BicOverlapper is a framework to support visual analysis of gene expression by means of biclustering.
Biclustering algorithms have become a spread technique to analyze microarray experiments. Since it is an unsupervised technique, biclustering is specially useful at discovering new knowledge about genes.
In order to improve the visualization of biclusters, we propose Overlapper, a visualization technique to simultaneously represent all biclusters from one or more biclustering algorithms, based on a force-directed layout. This visualization technique is integrated in BicOverlapper, along with several other visualization techniques and biclustering algorithms.
BicOverlapper is a visual framework that currently supports:
* Simultaneous visualization of one or more sets of biclusters, with a high degree of interaction
* Visualization of gene expression matrices as heatmaps and parallel coordinates
* Visualization of transcription regulatory networks
* Visualization of gene annotations
* Linkage of the different visualizations and data to achieve a broader analysis of the experiment
BicOverlapper was developed and is maintained by Rodrigo Santamaría, Roberto Therón and Luis Quintales, at the Department of Computers and Automation of the University of Salamanca. Special thanks to Javier Molpeceres for code contribution and to José Rafael García-Bermejo for english corrections. Questions and comments should be addressed to: rodri [at] usal [dot] es
If you want to cite Bicoverlapper, please use:
* Santamaría, R.; Therón, R. & Quintales, L. BicOverlapper: A tool for bicluster visualization. Bioinformatics, 2008, 24, 1212-1213 [ bibtex ]
* Santamaría, R.; Therón, R. & Quintales, L. A visual analytics approach for understanding biclustering results from microarray data. BMC Bioinformatics, 2008, 9 [ bibtex ]
* Santamaría, Rodrigo, Roberto Therón, and Luis Quintales. "BicOverlapper 2.0: visual analysis for gene expression." Bioinformatics (2014) 30 (12): 1785-1786 first published online March 3, 2014 doi:10.1093/bioinformatics/btu120
BicOverlapper is an open source project hosted by Google Code. The source can be downloaded at the Google Code project site.