Overview

exploRase is a MetNet tool written in R for the exploratory multivariate analysis of Systems Biology data. It provides a graphical user interface (GUI) on top of the analysis functionality provided by R and the Bioconductor project. exploRase is designed to be accessible to biologists analyzing omics data in the context of metabolic and regulatory networks.

Features

• Provides a biologist-accessible GUI to R analysis functionality, such as distance measures, clustering, pattern-finding, and modeling.
• Integrates the analysis with interactive graphics, using GGobi.
• Handles transcriptomic, metabolomic, and proteomic data.
• Simplifies the loading of experimental data into R and GGobi.
• Supports the storage of lists of "interesting" entities for future sessions.
• Links sortable tables of entity metadata to GGobi plots by color coding.
• Provides automatic access to AtGeneSearch, the web interface to MetNetDB.
• Saves calculated statistics.

Screenshots

ExploRase with GGobi graphics



ExploRase filter interface



ExploRase pattern finder

Components

• GTK+: The premier open-source graphical user interface toolkit.
• R: A sweet open-source platform for statistical computing.
• GGobi: The definitive open-source interactive graphics platform.
• rggobi: Lets R talk to ggobi.
• RGtk2: Lets R talk to GTK+.

Acknowledgements:

This work is funded by NSF Arabidopsis 2010 grants DB10209809 and DB10520267. The people involved in the development are Eun-Kyung Lee, Di Cook, Michael Lawrence, Heike Hofmann, Hai-Qing You, Eve Wurtele, Dongshin Kim, Jihong Kim, Hogeun An, and Heather Babka.

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