Software development for biclustering methods: The biclust GUI R package

Abstract

This thesis is centered around the subject of biclustering which is the simultaneous clustering of genes and conditions in a gene expression matrix. The focus will not be on the actual methods themselves, but on the software development of their implementation in a user-friendly Graphical User Interface. This GUI is packaged as RcmdrPlugin.BiclustGUI which is a plug-in for the already existing R-commander. The report will handle the implementation of several biclustering methods as well as ways to extract diagnostics and plots from the results, all by using the GUI. The second part of the report will handle the implementation of future new biclustering methods or diagnostic tools. Because the framework of RcmdrPlugin.BiclustGUI was created specifically for biclustering, this is can be achieved very easily. Thanks to easy-to-use scripts, developers can freely design their own GUI windows for their methods which can then later be added to RcmdrPlugin.BiclustGUI very quickly by the maintainer. The strength of these scripts lies in the fact that they do not rely on any knowledge of tcltk or Rcmdr which is normally required for creating such windows. This enables RcmdrPlugin.BiclustGUI to quickly gain a vast collection of biclustering methods which will then be accessible by non-R users through a simple point-and-click system. Further, it is also an attractive approach to easily connect biclustering methods with diagnostic and plotting packages to further investigate and visualize bicluster results.