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Research Projects

The following list is a sample of research projects that the lab is involved in.

Active

The 4DN DCIC data portal page lists available datasets and their associated metadata

4D Nucleome Data Portal

Collect, store, curate, display, and analyze data generated in the 4DN Network.

Cistrome Explorer provides scalable, interactive, and modular visualizations for epigenomics data with associated metadata.

Cistrome Explorer

Web-based Interactive Visual Analytics Tool for Exploring Epigenomics Data with Associated Metadata

High level summary of the patient’s profile and their medical data

Discovery

A tool for accessing and visualizing patient information from multiple providers.

Components of django_docker_engine

django-docker-engine

django-docker-engine is a Django app that manages the creation of, and proxies requests to, Docker containers.

Our review paper established an ontology of genomic visualization tools.

GenoCAT

GenoCAT provides a database of genomic visualization tools. Each tool has been sorted and grouped based on various attributes, and the website has been designed to help you find what you’re looking for.

Diverse Genomics Visualizations Using Gosling.js

Gosling

A Grammar-based Toolkit for Scalable and Interactive Genomics Data Visualization

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Halyos

Halyos is a tool for patients to explore their EHR data. It is designed to present patient data in a way that allows patients to better understand their health data.

HiGlass provides synchronized navigation of multiple views showing matrices from different experimental conditions, types or cell lines.

HiGlass

HiGlass is a tool for exploring genomic contact matrices and tracks. It can be configured to explore and compare contact matrices across multiple scales.

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HiPiler

HiPiler is an interactive visualization interface for the exploration and visualization of regions-of-interest such as loops in large genome interaction matrices.

HuBMAP data portal

HuBMAP Data Portal

Curate, display, and analyze data generated by the HuBMAP Consortium.

Longitudinal data visualization of samples taken in different timepoints.

OncoThreads

OncoThreads is a visualization tool for longitudinal cancer genomics data.

Precision VISSTA

An interactive visualization interface to explore time-varied mobile health and survey data, enabling precise recommendations for lifestyle modifications to improve inflammatory bowel disease (IBD) outcomes.

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SATORI

An ontology-guided visual exploration system that combines a powerful metadata search with a tree map and a node-link diagram that visualize the repository structure, provide context to retrieved data sets, and serve as an interface to drive semantic querying and browsing of the repository.

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Caleydo StratomeX

Integrative visualization of stratified heterogeneous data for disease subtype analysis.

tableschema-to-template

Given a YAML description of the data, generate an Excel template with input validation

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UpSetR

An R package to generate static UpSet plots.

Data-Driven Visual Consent will aid in shared decision making by allowing patients to take an active role in treatment planning.

Data-Driven Visual consent is a tool for patients to understand the risk of pursuing a surgical intervention. The application calculates personalized risk scores using patient data and preferences and renders an intuitive visualization.

Visual Integration Tool for Exploration of Spatial Single-Cell Experiments

Vitessce

Visual Integration Tool for Exploration of Spatial Single-Cell Experiments

High-Resolution Multiplexed Tissue Data on the Web

Viv

Library for Multiscale Visualization of High-Resolution Multiplexed Tissue Data on the Web

Inactive

Refinery incorporates the Satori tool for ontology-guided visual exploration of data sets within the system. The example shown is from the Harvard Stem Cell Institute Stem Cell Commons site, which is an instance of Refinery.

Refinery Platform

A cloud-based data management, analysis, and visualization platform for reproducible biomedical research.

Refinery Platform website
Refinery Platform repository