Research

Current Projects

StratomeX – Integrative Visualization for Tumor Subtype Characterization

Project Page | A tool for integrative visualization of cancer genomics data from The Cancer Genome Atlas project to identify and characterize tumor subtypes.

Refinery Platform

WebsiteGitHub | The Refinery Platform is a web-based data visualization and analysis system powered by an ISA-Tab-compatible data repository for public and private data sets. Analyses are implemented as Galaxy workflows and executed through the Galaxy API.

Nozzle – Interactive Reports for High-Throughput Data Analysis Pipelines

Website | GitHub | Nozzle is an R package for generation of reports in high-throughput data analysis pipelines. Nozzle reports are implemented in HTML, JavaScript, and Cascading Style Sheets (CSS), but report developers can use a simple R API to design and implement powerful reports with advanced features such as foldable sections, zoomable figures, sortable tables, and supplementary information.

Past Projects

REX – Retrieval of Experiments

Project Page | Probabilistic retrieval and visualization of biologically relevant microarray experiments from large collections of gene expression studies.

AEX – ArrayExpress Explorer

Project Page | An ontology-guided visual exploration tool for the ArrayExpress Archive built around a tree map visualization of a biomedical ontology.

Space Maps

Project Page | A glyph-based visualization method for very large gene expression data sets that cover hundreds or thousands of samples.

Prequips

Website | Prequips is a modular software platform for integration, visualization and analysis of complex LC/MS-MS proteomics data sets. The software provides access to data produced by proteomics analysis pipelines and bridges the gap to high-level analysis tools used in systems biology.

Prion Disease Database

Project PageWebsite | The Prion Disease Database (PDDB) is a public database that supports the prion disease research community by collecting, integrating, and presenting data from public sources and collaborating laboratories.

Mayday

Website | Mayday is a workbench for interactive visualization, analysis and storage of microarray data. It supports the development and integration of existing and novel analysis methods through a plugin interface.

Enhanced Heatmap

Project Page | A visualization method that allows integration of microarray data and meta information to guide the investigator during data exploration and analysis.