSetR-paper

Data and scripts for UpSetR paper.

gehlenborglab-website

Code for Gehlenborg Lab website.

crestree

Neural Crest Fate Decisions

aws-python-utilities

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

Jupyter Notebook

hapi-fhir-docker

A Docker build of the HAPI-FHIR stack

EHRtemporalVariability-shiny

Shiny app for EHRtemporalVariability R package

pic-sure

pic-sure-bdc-infrastructure

avillachlab-jenkins

pic-sure-hpds

spacemut

Spatial analysis of genome mutation patterns

pic-sure-all-in-one

Hail-on-Google-Cloud

Jupyter Notebook

pic-sure-hpds-genotype-load-example

Jupyter Notebook

picker

R scatterplot deck.gl widget inspired by vitessce

mHealthieR

R package to assess and evaluate longitudinal mHealth sensor data.

hypatio-app

pic-sure-r-adapter-hpds

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

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

Jupyter Notebook

django-dbmi-client

A Django application to integrate with DBMI services

pic-sure-auth-microapp

i2b2-Java-API

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

tev-server

Repository for tumor evolution visualization back end.

RaMeDiES

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

matrix_storage_benchmark

hail-workshop-2019

Hail workshop material for: i2b2tranSMART Foundation Harvard Symposium 2019

pic-sure-metadata-curation

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

pic-sure-bdc-frontend

IRCT

Merged IRCT Repository

music-ecrf-harmonization

hail-on-EMR

EMR cluster creation and Hail 0.2 installation

pklab

Kharchenko Lab Resources

docker-images

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

dbmi-fileservice

pic-sure-core-frontend

fhirquestionnaire

i2b2-to-PCORNET-CDM

i2b2 to PCORNET CDM Scripts

hpds-etl-sbg-cwl

service-workbench-infrastructure-tools

AWS lambda functions to extend SWB functionality

rcc_pathology

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.

i2b2v2-webclient

dcppc

Data Commons Pilot Phase Project

Jupyter Notebook

vitessce-grid

Simplified wrapper for react-grid-layout

pystarter

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

gehlenborg-lab-best-practices

Guidelines for creating medium-scale visualization software

IRCT-EXT

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

sci-aws-infrastructure

Rcheesecake

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

PIC-SURE-resources

PIC-SURE resource configuration files

Rcupcake

dbmisvc-stack

pic-sure-python-adapter-hpds

A Python client library for PIC-SURE-HPDS resources

stack

SciAuth-app-docker

pic-sure-r-client

Client library in R for connecting to PIC-SURE resources

pynxgu

GIC-ontology

ppm-data

pic-sure-bdc-release-control

exposomeDW_public

SciReg-docker

upset-faculty

Interactive UpSet plot for DBMI faculty areas of interest.

Jupyter Notebook

pic-sure-python-client

A client library for interacting with the PIC-SURE API

bmi713-visualization-lecture-2018

avillachlab-pic-sure-splunk-template

Dashboard templates for Splunk 8.0

single-cell-review-2020

Notesbooks for the 2020 single-cell review paper

secret-getter

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

SciAuthZ-app-docker

A small authorization service

COPDGene-WGS

Jupyter Notebook

sratoolkit

PIC-SURE-Frontend

A frontend for the PIC-SURE API

PICTURE

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

Jupyter Notebook